From 5b913e8fc76c3811f0bb73f83c096ef3b2281962 Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Wed, 29 Jul 2020 06:49:55 +0000
Subject: [PATCH 001/165] Update pytest requirement from <6 to <7

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/1.0.0b3...6.0.0)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>
---
 requirements.txt | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 mode change 100755 => 100644 setup.py

diff --git a/requirements.txt b/requirements.txt
index 672abb0..cf1e778 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
 schema-salad >= 5.0.20200220195218, <8
 junit-xml >= 1.8
-pytest < 6
+pytest < 7
diff --git a/setup.py b/setup.py
old mode 100755
new mode 100644
index 58663c6..128e127
--- a/setup.py
+++ b/setup.py
@@ -37,7 +37,7 @@
     install_requires=install_requires,
     test_suite="tests",
     setup_requires=[] + pytest_runner,
-    tests_require=["pytest<5"],
+    tests_require=["pytest<7"],
     entry_points={
         "console_scripts": [
             "cwltest=cwltest:main",

From 3b05d04a8027ae2977179ae053995aa1c5d9d569 Mon Sep 17 00:00:00 2001
From: Rupert Nash <rupert@nash.me.uk>
Date: Thu, 22 Apr 2021 17:20:42 +0100
Subject: [PATCH 002/165] allow exclusion of tests by name or number

---
 cwltest/__init__.py | 42 ++++++++++++++++++++++++++++++++++++------
 1 file changed, 36 insertions(+), 6 deletions(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index d192298..7f9f4e3 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -270,6 +270,18 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
         default=None,
         help="Run specific tests using their short names separated by comma",
     )
+    parser.add_argument(
+        "-N",
+        type=str,
+        default=None,
+        help="Exclude specific tests by number, format is 1,3-6,9",
+    )
+    parser.add_argument(
+        "-S",
+        type=str,
+        default=None,
+        help="Exclude specific tests by short names separated by comma",
+    )
     parser.add_argument(
         "--tool",
         type=str,
@@ -340,6 +352,15 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     return parser
 
+def expand_number_range(nr: str) -> List[int]:
+    ans: List[int] = []
+    for s in nr.split(","):
+        sp = s.split("-")
+        if len(sp) == 2:
+            ans.extend(range(int(sp[0]) - 1, int(sp[1])))
+        else:
+            ans.append(int(s) - 1)
+    return ans
 
 def main():  # type: () -> int
 
@@ -430,12 +451,7 @@ def main():  # type: () -> int
     if args.n is not None or args.s is not None:
         ntest = []
         if args.n is not None:
-            for s in args.n.split(","):
-                sp = s.split("-")
-                if len(sp) == 2:
-                    ntest.extend(list(range(int(sp[0]) - 1, int(sp[1]))))
-                else:
-                    ntest.append(int(s) - 1)
+            ntest = expand_number_range(args.n)
         if args.s is not None:
             for s in args.s.split(","):
                 test_number = get_test_number_by_key(tests, "short_name", s)
@@ -447,6 +463,20 @@ def main():  # type: () -> int
     else:
         ntest = list(range(0, len(tests)))
 
+    exclude_n = []
+    if args.N is not None:
+        exclude_n = expand_number_range(args.N)
+    if args.S is not None:
+        for s in args.S.split(","):
+            test_number = get_test_number_by_key(tests, "short_name", s)
+            if test_number:
+                exclude_n.append(test_number)
+            else:
+                _logger.error('Test with short name "%s" not found ', s)
+                return 1
+
+    ntest = list(filter(lambda x: x not in exclude_n, ntest))
+
     total = 0
     with ThreadPoolExecutor(max_workers=args.j) as executor:
         jobs = [

From ffed6d87e4ad024d464dc279759e11be8c8d794b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 23 Apr 2021 14:14:09 +0200
Subject: [PATCH 003/165] update release script for Python3.9 compat

---
 Makefile        |  6 ++---
 release-test.sh | 60 ++++++++++++++++++++++++-------------------------
 2 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/Makefile b/Makefile
index b5bcd1c..637cb4c 100644
--- a/Makefile
+++ b/Makefile
@@ -60,12 +60,12 @@ install: FORCE
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
 dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
-	./setup.py sdist bdist_wheel
+	python setup.py sdist bdist_wheel
 
 ## clean       : clean up all temporary / machine-generated files
 clean: FORCE
 	rm -f ${MODILE}/*.pyc tests/*.pyc
-	./setup.py clean --all || true
+	python setup.py clean --all || true
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
@@ -125,7 +125,7 @@ diff-cover.html: coverage-gcovr.xml coverage.xml
 
 ## test        : run the ${MODULE} test suite
 test: all
-	./setup.py test
+	python setup.py test
 
 sloccount.sc: ${PYSOURCES} Makefile
 	sloccount --duplicates --wide --details $^ > $@
diff --git a/release-test.sh b/release-test.sh
index a44e7c3..3fb3a1f 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -3,14 +3,15 @@
 set -e
 set -x
 
+export LC_ALL=C
+
 package=cwltest
 module=cwltest
 slug=${TRAVIS_PULL_REQUEST_SLUG:=common-workflow-language/${module}}
 repo=https://github.com/${slug}.git
 run_tests="bin/py.test --pyargs ${module}"
-pipver=18 # minimum required version of pip
-setupver=40.3 # minimum required version of setuptools
-PYVER=${PYVER:=3}
+pipver=20.3b1 # minimum required version of pip for Python 3.9
+setuptoolsver=41.1.0 # required for Python 3.9
 
 rm -Rf "testenv${PYVER}_"? || /bin/true
 
@@ -18,64 +19,63 @@ export HEAD=${TRAVIS_PULL_REQUEST_SHA:-$(git rev-parse HEAD)}
 
 if [ "${RELEASE_SKIP}" != "head" ]
 then
-	virtualenv "testenv${PYVER}_1" -p "python${PYVER}"
+	python3 -m venv testenv1
 	# First we test the head
 	# shellcheck source=/dev/null
-	source "testenv${PYVER}_1/bin/activate"
-	rm -f "testenv${PYVER}_1/lib/python-wheels/setuptools"*
-	pip install --force-reinstall -U pip==${pipver}
-	pip install setuptools==${setupver} wheel
+	source testenv1/bin/activate
+	rm -Rf testenv1/local
+	rm -f testenv1/lib/python-wheels/setuptools* \
+		&& pip install --force-reinstall -U pip==${pipver} \
+		&& pip install setuptools==${setuptoolsver} wheel
 	make install-dependencies
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} \
 		|| true; make install
-	mkdir "testenv${PYVER}_1/not-${module}"
+	mkdir testenv1/not-${module}
 	# if there is a subdir named '${module}' py.test will execute tests
 	# there instead of the installed module's tests
-
-	pushd "testenv${PYVER}_1/not-${module}"
+	pushd testenv1/not-${module}
 	# shellcheck disable=SC2086
 	../${run_tests}; popd
 fi
 
-
-virtualenv "testenv${PYVER}_2" -p "python${PYVER}"
-virtualenv "testenv${PYVER}_3" -p "python${PYVER}"
-virtualenv "testenv${PYVER}_4" -p "python${PYVER}"
-virtualenv "testenv${PYVER}_5" -p "python${PYVER}"
-
+python3 -m venv testenv2
+python3 -m venv testenv3
+python3 -m venv testenv4
+python3 -m venv testenv5
+rm -Rf testenv[2345]/local
 
 # Secondly we test via pip
 
-pushd "testenv${PYVER}_2"
+pushd testenv2
 # shellcheck source=/dev/null
 source bin/activate
-rm lib/python-wheels/setuptools* \
+rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setupver} wheel
+        && pip install setuptools==${setuptoolsver} wheel
 # The following can fail if you haven't pushed your commits to ${repo}
 pip install -e "git+${repo}@${HEAD}#egg=${package}"
 pushd src/${package}
 make install-dependencies
 make dist
 make test
-cp dist/${package}*tar.gz "../../../testenv${PYVER}_3/"
-cp dist/${module}*whl "../../../testenv${PYVER}_4/"
+cp dist/${package}*tar.gz ../../../testenv3/
+cp dist/${module}*whl ../../../testenv4/
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 popd # ../.. no subdir named ${proj} here, safe for py.testing the installed module
 # shellcheck disable=SC2086
 ${run_tests}
 popd
 
-# Is the source distribution in testenv${PYVER}_2 complete enough to build
+# Is the source distribution in testenv2 complete enough to build
 # another functional distribution?
 
-pushd "testenv${PYVER}_3/"
+pushd testenv3/
 # shellcheck source=/dev/null
 source bin/activate
-rm lib/python-wheels/setuptools* \
+rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setupver} wheel
+        && pip install setuptools==${setuptoolsver} wheel
 pip install ${package}*tar.gz
 pip install pytest\<5
 mkdir out
@@ -91,14 +91,14 @@ pushd ../not-${module}
 popd
 popd
 
-# Is the wheel in testenv${PYVER}_2 installable and will it pass the tests
+# Is the wheel in testenv2 installable and will it pass the tests
 
-pushd "testenv${PYVER}_4/"
+pushd testenv4/
 # shellcheck source=/dev/null
 source bin/activate
-rm lib/python-wheels/setuptools* \
+rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
-        && pip install setuptools==${setupver} wheel
+        && pip install setuptools==${setuptoolsver} wheel
 pip install ${module}*.whl
 pip install pytest\<5
 mkdir not-${module}

From 60dbec1b846e338dbda0a864326ef32fdb98de35 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 23 Apr 2021 14:46:33 +0200
Subject: [PATCH 004/165] make new release

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 128e127..26a4a1d 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@
 
 setup(
     name="cwltest",
-    version="2.0",
+    version="2.1",
     description="Common workflow language testing framework",
     long_description=open(README).read(),
     long_description_content_type="text/x-rst",

From 20810aaa6aa4bffcba14c8c6e52ada170fac28dd Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 23 Apr 2021 15:00:11 +0200
Subject: [PATCH 005/165] match Makefile to release-test.sh

---
 Makefile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 637cb4c..ca72a3f 100644
--- a/Makefile
+++ b/Makefile
@@ -156,11 +156,11 @@ release-test: FORCE
 
 release: FORCE
 	PYVER=3 ./release-test.sh
-	. testenv3_2/bin/activate && \
-		testenv3_2/src/${MODULE}/setup.py sdist bdist_wheel
-	. testenv3_2/bin/activate && \
+	. testenv2/bin/activate && \
+		testenv2/src/${MODULE}/setup.py sdist bdist_wheel
+	. testenv2/bin/activate && \
 		pip install twine && \
-		twine upload testenv3_2/src/${MODULE}/dist/*whl && \
+		twine upload testenv2/src/${MODULE}/dist/*whl && \
 		git tag ${VERSION} && git push --tags
 
 FORCE:

From a217026c37c9abe2f8fac9acdc529b09931d317f Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 23 Apr 2021 15:01:20 +0200
Subject: [PATCH 006/165] bump version in Makefile as well

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index ca72a3f..2d9ea30 100644
--- a/Makefile
+++ b/Makefile
@@ -30,7 +30,7 @@ DEVPKGS=pycodestyle diff_cover pylint coverage pydocstyle flake8 \
 	pytest pytest-xdist isort
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.0.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.1.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 

From 4f1fa3451e74a4add66f82f986703431cb243ed9 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 23 Apr 2021 15:04:52 +0200
Subject: [PATCH 007/165] Don't rely on setup.py being marked executable

---
 Makefile | 2 +-
 setup.py | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 mode change 100644 => 100755 setup.py

diff --git a/Makefile b/Makefile
index 2d9ea30..39aecd8 100644
--- a/Makefile
+++ b/Makefile
@@ -157,7 +157,7 @@ release-test: FORCE
 release: FORCE
 	PYVER=3 ./release-test.sh
 	. testenv2/bin/activate && \
-		testenv2/src/${MODULE}/setup.py sdist bdist_wheel
+		python testenv2/src/${MODULE}/setup.py sdist bdist_wheel
 	. testenv2/bin/activate && \
 		pip install twine && \
 		twine upload testenv2/src/${MODULE}/dist/*whl && \
diff --git a/setup.py b/setup.py
old mode 100644
new mode 100755

From 83f83afc449e932fdcfbc9fd6ed954e3a4f1e1a8 Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Thu, 29 Apr 2021 20:39:15 +0000
Subject: [PATCH 008/165] Upgrade to GitHub-native Dependabot

---
 .github/dependabot.yml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 .github/dependabot.yml

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..491deae
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+version: 2
+updates:
+- package-ecosystem: pip
+  directory: "/"
+  schedule:
+    interval: daily
+  open-pull-requests-limit: 10

From eabc56ec17ca37a68ad8dc237e9cb953b78218aa Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 25 Jun 2021 00:37:14 +0000
Subject: [PATCH 009/165] Update schema-salad requirement

Updates the requirements on [schema-salad](https://github.com/common-workflow-language/schema_salad) to permit the latest version.
- [Release notes](https://github.com/common-workflow-language/schema_salad/releases)
- [Commits](https://github.com/common-workflow-language/schema_salad/compare/5.0.20200220195218...8.0.20210624154013)

---
updated-dependencies:
- dependency-name: schema-salad
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
 mode change 100755 => 100644 setup.py

diff --git a/requirements.txt b/requirements.txt
index cf1e778..de7919c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
-schema-salad >= 5.0.20200220195218, <8
+schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
 pytest < 7
diff --git a/setup.py b/setup.py
old mode 100755
new mode 100644
index 26a4a1d..a98125b
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = ["schema-salad >= 5.0.20200220195218, < 8", "junit-xml >= 1.8"]
+install_requires = ["schema-salad >= 5.0.20200220195218, < 9", "junit-xml >= 1.8"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []

From eabe89614a1f7fb588ad49bda97a991740f43b1e Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 1 Sep 2021 15:35:43 +0200
Subject: [PATCH 010/165] modernize

---
 .github/workflows/ci-tests.yml                | 129 ++++++++++++++++++
 .travis.yml                                   |  64 ---------
 MANIFEST.in                                   |   3 +-
 Makefile                                      |  94 +++++++------
 cwltest/__init__.py                           |  44 +++---
 .../future/__init__.pyi => cwltest/py.typed   |   0
 cwltest/tests/test_categories.py              |   2 +-
 cwltest/tests/test_short_names.py             |   2 +-
 cwltest/tests/util.py                         |   4 +-
 mypy.ini                                      |  19 ++-
 mypy_requirements.txt                         |   3 +
 release-test.sh                               |  30 ++--
 requirements.txt                              |   1 +
 setup.cfg                                     |  14 +-
 setup.py                                      |  30 +++-
 test-requirements.txt                         |   3 +
 tox.ini                                       |  88 ++++++------
 travis/os_install.sh                          |  17 ---
 typeshed/{2and3 => }/avro/__init__.pyi        |   0
 typeshed/{2and3 => }/avro/schema.pyi          |   0
 .../{2and3 => }/cachecontrol/__init__.pyi     |   0
 typeshed/{2and3 => }/cachecontrol/adapter.pyi |   0
 typeshed/{2and3 => }/cachecontrol/cache.pyi   |   0
 .../cachecontrol/caches/__init__.pyi          |   0
 .../cachecontrol/caches/file_cache.pyi        |   0
 typeshed/{2and3 => }/cachecontrol/compat.pyi  |   0
 .../{2and3 => }/cachecontrol/controller.pyi   |   0
 .../{2and3 => }/cachecontrol/filewrapper.pyi  |   0
 .../{2and3 => }/cachecontrol/serialize.pyi    |   0
 typeshed/{2and3 => }/cachecontrol/wrapper.pyi |   0
 .../__init__.py => future/__init__.pyi}       |   0
 .../{2and3 => }/future/utils/__init__.pyi     |   0
 typeshed/{2and3 => }/galaxy/__init__.pyi      |   0
 .../galaxy/exceptions/__init__.pyi            |   0
 .../galaxy/exceptions/error_codes.pyi         |   0
 typeshed/{2and3 => }/galaxy/jobs/__init__.pyi |   0
 .../galaxy/jobs/metrics/__init__.pyi          |   0
 .../galaxy/jobs/metrics/collectl/__init__.pyi |   0
 .../galaxy/jobs/metrics/collectl/cli.pyi      |   0
 .../jobs/metrics/collectl/processes.pyi       |   0
 .../galaxy/jobs/metrics/collectl/stats.pyi    |   0
 .../jobs/metrics/collectl/subsystems.pyi      |   0
 .../galaxy/jobs/metrics/formatting.pyi        |   0
 .../jobs/metrics/instrumenters/__init__.pyi   |   0
 .../jobs/metrics/instrumenters/collectl.pyi   |   0
 .../jobs/metrics/instrumenters/core.pyi       |   0
 .../jobs/metrics/instrumenters/cpuinfo.pyi    |   0
 .../galaxy/jobs/metrics/instrumenters/env.pyi |   0
 .../jobs/metrics/instrumenters/meminfo.pyi    |   0
 .../jobs/metrics/instrumenters/uname.pyi      |   0
 .../galaxy/objectstore/__init__.pyi           |   0
 .../galaxy/objectstore/azure_blob.pyi         |   0
 .../{2and3 => }/galaxy/objectstore/pulsar.pyi |   0
 .../{2and3 => }/galaxy/objectstore/rods.pyi   |   0
 .../{2and3 => }/galaxy/objectstore/s3.pyi     |   0
 .../objectstore/s3_multipart_upload.pyi       |   0
 .../{2and3 => }/galaxy/tools/__init__.pyi     |   0
 .../{2and3 => }/galaxy/tools/cwl/__init__.pyi |   0
 .../galaxy/tools/cwl/cwltool_deps.pyi         |   0
 .../{2and3 => }/galaxy/tools/cwl/parser.pyi   |   0
 .../galaxy/tools/cwl/representation.pyi       |   0
 .../galaxy/tools/cwl/runtime_actions.pyi      |   0
 .../{2and3 => }/galaxy/tools/cwl/schema.pyi   |   0
 .../galaxy/tools/deps/__init__.pyi            |   0
 .../galaxy/tools/deps/brew_exts.pyi           |   0
 .../galaxy/tools/deps/brew_util.pyi           |   0
 .../galaxy/tools/deps/commands.pyi            |   0
 .../galaxy/tools/deps/conda_compat.pyi        |   0
 .../galaxy/tools/deps/conda_util.pyi          |   0
 .../deps/container_resolvers/__init__.pyi     |   0
 .../deps/container_resolvers/explicit.pyi     |   0
 .../tools/deps/container_resolvers/mulled.pyi |   0
 .../galaxy/tools/deps/containers.pyi          |   0
 .../galaxy/tools/deps/dependencies.pyi        |   0
 .../galaxy/tools/deps/docker_util.pyi         |   0
 .../galaxy/tools/deps/dockerfiles.pyi         |   0
 .../galaxy/tools/deps/installable.pyi         |   0
 .../galaxy/tools/deps/mulled/__init__.pyi     |   0
 .../galaxy/tools/deps/mulled/_cli.pyi         |   0
 .../galaxy/tools/deps/mulled/mulled_build.pyi |   0
 .../deps/mulled/mulled_build_channel.pyi      |   0
 .../tools/deps/mulled/mulled_build_files.pyi  |   0
 .../tools/deps/mulled/mulled_build_tool.pyi   |   0
 .../tools/deps/mulled/mulled_search.pyi       |   0
 .../galaxy/tools/deps/mulled/util.pyi         |   0
 .../galaxy/tools/deps/requirements.pyi        |   0
 .../galaxy/tools/deps/resolvers/__init__.pyi  |   0
 .../resolvers/brewed_tool_shed_packages.pyi   |   0
 .../galaxy/tools/deps/resolvers/conda.pyi     |   0
 .../tools/deps/resolvers/galaxy_packages.pyi  |   0
 .../galaxy/tools/deps/resolvers/homebrew.pyi  |   0
 .../galaxy/tools/deps/resolvers/modules.pyi   |   0
 .../tools/deps/resolvers/resolver_mixins.pyi  |   0
 .../deps/resolvers/tool_shed_packages.pyi     |   0
 .../resolvers/unlinked_tool_shed_packages.pyi |   0
 .../galaxy/tools/deps/singularity_util.pyi    |   0
 .../{2and3 => }/galaxy/tools/deps/views.pyi   |   0
 typeshed/{2and3 => }/galaxy/tools/fetcher.pyi |   0
 typeshed/{2and3 => }/galaxy/tools/lint.pyi    |   0
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 .../galaxy/tools/linters/__init__.pyi         |   0
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 .../{2and3 => }/galaxy/util/lazy_process.pyi  |   0
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 typeshed/{2and3 => }/galaxy/util/odict.pyi    |   0
 typeshed/{2and3 => }/galaxy/util/oset.pyi     |   0
 .../{2and3 => }/galaxy/util/plugin_config.pyi |   0
 .../{2and3 => }/galaxy/util/properties.pyi    |   0
 .../{2and3 => }/galaxy/util/simplegraph.pyi   |   0
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 typeshed/{2and3 => }/galaxy/util/specs.pyi    |   0
 typeshed/{2and3 => }/galaxy/util/sqlite.pyi   |   0
 .../{2and3 => }/galaxy/util/submodules.pyi    |   0
 typeshed/{2and3 => }/galaxy/util/topsort.pyi  |   0
 .../{2and3 => }/galaxy/util/xml_macros.pyi    |   0
 typeshed/{2and3 => }/junit_xml.pyi            |   0
 typeshed/{2and3 => }/mistune.pyi              |   0
 typeshed/{2and3 => }/rdflib/__init__.pyi      |   0
 typeshed/{2and3 => }/rdflib/events.pyi        |   0
 typeshed/{2and3 => }/rdflib/exceptions.pyi    |   0
 typeshed/{2and3 => }/rdflib/graph.pyi         |   0
 typeshed/{2and3 => }/rdflib/namespace.pyi     |   0
 typeshed/{2and3 => }/rdflib/parser.pyi        |   0
 typeshed/{2and3 => }/rdflib/plugin.pyi        |   0
 .../{2and3 => }/rdflib/plugins/__init__.pyi   |   0
 .../rdflib/plugins/parsers/__init__.pyi       |   0
 .../rdflib/plugins/parsers/notation3.pyi      |   0
 typeshed/{2and3 => }/rdflib/query.pyi         |   0
 typeshed/{2and3 => }/rdflib/serializer.pyi    |   0
 typeshed/{2and3 => }/rdflib/store.pyi         |   0
 typeshed/{2and3 => }/rdflib/term.pyi          |   0
 typeshed/{2and3 => }/rdflib/util.pyi          |   0
 typeshed/{3/urllib => ruamel}/__init__.py     |   0
 typeshed/{2and3 => }/select.pyi               |   0
 typeshed/{2and3 => }/shellescape/__init__.pyi |   0
 typeshed/{2and3 => }/shellescape/main.pyi     |   0
 typeshed/urllib/__init__.py                   |   0
 typeshed/{3 => }/urllib/parse.pyi             |   0
 typeshed/{3 => }/urllib/subprocess.pyi        |   0
 184 files changed, 331 insertions(+), 216 deletions(-)
 create mode 100644 .github/workflows/ci-tests.yml
 delete mode 100644 .travis.yml
 rename typeshed/2and3/future/__init__.pyi => cwltest/py.typed (100%)
 create mode 100644 mypy_requirements.txt
 create mode 100644 test-requirements.txt
 delete mode 100644 travis/os_install.sh
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diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
new file mode 100644
index 0000000..cf34d1d
--- /dev/null
+++ b/.github/workflows/ci-tests.yml
@@ -0,0 +1,129 @@
+name: Continous integration tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+
+  tox:
+    name: CI tests via Tox
+
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        py-ver-major: [3]
+        py-ver-minor: [6, 7, 8, 9]
+        step: [lint, unit, mypy]
+
+    env:
+      py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
+      TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.py-semver }}
+
+      - name: Cache for pip
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt', 'tox.ini') }}
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install tox tox-gh-actions
+
+      - name: MyPy cache
+        if: ${{ matrix.step == 'mypy' }}
+        uses: actions/cache@v2
+        with:
+          path: .mypy_cache/${{ env.py-semver }}
+          key: mypy-${{ env.py-semver }}
+
+      - name: Test with tox
+        run: tox
+
+      - name: Upload coverage to Codecov
+        if: ${{ matrix.step == 'unit' }}
+        uses: codecov/codecov-action@v1
+        with:
+          fail_ci_if_error: true
+
+  tox-style:
+    name: CI linters via Tox
+
+    runs-on: ubuntu-20.04
+
+    strategy:
+      matrix:
+        step: [lint-readme, pydocstyle]
+
+    env:
+      py-semver: 3.9
+      TOXENV: ${{ format('py39-{0}', matrix.step) }}
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ env.py-semver }}
+
+      - name: Cache for pip
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
+
+      - name: Upgrade setuptools and install tox
+        run: |
+          pip install -U pip setuptools wheel
+          pip install tox tox-gh-actions
+
+      - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
+        name: Create local branch for diff-quality for PRs
+        run: git branch ${{github.base_ref}} origin/${{github.base_ref}}
+
+      - name: Test with tox
+        run: tox
+
+  release_test:
+    name: cwltest release test
+
+    runs-on: ubuntu-20.04
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Cache for pip
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-release-${{ hashFiles('requirements.txt', 'test-requirements.txt') }}
+
+      - name: Install packages
+        run: |
+          pip install -U pip setuptools wheel
+          pip install virtualenv
+
+      - name: Release test
+        env:
+          RELEASE_SKIP: head
+        run: ./release-test.sh
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 89a8f69..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,64 +0,0 @@
-services:
-  - docker
-
-matrix:
-  include:
-    - os: linux
-      language: python
-      python: 3.5
-      script:
-        - tox
-        - RELEASE_SKIP=head PYVER=3 ${TRAVIS_BUILD_DIR}/release-test.sh
-    - os: linux
-      language: python
-      python: 3.6
-      script:
-        - tox
-        - RELEASE_SKIP=head PYVER=3 ${TRAVIS_BUILD_DIR}/release-test.sh
-    - os: linux
-      language: python
-      python: 3.7
-      script:
-        - tox
-        - RELEASE_SKIP=head PYVER=3 ${TRAVIS_BUILD_DIR}/release-test.sh
-    - os: linux
-      language: python
-      python: 3.8
-      script:
-        - tox
-        - RELEASE_SKIP=head PYVER=3 ${TRAVIS_BUILD_DIR}/release-test.sh
-    - os: osx
-      language: generic
-      env: TRAVIS_PYTHON_VERSION=3.5 PYENV_VERSION=3.5.4
-    - os: osx
-      language: generic
-      env: TRAVIS_PYTHON_VERSION=3.6 PYENV_VERSION=3.6.3
-    - os: osx
-      language: generic
-      env: TRAVIS_PYTHON_VERSION=3.7 PYENV_VERSION=3.7.5
-    - os: osx
-      language: generic
-      env: TRAVIS_PYTHON_VERSION=3.8 PYENV_VERSION=3.8.0
-
-install:
-  - source $TRAVIS_BUILD_DIR/travis/os_install.sh
-  - pip install tox-travis
-
-script:
-  - tox
-
-before_cache:
-  - brew cleanup
-cache:
-  pip: true
-  directories:
-    - .mypy_cache
-    - $HOME/.pyenv_cache
-    - $HOME/Library/Caches/Homebrew
-    - $HOME/.pyenv/versions
-
-branches:
-  only:
-    - master
-notifications:
-  email: false
diff --git a/MANIFEST.in b/MANIFEST.in
index 46873cc..6e775fd 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,7 +1,8 @@
-include Makefile gittaggers.py
+include Makefile gittaggers.py test-requirements.txt mypy_requirements.txt requirements.txt
 include cwltest/cwltest-schema.yml
 include cwltest/tests/*
 include cwltest/tests/test-data/*
 include cwltest/tests/test-data/v1.0/*
+recursive-include typeshed *.py?
 global-exclude *~
 global-exclude *.pyc
diff --git a/Makefile b/Makefile
index 39aecd8..e67f0e1 100644
--- a/Makefile
+++ b/Makefile
@@ -15,36 +15,36 @@
 #
 # Contact: common-workflow-language@googlegroups.com
 
-# make pycodestyle to check for basic Python code compliance
-# make autopep8 to fix most pep8 errors
+# make format to fix most python formatting errors
 # make pylint to check Python code for enhanced compliance including naming
 #  and documentation
 # make coverage-report to check coverage of the python scripts by the tests
 
 MODULE=cwltest
+PACKAGE=cwltest
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pycodestyle diff_cover pylint coverage pydocstyle flake8 \
-	pytest pytest-xdist isort
+DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
+	isort wheel autoflake flake8-bugbear pyupgrade bandit \
+	-rtest-requirements.txt -rmypy_requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.1.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.2.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
-mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
 
 ## all         : default task
-all: FORCE
-	pip install -e .
+all: dev
 
 ## help        : print this help message and exit
 help: Makefile
 	@sed -n 's/^##//p' $<
 
-install-dependencies: install-dep
 ## install-dep : install most of the development dependencies via pip
-install-dep:
+install-dep: install-dependencies
+
+install-dependencies: FORCE
 	pip install --upgrade $(DEVPKGS)
 	pip install -r requirements.txt
 
@@ -52,10 +52,14 @@ install-dep:
 install-deb-dep:
 	sudo apt-get install $(DEBDEVPKGS)
 
-## install     : install the ${MODULE} module and schema-salad-tool
+## install     : install the ${MODULE} module and cwltest
 install: FORCE
 	pip install .
 
+## dev     : install the ${MODULE} module in dev mode
+dev: install-dep
+	pip install -e .
+
 ## dist        : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
@@ -71,8 +75,11 @@ clean: FORCE
 
 # Linting and code style related targets
 ## sorting imports using isort: https://github.com/timothycrosley/isort
-sort_imports:
-	isort ${MODULE}/*.py tests/*.py setup.py
+sort_imports: $(PYSOURCES)
+	isort $^
+
+remove_unused_imports: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+	autoflake --in-place --remove-all-unused-imports $^
 
 pep257: pydocstyle
 ## pydocstyle      : check Python code style
@@ -83,18 +90,21 @@ pydocstyle_report.txt: $(PYSOURCES)
 	pydocstyle setup.py $^ > $@ 2>&1 || true
 
 diff_pydocstyle_report: pydocstyle_report.txt
-	diff-quality --violations=pycodestyle --fail-under=100 $^
+	diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
 
 ## format      : check/fix all code indentation and formatting (runs black)
 format:
-	black --exclude cwltool/schemas setup.py cwltest
+	black setup.py cwltest setup.py
+
+format-check:
+	black --diff --check setup.py cwltest
 
 ## pylint      : run static code analysis on Python code
 pylint: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
                 $^ -j0|| true
 
-pylint_report.txt: ${PYSOURCES}
+pylint_report.txt: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
 		$^ -j0> $@ || true
 
@@ -102,36 +112,39 @@ diff_pylint_report: pylint_report.txt
 	diff-quality --violations=pylint pylint_report.txt
 
 .coverage: $(PYSOURCES) all
-	coverage run ./setup.py test
+	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= -n auto ${PYTEST_EXTRA}"
 
 coverage.xml: .coverage
-	python-coverage xml
+	coverage xml
 
 coverage.html: htmlcov/index.html
 
 htmlcov/index.html: .coverage
-	python-coverage html
+	coverage html
 	@echo Test coverage of the Python code is now in htmlcov/index.html
 
 coverage-report: .coverage
-	python-coverage report
+	coverage report
 
-diff-cover: coverage-gcovr.xml coverage.xml
-	diff-cover coverage-gcovr.xml coverage.xml
+diff-cover: coverage.xml
+	diff-cover $^
 
-diff-cover.html: coverage-gcovr.xml coverage.xml
-	diff-cover coverage-gcovr.xml coverage.xml \
-		--html-report diff-cover.html
+diff-cover.html: coverage.xml
+	diff-cover $^ --html-report $@
 
 ## test        : run the ${MODULE} test suite
-test: all
-	python setup.py test
+test: $(PYSOURCES) all
+	python setup.py test ${PYTEST_EXTRA}
+
+## testcov     : run the ${MODULE} test suite and collect coverage
+testcov: $(PYSOURCES)
+	python setup.py test --addopts "--cov" ${PYTEST_EXTRA}
 
-sloccount.sc: ${PYSOURCES} Makefile
+sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@
 
 ## sloccount   : count lines of code
-sloccount: ${PYSOURCES} Makefile
+sloccount: $(PYSOURCES) Makefile
 	sloccount $^
 
 list-author-emails:
@@ -139,30 +152,33 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: ${PYSOURCES}
+mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
-		rm -Rf typeshed/2and3/ruamel/yaml ; \
+		rm -Rf typeshed/ruamel/yaml ; \
 		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			typeshed/2and3/ruamel/ ; \
+			typeshed/ruamel/ ; \
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
-	MYPYPATH=$$MYPYPATH:typeshed/3:typeshed/2and3 mypy --disallow-untyped-calls \
-		 --warn-redundant-casts \
-		 ${MODULE}
+	MYPYPATH=$$MYPYPATH:typeshed mypy $^
+
+pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
+	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
 	./release-test.sh
 
-release: FORCE
-	PYVER=3 ./release-test.sh
+release: release-test
 	. testenv2/bin/activate && \
-		python testenv2/src/${MODULE}/setup.py sdist bdist_wheel
+		python testenv2/src/${PACKAGE}/setup.py sdist bdist_wheel
 	. testenv2/bin/activate && \
 		pip install twine && \
-		twine upload testenv2/src/${MODULE}/dist/*whl && \
+		twine upload testenv2/src/${PACKAGE}/dist/* && \
 		git tag ${VERSION} && git push --tags
 
+flake8: $(PYSOURCES)
+	flake8 $^
+
 FORCE:
 
 # Use this to print the value of a Makefile variable
diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 7f9f4e3..33eb121 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -38,10 +38,10 @@
 DEFAULT_TIMEOUT = 600  # 10 minutes
 
 if sys.version_info < (3, 0):
-    import subprocess32 as subprocess
+    import subprocess32 as subprocess  # nosec
     from pipes import quote
 else:
-    import subprocess
+    import subprocess  # nosec
     from shlex import quote
 
 templock = threading.Lock()
@@ -145,7 +145,7 @@ def run_test(
 
         start_time = time.time()
         stderr = subprocess.PIPE if not args.verbose else None
-        process = subprocess.Popen(test_command, stdout=subprocess.PIPE, stderr=stderr, universal_newlines=True, cwd=cwd)
+        process = subprocess.Popen(test_command, stdout=subprocess.PIPE, stderr=stderr, universal_newlines=True, cwd=cwd)  # nosec
         outstr, outerr = process.communicate(timeout=timeout)
         return_code = process.poll()
         duration = time.time() - start_time
@@ -189,16 +189,16 @@ def run_test(
         _logger.error(outerr)
     except KeyboardInterrupt:
         _logger.error(
-            u"""Test %i interrupted: %s""",
+            """Test %i interrupted: %s""",
             test_number,
-            u" ".join([quote(tc) for tc in test_command]),
+            " ".join([quote(tc) for tc in test_command]),
         )
         raise
     except subprocess.TimeoutExpired:
         _logger.error(
-            u"""Test %i timed out: %s""",
+            """Test %i timed out: %s""",
             test_number,
-            u" ".join([quote(tc) for tc in test_command]),
+            " ".join([quote(tc) for tc in test_command]),
         )
         _logger.error(test.get("doc"))
         return TestResult(2, outstr, outerr, timeout, args.classname, "Test timed out")
@@ -379,17 +379,27 @@ def main():  # type: () -> int
         return 1
 
     schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
-    cache = {"https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode("utf-8")}  # type: Optional[Dict[str, Union[str, Graph, bool]]]
-    (document_loader,
-     avsc_names,
-     schema_metadata,
-     metaschema_loader) = schema_salad.schema.load_schema("https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache)
+    cache = {
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
+            "utf-8"
+        )
+    }  # type: Optional[Dict[str, Union[str, Graph, bool]]]
+    (
+        document_loader,
+        avsc_names,
+        schema_metadata,
+        metaschema_loader,
+    ) = schema_salad.schema.load_schema(
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
+    )
 
     if not isinstance(avsc_names, schema_salad.avro.schema.Names):
         print(avsc_names)
         return 1
 
-    tests, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, args.test, True)
+    tests, metadata = schema_salad.schema.load_and_validate(
+        document_loader, avsc_names, args.test, True
+    )
 
     failures = 0
     unsupported = 0
@@ -421,7 +431,7 @@ def main():  # type: () -> int
         tags = args.tags.split(",")
         for t in alltests:
             ts = t.get("tags", [])
-            if any((tag in ts for tag in tags)):
+            if any(tag in ts for tag in tags):
                 tests.append(t)
 
     for t in tests:
@@ -441,10 +451,10 @@ def main():  # type: () -> int
         for i, t in enumerate(tests):
             if t.get("short_name"):
                 print(
-                    u"[%i] %s: %s" % (i + 1, t["short_name"], t.get("doc", "").strip())
+                    "[%i] %s: %s" % (i + 1, t["short_name"], t.get("doc", "").strip())
                 )
             else:
-                print(u"[%i] %s" % (i + 1, t.get("doc", "").strip()))
+                print("[%i] %s" % (i + 1, t.get("doc", "").strip()))
 
         return 0
 
@@ -495,7 +505,7 @@ def main():  # type: () -> int
             for i, job in zip(ntest, jobs):
                 test_result = job.result()
                 test_case = test_result.create_test_case(tests[i])
-                test_case.url = "cwltest:{}#{}".format(suite_name, i + 1)
+                test_case.url = f"cwltest:{suite_name}#{i + 1}"
                 total += 1
                 tags = tests[i].get("tags", [])
                 for t in tags:
diff --git a/typeshed/2and3/future/__init__.pyi b/cwltest/py.typed
similarity index 100%
rename from typeshed/2and3/future/__init__.pyi
rename to cwltest/py.typed
diff --git a/cwltest/tests/test_categories.py b/cwltest/tests/test_categories.py
index 3ec6719..71798e9 100644
--- a/cwltest/tests/test_categories.py
+++ b/cwltest/tests/test_categories.py
@@ -5,7 +5,7 @@
 from os import sep as p
 
 from .util import run_with_mock_cwl_runner, get_data
-import xml.etree.ElementTree as ET
+import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
 
 class TestCategories(unittest.TestCase):
diff --git a/cwltest/tests/test_short_names.py b/cwltest/tests/test_short_names.py
index ca0367a..6efda7f 100644
--- a/cwltest/tests/test_short_names.py
+++ b/cwltest/tests/test_short_names.py
@@ -4,7 +4,7 @@
 from os import linesep as n
 
 from .util import run_with_mock_cwl_runner, get_data
-import xml.etree.ElementTree as ET
+import defusedxml.ElementTree as ET
 
 
 class TestShortNames(unittest.TestCase):
diff --git a/cwltest/tests/util.py b/cwltest/tests/util.py
index 3a2bc77..414db00 100644
--- a/cwltest/tests/util.py
+++ b/cwltest/tests/util.py
@@ -1,7 +1,7 @@
 import os
 import sys
 
-import subprocess
+import subprocess  # nosec
 
 from pkg_resources import (
     Requirement,
@@ -25,7 +25,7 @@ def get_data(filename):
 
 
 def run_with_mock_cwl_runner(args):
-    process = subprocess.Popen(
+    process = subprocess.Popen(  # nosec
         ["cwltest", "--tool", "mock-cwl-runner"] + args,
         stdout=subprocess.PIPE,
         stderr=subprocess.PIPE,
diff --git a/mypy.ini b/mypy.ini
index 2d48495..6a442f8 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,8 +1,13 @@
 [mypy]
-# --strict options as of mypy 0.720
+show_error_context = true
+show_column_numbers = true
+show_error_codes = true
+pretty = true
+
+# --strict options as of mypy 0.910
 warn_unused_configs = True
-disallow_subclassing_any = True
 disallow_any_generics = True
+disallow_subclassing_any = True
 disallow_untyped_calls = True
 disallow_untyped_defs = True
 disallow_incomplete_defs = True
@@ -12,14 +17,8 @@ no_implicit_optional = True
 warn_redundant_casts = True
 warn_unused_ignores = True
 warn_return_any = True
-implicit_reexport = True
-
-[mypy-schema_salad.tests.*]
-ignore_errors = True
+implicit_reexport = False
+strict_equality = True
 
 [mypy-ruamel.*]
 ignore_errors = True
-
-[mypy-cwltest.tests.*]
-ignore_errors = True
-
diff --git a/mypy_requirements.txt b/mypy_requirements.txt
new file mode 100644
index 0000000..e33b163
--- /dev/null
+++ b/mypy_requirements.txt
@@ -0,0 +1,3 @@
+mypy==0.910
+types-setuptools
+types-requests
diff --git a/release-test.sh b/release-test.sh
index 3fb3a1f..dcb6d90 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -7,15 +7,21 @@ export LC_ALL=C
 
 package=cwltest
 module=cwltest
-slug=${TRAVIS_PULL_REQUEST_SLUG:=common-workflow-language/${module}}
-repo=https://github.com/${slug}.git
+if [ "$GITHUB_ACTIONS" = "true" ]; then
+    # We are running as a GH Action
+    repo=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}.git
+    HEAD=${GITHUB_REF}
+else
+    repo=https://github.com/common-workflow-language/cwltest.git
+    HEAD=$(git rev-parse HEAD)
+fi
 run_tests="bin/py.test --pyargs ${module}"
 pipver=20.3b1 # minimum required version of pip for Python 3.9
 setuptoolsver=41.1.0 # required for Python 3.9
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
-rm -Rf "testenv${PYVER}_"? || /bin/true
+rm -Rf testenv? || /bin/true
 
-export HEAD=${TRAVIS_PULL_REQUEST_SHA:-$(git rev-parse HEAD)}
 
 if [ "${RELEASE_SKIP}" != "head" ]
 then
@@ -27,10 +33,9 @@ then
 	rm -f testenv1/lib/python-wheels/setuptools* \
 		&& pip install --force-reinstall -U pip==${pipver} \
 		&& pip install setuptools==${setuptoolsver} wheel
-	make install-dependencies
+	pip install -rtest-requirements.txt
 	make test
-	pip uninstall -y ${package} || true; pip uninstall -y ${package} \
-		|| true; make install
+	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 	mkdir testenv1/not-${module}
 	# if there is a subdir named '${module}' py.test will execute tests
 	# there instead of the installed module's tests
@@ -56,7 +61,7 @@ rm -f lib/python-wheels/setuptools* \
 # The following can fail if you haven't pushed your commits to ${repo}
 pip install -e "git+${repo}@${HEAD}#egg=${package}"
 pushd src/${package}
-make install-dependencies
+pip install -rtest-requirements.txt
 make dist
 make test
 cp dist/${package}*tar.gz ../../../testenv3/
@@ -76,13 +81,16 @@ source bin/activate
 rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
-pip install ${package}*tar.gz
-pip install pytest\<5
+package_tar=$(find . -name "${package}*tar.gz")
+pip install "-r${DIR}/test-requirements.txt"
+pip install "${package_tar}"
 mkdir out
 tar --extract --directory=out -z -f ${package}*.tar.gz
 pushd out/${package}*
 make dist
 make test
+pip install "-r${DIR}/mypy_requirements.txt"
+make mypy
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 mkdir ../not-${module}
 pushd ../not-${module}
@@ -100,7 +108,7 @@ rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
 pip install ${module}*.whl
-pip install pytest\<5
+pip install "-r${DIR}/test-requirements.txt"
 mkdir not-${module}
 pushd not-${module}
 # shellcheck disable=SC2086
diff --git a/requirements.txt b/requirements.txt
index de7919c..9eadc1f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
 schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
 pytest < 7
+defusedxml
diff --git a/setup.cfg b/setup.cfg
index 6c900c5..aae8e39 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,10 +1,14 @@
 [flake8]
 ignore = E124,E128,E129,E201,E202,E225,E226,E231,E265,E271,E302,E303,F401,E402,E501,W503,E731,F811,F821,F841
-
-[easy_install]
-
-[tool:pytest]
-testpaths = cwltest/tests
+max-line-length = 88
+extend-ignore = E203, W503
 
 [aliases]
 test=pytest
+
+[tool:isort]
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88
diff --git a/setup.py b/setup.py
index a98125b..bb098fb 100644
--- a/setup.py
+++ b/setup.py
@@ -15,15 +15,19 @@
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = ["schema-salad >= 5.0.20200220195218, < 9", "junit-xml >= 1.8"]
+install_requires = [
+    "schema-salad >= 5.0.20200220195218, < 9",
+    "junit-xml >= 1.8",
+    "defusedxml",
+]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
-pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []
+pytest_runner = ["pytest < 7", "pytest-runner"] if needs_pytest else []
 
 setup(
     name="cwltest",
-    version="2.1",
-    description="Common workflow language testing framework",
+    version="2.2",  # update the VERSION prefix in the Makefile as well 🙂
+    description="Common Workflow Language testing framework",
     long_description=open(README).read(),
     long_description_content_type="text/x-rst",
     author="Common workflow language working group",
@@ -31,12 +35,13 @@
     url="https://github.com/common-workflow-language/cwltest",
     download_url="https://github.com/common-workflow-language/cwltest",
     license="Apache 2.0",
+    python_requires=">=3.6, <4",
+    setup_requires=[] + pytest_runner,
     packages=["cwltest", "cwltest.tests"],
-    package_data={"cwltest.tests": ["test-data/*"]},
+    package_data={"cwltest": ["py.typed"], "cwltest.tests": ["test-data/*"]},
     include_package_data=True,
     install_requires=install_requires,
     test_suite="tests",
-    setup_requires=[] + pytest_runner,
     tests_require=["pytest<7"],
     entry_points={
         "console_scripts": [
@@ -46,5 +51,16 @@
     },
     zip_safe=True,
     cmdclass={"egg_info": tagger},
-    python_requires=">=3.5, <4",
+    classifiers=[
+        "Environment :: Console",
+        "License :: OSI Approved :: Apache Software License",
+        "Operating System :: POSIX",
+        "Operating System :: MacOS :: MacOS X",
+        "Development Status :: 5 - Production/Stable",
+        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Typing :: Typed",
+    ],
 )
diff --git a/test-requirements.txt b/test-requirements.txt
new file mode 100644
index 0000000..fb43315
--- /dev/null
+++ b/test-requirements.txt
@@ -0,0 +1,3 @@
+pytest >= 6.2, < 6.3
+pytest-cov
+pytest-xdist
diff --git a/tox.ini b/tox.ini
index 179e640..c0f3f1a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,65 +1,78 @@
 [tox]
 envlist =
-  py{36,37,38}-lint,
-  py{35,36,37,38}-unit,
-  py{35,36,37,38}-mypy,
-  py37-pipconflictchecker,
-  py37-lint-readme,
-  py37-pydocstyle
+  py{36,37,38,39}-lint,
+  py{36,37,38,39}-unit,
+  py{36,37,38,39}-bandit,
+  py{36,37,38,39}-mypy,
+  py39-pipconflictchecker,
+  py39-lint-readme,
+  py39-pydocstyle
 
 skipsdist = True
 skip_missing_interpreters = True
 
-[travis]
-os =
-  linux: py35-{unit,mypy}, py{36,38}-{lint,unit,mypy}, py37-{unit,mypy,pipconflictchecker,lint-readme,pydocstyle}
-  osx: py{35,36,38}-{unit,mypy}, py37-{unit,mypy}
+[pytest]
+addopts=-n auto --pyargs cwltest
+testpaths = cwltest/tests
+
+[gh-actions]
 python =
-  3.4: py34
-  3.5: py35
   3.6: py36
   3.7: py37
   3.8: py38
+  3.9: py39
 
 [testenv]
+description =
+  py{36,37,38,39}-unit: Run the unit tests
+  py{36,37,38,39}-lint: Lint the Python code
+  py{36,37,38,39}-bandit: Search for common security issues
+  py{36,37,38,39}-mypy: Check for type safety
+  py39-pydocstyle: docstring style checker
+  py39-lint-readme: Lint the README.rst->.md conversion
+
 passenv =
   CI
-  TRAVIS
-  TRAVIS_*
+  GITHUB_*
 deps =
-  -rrequirements.txt
-  py{35,36,37,38}-unit: codecov
-  py{35,36,37,38}-unit: pytest-xdist
-  py{35,36,37,38}-unit: pytest-cov
-  py{36,37,38}-lint: flake8
-  py{35,36,37,38}-mypy: mypy==0.782
+  py{36,37,38,39}-{unit,lint,bandit,mypy}: -rrequirements.txt
+  py{36,37,38,39}-{unit,mypy}: -rtest-requirements.txt
+  py{36,37,38,39}-lint: flake8-bugbear
+  py{36,37,38,39}-lint: black
+  py{36,37,38,39}-bandit: bandit
+  py{36,37,38,39}-mypy: -rmypy_requirements.txt
 
 setenv =
-  py{35,36,37,38}-unit: LC_ALL = C
+  py{36,37,38,39}-unit: LC_ALL = C.UTF-8
 
 commands =
-  py{35,36,37,38}-unit: python -m pip install -U pip setuptools wheel
-  py{35,36,37,38}-unit: python -m pip install -e .
-  py{35,36,37,38}-unit: coverage run --parallel-mode -m pytest --strict {posargs}
-  py{35,36,37,38}-unit: coverage combine
-  py{35,36,37,38}-unit: coverage report
-  py{35,36,37,38}-unit: coverage xml
-  py{35,36,37,38}-unit: codecov --file coverage.xml
-  py{36,37,38}-lint: flake8 cwltest setup.py
-  py{35,36,37,38}-mypy: make mypy
+  py{36,37,38,39}-unit: python -m pip install -U pip setuptools wheel
+  py{36,37,38,39}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py{36,37,38,39}-bandit: bandit --recursive cwltest
+  py{36,37,38,39}-lint: make flake8
+  py{36,37,38,39}-lint: make format-check
+  py{36,37,38,39}-mypy: make mypy
 
 whitelist_externals =
-  py{36,37,38}-lint: flake8
-  py{35,36,37,38}-mypy: make
+  py{36,37,38,39}-lint: flake8
+  py{36,37,38,39}-lint: black
+  py{36,37,38,39}-{mypy,shellcheck,lint,unit}: make
+
+[testenv:py39-pydocstyle]
+whitelist_externals = make
+commands = make diff_pydocstyle_report
+deps =
+    pydocstyle
+    diff-cover
 
-[testenv:py37-pipconflictchecker]
+[testenv:py39-pipconflictchecker]
 commands = pipconflictchecker
 whitelist_externals = pipconflictchecker
 deps =
   pip-conflict-checker
   pip==9.0.3
 
-[testenv:py37-lint-readme]
+[testenv:py39-lint-readme]
 commands =
   python setup.py sdist
   python setup.py bdist_wheel
@@ -68,10 +81,3 @@ deps =
     twine
     wheel
     readme_renderer[md]
-
-[testenv:py37-pydocstyle]
-whitelist_externals = make
-commands = make diff_pydocstyle_report
-deps =
-    pydocstyle
-    diff-cover
diff --git a/travis/os_install.sh b/travis/os_install.sh
deleted file mode 100644
index 1336699..0000000
--- a/travis/os_install.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-if [[ $TRAVIS_OS_NAME == 'linux' ]]; then
-    echo No special install needed on Linux
-    #wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list;
-    #sudo apt-key add .travis.singularity_key.txt;
-    #sudo apt-get update;
-    #sudo apt-get install -y singularity-container;
-elif [[ $TRAVIS_OS_NAME == "osx" ]]; then
-    pyenv install $PYENV_VERSION -s;
-    eval "$(pyenv init -)";
-    pyenv global $PYENV_VERSION;
-    pip install -U virtualenv;
-    VIRTUAL_ENV="$HOME/ve-pyenv-$PYENV_VERSION";
-    virtualenv -p "$(which python)" ${VIRTUALENV_EXTRA_ARGS:-} "$VIRTUAL_ENV";
-    source "$VIRTUAL_ENV/bin/activate";
-fi
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rename to typeshed/rdflib/events.pyi
diff --git a/typeshed/2and3/rdflib/exceptions.pyi b/typeshed/rdflib/exceptions.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/exceptions.pyi
rename to typeshed/rdflib/exceptions.pyi
diff --git a/typeshed/2and3/rdflib/graph.pyi b/typeshed/rdflib/graph.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/graph.pyi
rename to typeshed/rdflib/graph.pyi
diff --git a/typeshed/2and3/rdflib/namespace.pyi b/typeshed/rdflib/namespace.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/namespace.pyi
rename to typeshed/rdflib/namespace.pyi
diff --git a/typeshed/2and3/rdflib/parser.pyi b/typeshed/rdflib/parser.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/parser.pyi
rename to typeshed/rdflib/parser.pyi
diff --git a/typeshed/2and3/rdflib/plugin.pyi b/typeshed/rdflib/plugin.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/plugin.pyi
rename to typeshed/rdflib/plugin.pyi
diff --git a/typeshed/2and3/rdflib/plugins/__init__.pyi b/typeshed/rdflib/plugins/__init__.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/plugins/__init__.pyi
rename to typeshed/rdflib/plugins/__init__.pyi
diff --git a/typeshed/2and3/rdflib/plugins/parsers/__init__.pyi b/typeshed/rdflib/plugins/parsers/__init__.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/plugins/parsers/__init__.pyi
rename to typeshed/rdflib/plugins/parsers/__init__.pyi
diff --git a/typeshed/2and3/rdflib/plugins/parsers/notation3.pyi b/typeshed/rdflib/plugins/parsers/notation3.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/plugins/parsers/notation3.pyi
rename to typeshed/rdflib/plugins/parsers/notation3.pyi
diff --git a/typeshed/2and3/rdflib/query.pyi b/typeshed/rdflib/query.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/query.pyi
rename to typeshed/rdflib/query.pyi
diff --git a/typeshed/2and3/rdflib/serializer.pyi b/typeshed/rdflib/serializer.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/serializer.pyi
rename to typeshed/rdflib/serializer.pyi
diff --git a/typeshed/2and3/rdflib/store.pyi b/typeshed/rdflib/store.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/store.pyi
rename to typeshed/rdflib/store.pyi
diff --git a/typeshed/2and3/rdflib/term.pyi b/typeshed/rdflib/term.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/term.pyi
rename to typeshed/rdflib/term.pyi
diff --git a/typeshed/2and3/rdflib/util.pyi b/typeshed/rdflib/util.pyi
similarity index 100%
rename from typeshed/2and3/rdflib/util.pyi
rename to typeshed/rdflib/util.pyi
diff --git a/typeshed/3/urllib/__init__.py b/typeshed/ruamel/__init__.py
similarity index 100%
rename from typeshed/3/urllib/__init__.py
rename to typeshed/ruamel/__init__.py
diff --git a/typeshed/2and3/select.pyi b/typeshed/select.pyi
similarity index 100%
rename from typeshed/2and3/select.pyi
rename to typeshed/select.pyi
diff --git a/typeshed/2and3/shellescape/__init__.pyi b/typeshed/shellescape/__init__.pyi
similarity index 100%
rename from typeshed/2and3/shellescape/__init__.pyi
rename to typeshed/shellescape/__init__.pyi
diff --git a/typeshed/2and3/shellescape/main.pyi b/typeshed/shellescape/main.pyi
similarity index 100%
rename from typeshed/2and3/shellescape/main.pyi
rename to typeshed/shellescape/main.pyi
diff --git a/typeshed/urllib/__init__.py b/typeshed/urllib/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/typeshed/3/urllib/parse.pyi b/typeshed/urllib/parse.pyi
similarity index 100%
rename from typeshed/3/urllib/parse.pyi
rename to typeshed/urllib/parse.pyi
diff --git a/typeshed/3/urllib/subprocess.pyi b/typeshed/urllib/subprocess.pyi
similarity index 100%
rename from typeshed/3/urllib/subprocess.pyi
rename to typeshed/urllib/subprocess.pyi

From a1123671152b20a0d54ff089d50d0bd2b2101abb Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 1 Sep 2021 15:48:51 +0200
Subject: [PATCH 011/165] pyupgrade to 3.6+ syntax

---
 cwltest/__init__.py              | 68 +++++++++++++++++---------------
 cwltest/tests/test_categories.py | 26 ++++++++++--
 cwltest/tests/test_prepare.py    |  6 +--
 cwltest/utils.py                 | 28 ++++++-------
 4 files changed, 75 insertions(+), 53 deletions(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 33eb121..dcf9df7 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -37,12 +37,8 @@
 UNSUPPORTED_FEATURE = 33
 DEFAULT_TIMEOUT = 600  # 10 minutes
 
-if sys.version_info < (3, 0):
-    import subprocess32 as subprocess  # nosec
-    from pipes import quote
-else:
-    import subprocess  # nosec
-    from shlex import quote
+import subprocess  # nosec
+from shlex import quote
 
 templock = threading.Lock()
 
@@ -55,7 +51,7 @@ def prepare_test_command(
     cwd,  # type: str
     verbose=False,  # type: bool
 ):  # type: (...) -> List[str]
-    """ Turn the test into a command line. """
+    """Turn the test into a command line."""
     test_command = [tool]
     test_command.extend(args)
 
@@ -72,26 +68,26 @@ def prepare_test_command(
             outdir = tempfile.mkdtemp(prefix=os.path.abspath(os.path.curdir))
             test_command.extend(
                 [
-                    "--tmp-outdir-prefix={}".format(outdir),
-                    "--tmpdir-prefix={}".format(outdir),
+                    f"--tmp-outdir-prefix={outdir}",
+                    f"--tmpdir-prefix={outdir}",
                 ]
             )
         else:
             outdir = tempfile.mkdtemp()
-    test_command.extend(["--outdir={}".format(outdir)])
+    test_command.extend([f"--outdir={outdir}"])
     if not verbose:
         test_command.extend(["--quiet"])
 
     cwd = schema_salad.ref_resolver.file_uri(cwd)
     toolpath = test["tool"]
     if toolpath.startswith(cwd):
-        toolpath = toolpath[len(cwd)+1:]
+        toolpath = toolpath[len(cwd) + 1 :]
     test_command.extend([os.path.normcase(toolpath)])
 
     jobpath = test.get("job")
     if jobpath:
         if jobpath.startswith(cwd):
-            jobpath = jobpath[len(cwd)+1:]
+            jobpath = jobpath[len(cwd) + 1 :]
         test_command.append(os.path.normcase(jobpath))
     return test_command
 
@@ -108,7 +104,7 @@ def run_test(
     global templock
 
     out = {}  # type: Dict[str,Any]
-    outdir = outstr = outerr = u""
+    outdir = outstr = outerr = ""
     test_command = []  # type: List[str]
     duration = 0.0
     prefix = ""
@@ -145,7 +141,13 @@ def run_test(
 
         start_time = time.time()
         stderr = subprocess.PIPE if not args.verbose else None
-        process = subprocess.Popen(test_command, stdout=subprocess.PIPE, stderr=stderr, universal_newlines=True, cwd=cwd)  # nosec
+        process = subprocess.Popen(  # nosec
+            test_command,
+            stdout=subprocess.PIPE,
+            stderr=stderr,
+            universal_newlines=True,
+            cwd=cwd,
+        )
         outstr, outerr = process.communicate(timeout=timeout)
         return_code = process.poll()
         duration = time.time() - start_time
@@ -167,25 +169,25 @@ def run_test(
         if test.get("should_fail", False):
             return TestResult(0, outstr, outerr, duration, args.classname)
         _logger.error(
-            u"""Test %i failed: %s""",
+            """Test %i failed: %s""",
             test_number,
             " ".join([quote(tc) for tc in test_command]),
         )
         _logger.error(test.get("doc"))
         if err.returncode == UNSUPPORTED_FEATURE:
-            _logger.error(u"Does not support required feature")
+            _logger.error("Does not support required feature")
         else:
-            _logger.error(u"Returned non-zero")
+            _logger.error("Returned non-zero")
         _logger.error(outerr)
         return TestResult(1, outstr, outerr, duration, args.classname, str(err))
     except (yamlscanner.ScannerError, TypeError) as err:
         _logger.error(
-            u"""Test %i failed: %s""",
+            """Test %i failed: %s""",
             test_number,
-            u" ".join([quote(tc) for tc in test_command]),
+            " ".join([quote(tc) for tc in test_command]),
         )
         _logger.error(outstr)
-        _logger.error(u"Parse error %s", str(err))
+        _logger.error("Parse error %s", str(err))
         _logger.error(outerr)
     except KeyboardInterrupt:
         _logger.error(
@@ -204,7 +206,7 @@ def run_test(
         return TestResult(2, outstr, outerr, timeout, args.classname, "Test timed out")
     finally:
         if process is not None and process.returncode is None:
-            _logger.error(u"""Terminating lingering process""")
+            _logger.error("""Terminating lingering process""")
             process.terminate()
             for _ in range(0, 3):
                 time.sleep(1)
@@ -217,24 +219,24 @@ def run_test(
 
     if test.get("should_fail", False):
         _logger.warning(
-            u"""Test %i failed: %s""",
+            """Test %i failed: %s""",
             test_number,
-            u" ".join([quote(tc) for tc in test_command]),
+            " ".join([quote(tc) for tc in test_command]),
         )
         _logger.warning(test.get("doc"))
-        _logger.warning(u"Returned zero but it should be non-zero")
+        _logger.warning("Returned zero but it should be non-zero")
         return TestResult(1, outstr, outerr, duration, args.classname)
 
     try:
         compare(test.get("output"), out)
     except CompareFail as ex:
         _logger.warning(
-            u"""Test %i failed: %s""",
+            """Test %i failed: %s""",
             test_number,
-            u" ".join([quote(tc) for tc in test_command]),
+            " ".join([quote(tc) for tc in test_command]),
         )
         _logger.warning(test.get("doc"))
-        _logger.warning(u"Compare failure %s", ex)
+        _logger.warning("Compare failure %s", ex)
         fail_message = str(ex)
 
     if outdir:
@@ -345,13 +347,14 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     pkg = pkg_resources.require("cwltest")
     if pkg:
-        ver = u"%s %s" % (sys.argv[0], pkg[0].version)
+        ver = f"{sys.argv[0]} {pkg[0].version}"
     else:
-        ver = u"%s %s" % (sys.argv[0], "unknown version")
+        ver = "{} {}".format(sys.argv[0], "unknown version")
     parser.add_argument("--version", action="https://github.com/version", version=ver)
 
     return parser
 
+
 def expand_number_range(nr: str) -> List[int]:
     ans: List[int] = []
     for s in nr.split(","):
@@ -362,6 +365,7 @@ def expand_number_range(nr: str) -> List[int]:
             ans.append(int(s) - 1)
     return ans
 
+
 def main():  # type: () -> int
 
     args = arg_parser().parse_args(sys.argv[1:])
@@ -558,12 +562,12 @@ def main():  # type: () -> int
             else:
                 color = "yellow"
 
-            with open("{}/{}.json".format(args.badgedir, t), "w") as out:
+            with open(f"{args.badgedir}/{t}.json", "w") as out:
                 out.write(
                     json.dumps(
                         {
-                            "subject": "{}".format(t),
-                            "status": "{}%".format(percent),
+                            "subject": f"{t}",
+                            "status": f"{percent}%",
                             "color": color,
                         }
                     )
diff --git a/cwltest/tests/test_categories.py b/cwltest/tests/test_categories.py
index 71798e9..d1e1de2 100644
--- a/cwltest/tests/test_categories.py
+++ b/cwltest/tests/test_categories.py
@@ -8,11 +8,17 @@
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
 
+
 class TestCategories(unittest.TestCase):
     maxDiff = None
 
     def test_unsupported_with_required_tests(self):
-        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/required-unsupported.yml"))]
+        args = [
+            "--test",
+            schema_salad.ref_resolver.file_uri(
+                get_data("tests/test-data/required-unsupported.yml")
+            ),
+        ]
         try:
             cwd = os.getcwd()
             os.chdir(get_data("tests/test-data/"))
@@ -47,7 +53,12 @@ def test_unsupported_with_required_tests(self):
         )
 
     def test_unsupported_with_optional_tests(self):
-        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-unsupported.yml"))]
+        args = [
+            "--test",
+            schema_salad.ref_resolver.file_uri(
+                get_data("tests/test-data/optional-unsupported.yml")
+            ),
+        ]
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
         self.assertEqual(error_code, 0)
         self.assertEqual(
@@ -58,7 +69,12 @@ def test_unsupported_with_optional_tests(self):
         )
 
     def test_error_with_optional_tests(self):
-        args = ["--test", schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-error.yml"))]
+        args = [
+            "--test",
+            schema_salad.ref_resolver.file_uri(
+                get_data("tests/test-data/optional-error.yml")
+            ),
+        ]
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
         self.assertEqual(error_code, 1)
         self.assertIn("1 failures", stderr)
@@ -67,7 +83,9 @@ def test_category_in_junit_xml(self):
         junit_xml_report = get_data("tests/test-data/junit-report.xml")
         args = [
             "--test",
-            schema_salad.ref_resolver.file_uri(get_data("tests/test-data/optional-error.yml")),
+            schema_salad.ref_resolver.file_uri(
+                get_data("tests/test-data/optional-error.yml")
+            ),
             "--junit-xml",
             junit_xml_report,
         ]
diff --git a/cwltest/tests/test_prepare.py b/cwltest/tests/test_prepare.py
index 3d93487..d09f039 100644
--- a/cwltest/tests/test_prepare.py
+++ b/cwltest/tests/test_prepare.py
@@ -4,10 +4,10 @@
 
 
 class TestPrepareCommand(unittest.TestCase):
-    """ Test prepare_test_command() """
+    """Test prepare_test_command()"""
 
     def test_unix_relative_path(self):
-        """ Confirm unix style to windows style path corrections. """
+        """Confirm unix style to windows style path corrections."""
         command = prepare_test_command(
             tool="cwl-runner",
             args=[],
@@ -19,7 +19,7 @@ def test_unix_relative_path(self):
                 "job": "v1.0/bwa-mem-job.json",
                 "tags": ["required"],
             },
-            cwd=os.getcwd()
+            cwd=os.getcwd(),
         )
         if os.name == "nt":
             self.assertEqual(command[3], "v1.0\\bwa-mem-tool.cwl")
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 034b538..13ea3fb 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -7,7 +7,7 @@
 REQUIRED = "required"
 
 
-class TestResult(object):
+class TestResult:
 
     """Encapsulate relevant test result data."""
 
@@ -30,12 +30,12 @@ def __init__(
 
     def create_test_case(self, test):
         # type: (Dict[Text, Any]) -> junit_xml.TestCase
-        doc = test.get(u"doc", "N/A").strip()
+        doc = test.get("doc", "N/A").strip()
         if test.get("tags"):
             category = ", ".join(test["tags"])
         else:
             category = REQUIRED
-        short_name = test.get(u"short_name")
+        short_name = test.get("short_name")
         case = junit_xml.TestCase(
             doc,
             elapsed_sec=self.duration,
@@ -53,12 +53,12 @@ class CompareFail(Exception):
     @classmethod
     def format(cls, expected, actual, cause=None):
         # type: (Any, Any, Any) -> CompareFail
-        message = u"expected: %s\ngot: %s" % (
+        message = "expected: {}\ngot: {}".format(
             json.dumps(expected, indent=4, sort_keys=True),
             json.dumps(actual, indent=4, sort_keys=True),
         )
         if cause:
-            message += u"\ncaused by: %s" % cause
+            message += "\ncaused by: %s" % cause
         return cls(message)
 
 
@@ -84,7 +84,7 @@ def compare_location(expected, actual):
         raise CompareFail.format(
             expected,
             actual,
-            u"%s does not end with %s" % (actual[comp], expected[comp]),
+            f"{actual[comp]} does not end with {expected[comp]}",
         )
 
 
@@ -98,7 +98,7 @@ def compare_contents(expected, actual):
             expected,
             actual,
             json.dumps(
-                u"Output file contents do not match: actual '%s' is not equal to expected '%s'"
+                "Output file contents do not match: actual '%s' is not equal to expected '%s'"
                 % (actual_contents, expected_contents)
             ),
         )
@@ -111,7 +111,7 @@ def check_keys(keys, expected, actual):
             compare(expected.get(k), actual.get(k))
         except CompareFail as e:
             raise CompareFail.format(
-                expected, actual, u"field '%s' failed comparison: %s" % (k, str(e))
+                expected, actual, f"field '{k}' failed comparison: {str(e)}"
             )
 
 
@@ -128,11 +128,11 @@ def compare_directory(expected, actual):
     # type: (Dict[str,Any], Dict[str,Any]) -> None
     if actual.get("class") != "Directory":
         raise CompareFail.format(
-            expected, actual, u"expected object with a class 'Directory'"
+            expected, actual, "expected object with a class 'Directory'"
         )
     if "listing" not in actual:
         raise CompareFail.format(
-            expected, actual, u"'listing' is mandatory field in Directory object"
+            expected, actual, "'listing' is mandatory field in Directory object"
         )
     for i in expected["listing"]:
         found = False
@@ -147,7 +147,7 @@ def compare_directory(expected, actual):
             raise CompareFail.format(
                 expected,
                 actual,
-                u"%s not found" % json.dumps(i, indent=4, sort_keys=True),
+                "%s not found" % json.dumps(i, indent=4, sort_keys=True),
             )
     compare_file(expected, actual)
 
@@ -159,12 +159,12 @@ def compare_dict(expected, actual):
             compare(expected[c], actual.get(c))
         except CompareFail as e:
             raise CompareFail.format(
-                expected, actual, u"failed comparison for key '%s': %s" % (c, e)
+                expected, actual, f"failed comparison for key '{c}': {e}"
             )
     extra_keys = set(actual.keys()).difference(list(expected.keys()))
     for k in extra_keys:
         if actual[k] is not None:
-            raise CompareFail.format(expected, actual, u"unexpected key '%s'" % k)
+            raise CompareFail.format(expected, actual, "unexpected key '%s'" % k)
 
 
 def compare(expected, actual):  # type: (Any, Any) -> None
@@ -190,7 +190,7 @@ def compare(expected, actual):  # type: (Any, Any) -> None
                 raise CompareFail.format(expected, actual)
 
             if len(expected) != len(actual):
-                raise CompareFail.format(expected, actual, u"lengths don't match")
+                raise CompareFail.format(expected, actual, "lengths don't match")
             for c in range(0, len(expected)):
                 try:
                     compare(expected[c], actual[c])

From 6c38dbe195022babfeb78acc6e5f643392b23bd8 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 1 Sep 2021 16:01:24 +0200
Subject: [PATCH 012/165] sort inputs

---
 cwltest/__init__.py | 26 ++++++++++++--------------
 cwltest/utils.py    |  3 +--
 2 files changed, 13 insertions(+), 16 deletions(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index dcf9df7..d2d40aa 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -5,28 +5,29 @@
 import logging
 import os
 import shutil
+import subprocess  # nosec
 import sys
 import tempfile
 import threading
 import time
-from typing import Any, Dict, List, Optional, Set, Text, Union
-from concurrent.futures import ThreadPoolExecutor
 from collections import defaultdict
-from rdflib import Graph
+from concurrent.futures import ThreadPoolExecutor
+from shlex import quote
+from typing import Any, Dict, List, Optional, Set, Union
 
-import ruamel.yaml as yaml
+import junit_xml
+import pkg_resources  # part of setuptools
 import ruamel.yaml.scanner as yamlscanner
+import schema_salad.avro.schema
 import schema_salad.ref_resolver
 import schema_salad.schema
-import schema_salad.avro.schema
-import pkg_resources  # part of setuptools
+from rdflib import Graph
 
-import junit_xml
 from cwltest.utils import (
-    compare,
+    REQUIRED,
     CompareFail,
     TestResult,
-    REQUIRED,
+    compare,
     get_test_number_by_key,
 )
 
@@ -37,9 +38,6 @@
 UNSUPPORTED_FEATURE = 33
 DEFAULT_TIMEOUT = 600  # 10 minutes
 
-import subprocess  # nosec
-from shlex import quote
-
 templock = threading.Lock()
 
 
@@ -391,8 +389,8 @@ def main():  # type: () -> int
     (
         document_loader,
         avsc_names,
-        schema_metadata,
-        metaschema_loader,
+        _,
+        _,
     ) = schema_salad.schema.load_schema(
         "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
     )
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 13ea3fb..984d8a8 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -1,6 +1,5 @@
 import json
-
-from typing import Any, Dict, Set, Text, List, Optional
+from typing import Any, Dict, List, Optional, Set, Text
 
 import junit_xml
 

From 097088ecfd599c7a096e9d3fc05d458456d2a641 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 1 Sep 2021 16:18:17 +0200
Subject: [PATCH 013/165] print command in verbose mode

---
 cwltest/__init__.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index d2d40aa..577a19f 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -96,6 +96,7 @@ def run_test(
     test_number,  # type: int
     total_tests,  # type: int
     timeout,  # type: int
+    junit_verbose=False,  # type: bool
     verbose=False,  # type: bool
 ):  # type: (...) -> TestResult
 
@@ -115,7 +116,7 @@ def run_test(
         process = None  # type: Optional[subprocess.Popen[str]]
         cwd = os.getcwd()
         test_command = prepare_test_command(
-            args.tool, args.args, args.testargs, test, cwd, verbose
+            args.tool, args.args, args.testargs, test, cwd, junit_verbose
         )
 
         if test.get("short_name"):
@@ -135,6 +136,8 @@ def run_test(
                 "%sTest [%i/%i] %s%s\n"
                 % (prefix, test_number, total_tests, test.get("doc"), suffix)
             )
+        if verbose:
+            sys.stderr.write(f"Running: {' '.join(test_command)}\n")
         sys.stderr.flush()
 
         start_time = time.time()
@@ -386,12 +389,7 @@ def main():  # type: () -> int
             "utf-8"
         )
     }  # type: Optional[Dict[str, Union[str, Graph, bool]]]
-    (
-        document_loader,
-        avsc_names,
-        _,
-        _,
-    ) = schema_salad.schema.load_schema(
+    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
         "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
     )
 
@@ -500,6 +498,7 @@ def main():  # type: () -> int
                 len(tests),
                 args.timeout,
                 args.junit_verbose,
+                args.verbose,
             )
             for i in ntest
         ]

From e27d9bed1e48ad54727ac24874339d6f2b36304e Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 5 Oct 2021 17:55:57 +0200
Subject: [PATCH 014/165] update badges

---
 README.rst   | 49 ++++++++++++++++++++++++++++++++++++++-----------
 appveyor.yml | 48 ------------------------------------------------
 2 files changed, 38 insertions(+), 59 deletions(-)
 delete mode 100644 appveyor.yml

diff --git a/README.rst b/README.rst
index decd324..bd0df40 100644
--- a/README.rst
+++ b/README.rst
@@ -1,30 +1,57 @@
-|Linux Build Status| |Windows Build status| |Code coverage|
+==========================================
+Common Workflow Language testing framework
+==========================================
+
+|Linux Build Status| |Code coverage|
+
+PyPI: |PyPI Version| |PyPI Downloads Month| |Total PyPI Downloads|
 
-.. |Linux Build Status| image:: https://img.shields.io/travis/common-workflow-language/cwltest/master.svg?label=unix%20build
-   :target: https://travis-ci.org/common-workflow-language/cwltest
-.. |Windows Build status| image:: https://img.shields.io/appveyor/ci/mr-c/cwltest/master.svg?label=windows%20build
-   :target: https://ci.appveyor.com/project/mr-c/cwltest/branch/master
+Conda: |Conda Version| |Conda Installs|
+
+.. |Linux Build Status| image:: https://github.com/common-workflow-language/cwltest/actions/workflows/ci-tests.yml/badge.svg?branch=main
+   :target: https://github.com/common-workflow-language/cwltest/actions/workflows/ci-tests.yml
 .. |Code coverage| image:: https://codecov.io/gh/common-workflow-language/cwltest/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/common-workflow-language/cwltest
 
-==========================================
-Common workflow language testing framework
-==========================================
+.. |PyPI Version| image:: https://badge.fury.io/py/cwltest.svg
+   :target: https://badge.fury.io/py/cwltest
+
+.. |PyPI Downloads Month| image:: https://pepy.tech/badge/cwltest/month
+   :target: https://pepy.tech/project/cwltest
+
+.. |Total PyPI Downloads| image:: https://static.pepy.tech/personalized-badge/cwltest?period=total&units=international_system&left_color=black&right_color=orange&left_text=Total%20PyPI%20Downloads
+   :target: https://pepy.tech/project/cwltest
+
+.. |Conda Version| image:: https://anaconda.org/bioconda/cwltest/badges/version.svg
+   :target: https://anaconda.org/bioconda/cwltest
+
+.. |Conda Installs| image:: https://anaconda.org/bioconda/cwltest/badges/downloads.svg
+   :target: https://anaconda.org/bioconda/cwltest
 
 This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 2.7, 3.4, 3.5, 3.6, and 3.7
+This is written and tested for Python 3.6, 3.7, 3.8, and 3.9
 
 Install
 -------
 
-Installing the official package from PyPi::
+Installing the official package from PyPi
+
+.. code:: bash
 
   pip install cwltest
 
-Or from source::
+Or from bioconda
+
+.. code:: bash
+
+  conda install -c bioconda cwltest
+
+Or from source
+
+.. code:: bash
 
   git clone https://github.com/common-workflow-language/cwltest.git
   cd cwltest && python setup.py install
diff --git a/appveyor.yml b/appveyor.yml
deleted file mode 100644
index 8ca6123..0000000
--- a/appveyor.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-version: .{build}-{branch}
-
-cache:
- - '%LOCALAPPDATA%\pip\Cache'
-
-environment:
-
-  SYSTEMROOT: "C:\\WINDOWS"
-
-  matrix:
-    - PYTHON: "C:\\Python35-x64"
-      PYTHON_VERSION: "3.5.x"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python36-x64"
-      PYTHON_VERSION: "3.6.x"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python37-x64"
-      PYTHON_VERSION: "3.7.x"
-      PYTHON_ARCH: "64"
-
-    - PYTHON: "C:\\Python38-x64"
-      PYTHON_VERSION: "3.8.x"
-      PYTHON_ARCH: "64"
-
-install:
-  - "%PYTHON%\\python.exe -m pip install -U pip setuptools^>=20.3"
-  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-  # Note the use of a `^` to escape the `>`
-
-build_script:
-  - |
-        %PYTHON%\\python.exe -m pip install -U wheel pytest pytest-xdist
-        %PYTHON%\\python.exe -m pip install -e .
-
-test_script:
-  - |
-        %PYTHON%\\python.exe setup.py test --addopts "--verbose -p no:cacheprovider --junit-xml=tests.xml"
-
-on_finish:
-  - ps: |
-      $wc = New-Object 'System.Net.WebClient'
-      $wc.UploadFile("https://ci.appveyor.com/api/testresults/junit/$($Env:APPVEYOR_JOB_ID)", (Resolve-Path .\tests.xml))
-
-branches:
-  only:
-    - master

From f69e1249cc44e916ba2c2df3886c52691275ebb7 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Mon, 15 Nov 2021 10:39:39 -0500
Subject: [PATCH 015/165] Collect output from timed-out tests

This should fix https://github.com/common-workflow-language/cwltest/issues/121
---
 cwltest/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 577a19f..3dc97c8 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -204,6 +204,10 @@ def run_test(
             " ".join([quote(tc) for tc in test_command]),
         )
         _logger.error(test.get("doc"))
+        # Kill and re-communicate to get the logs and reap the child, as
+        # instructed in the subprocess docs.
+        process.kill()
+        outstr, outerr = process.communicate()
         return TestResult(2, outstr, outerr, timeout, args.classname, "Test timed out")
     finally:
         if process is not None and process.returncode is None:

From af69301f47f8a15520e228d9a8c05ae9e0176fa0 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 15 Nov 2021 18:02:57 +0100
Subject: [PATCH 016/165] only if we got a Process object back

---
 cwltest/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 3dc97c8..9e0ec7a 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -206,8 +206,9 @@ def run_test(
         _logger.error(test.get("doc"))
         # Kill and re-communicate to get the logs and reap the child, as
         # instructed in the subprocess docs.
-        process.kill()
-        outstr, outerr = process.communicate()
+        if process:
+            process.kill()
+            outstr, outerr = process.communicate()
         return TestResult(2, outstr, outerr, timeout, args.classname, "Test timed out")
     finally:
         if process is not None and process.returncode is None:

From 027e688bb2f0292c497c24d0e50abb1396e14827 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 15 Nov 2021 18:29:02 +0100
Subject: [PATCH 017/165] modernize tests

---
 cwltest/tests/test_argparse.py    |  27 ++---
 cwltest/tests/test_categories.py  | 159 +++++++++++++++---------------
 cwltest/tests/test_compare.py     | 107 ++++++++++----------
 cwltest/tests/test_prepare.py     |  47 +++++----
 cwltest/tests/test_short_names.py |  94 +++++++++---------
 5 files changed, 207 insertions(+), 227 deletions(-)

diff --git a/cwltest/tests/test_argparse.py b/cwltest/tests/test_argparse.py
index 6a5c067..729cd5c 100644
--- a/cwltest/tests/test_argparse.py
+++ b/cwltest/tests/test_argparse.py
@@ -1,20 +1,13 @@
-import unittest
 from cwltest import arg_parser
 
 
-class TestArgparse(unittest.TestCase):
-    def setUp(self):
-        self.parser = arg_parser()
-
-    def test_arg(self):
-        parsed = self.parser.parse_args(
-            ["--test", "test_name", "-n", "52", "--tool", "cwltool", "-j", "4"]
-        )
-        self.assertEqual(parsed.test, "test_name")
-        self.assertEqual(parsed.n, "52")
-        self.assertEqual(parsed.tool, "cwltool")
-        self.assertEqual(parsed.j, 4)
-
-
-if __name__ == "__main__":
-    unittest.main()
+def test_arg():
+    """Basic test of the argparse."""
+    parser = arg_parser()
+    parsed = parser.parse_args(
+        ["--test", "test_name", "-n", "52", "--tool", "cwltool", "-j", "4"]
+    )
+    assert parsed.test == "test_name"
+    assert parsed.n == "52"
+    assert parsed.tool == "cwltool"
+    assert parsed.j == 4
diff --git a/cwltest/tests/test_categories.py b/cwltest/tests/test_categories.py
index d1e1de2..77e8711 100644
--- a/cwltest/tests/test_categories.py
+++ b/cwltest/tests/test_categories.py
@@ -1,97 +1,92 @@
-import unittest
 import re
 import os
 from os import linesep as n
 from os import sep as p
+from pathlib import Path
 
 from .util import run_with_mock_cwl_runner, get_data
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
 
 
-class TestCategories(unittest.TestCase):
-    maxDiff = None
+def test_unsupported_with_required_tests():
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/required-unsupported.yml")
+        ),
+    ]
+    try:
+        cwd = os.getcwd()
+        os.chdir(get_data("tests/test-data/"))
+        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    finally:
+        os.chdir(cwd)
 
-    def test_unsupported_with_required_tests(self):
-        args = [
-            "--test",
-            schema_salad.ref_resolver.file_uri(
-                get_data("tests/test-data/required-unsupported.yml")
-            ),
-        ]
-        try:
-            cwd = os.getcwd()
-            os.chdir(get_data("tests/test-data/"))
-            error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        finally:
-            os.chdir(cwd)
+    assert error_code == 1
+    print(stderr)
+    stderr = re.sub(r" '?--outdir=[^ ]*", "", stderr)
+    if os.name == "nt":
+        q = "'"
+    else:
+        q = ""
+    assert (
+        "Test [1/2] Required test that is unsupported (without tags){n}"
+        "{n}"
+        "Test 1 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        "Required test that is unsupported (without tags){n}"
+        "Does not support required feature{n}"
+        "{n}"
+        "Test [2/2] Required test that is unsupported (with tags){n}"
+        "{n}"
+        "Test 2 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        "Required test that is unsupported (with tags){n}"
+        "Does not support required feature{n}"
+        "{n}"
+        "0 tests passed, 2 failures, 0 unsupported features{n}".format(n=n, p=p, q=q)
+    ) == stderr
 
-        self.assertEqual(error_code, 1)
-        print(stderr)
-        stderr = re.sub(r" '?--outdir=[^ ]*", "", stderr)
-        if os.name == "nt":
-            q = "'"
-        else:
-            q = ""
-        self.assertEqual(
-            "Test [1/2] Required test that is unsupported (without tags){n}"
-            "{n}"
-            "Test 1 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
-            "Required test that is unsupported (without tags){n}"
-            "Does not support required feature{n}"
-            "{n}"
-            "Test [2/2] Required test that is unsupported (with tags){n}"
-            "{n}"
-            "Test 2 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
-            "Required test that is unsupported (with tags){n}"
-            "Does not support required feature{n}"
-            "{n}"
-            "0 tests passed, 2 failures, 0 unsupported features{n}".format(
-                n=n, p=p, q=q
-            ),
-            stderr,
-        )
 
-    def test_unsupported_with_optional_tests(self):
-        args = [
-            "--test",
-            schema_salad.ref_resolver.file_uri(
-                get_data("tests/test-data/optional-unsupported.yml")
-            ),
-        ]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        self.assertEqual(error_code, 0)
-        self.assertEqual(
-            "Test [1/1] Optional test that is unsupported{n}{n}"
-            "0 tests passed, 1 unsupported "
-            "features{n}".format(n=n),
-            stderr,
-        )
+def test_unsupported_with_optional_tests():
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/optional-unsupported.yml")
+        ),
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert error_code == 0
+    assert (
+        "Test [1/1] Optional test that is unsupported{n}{n}"
+        "0 tests passed, 1 unsupported "
+        "features{n}".format(n=n)
+    ) == stderr
+
+
+def test_error_with_optional_tests():
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/optional-error.yml")
+        ),
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert error_code == 1
+    assert "1 failures" in stderr
 
-    def test_error_with_optional_tests(self):
-        args = [
-            "--test",
-            schema_salad.ref_resolver.file_uri(
-                get_data("tests/test-data/optional-error.yml")
-            ),
-        ]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        self.assertEqual(error_code, 1)
-        self.assertIn("1 failures", stderr)
 
-    def test_category_in_junit_xml(self):
-        junit_xml_report = get_data("tests/test-data/junit-report.xml")
-        args = [
-            "--test",
-            schema_salad.ref_resolver.file_uri(
-                get_data("tests/test-data/optional-error.yml")
-            ),
-            "--junit-xml",
-            junit_xml_report,
-        ]
-        run_with_mock_cwl_runner(args)
-        tree = ET.parse(junit_xml_report)
-        root = tree.getroot()
-        category = root.find("testsuite").find("testcase").attrib["class"]
-        self.assertEqual(category, "js, init_work_dir")
-        os.remove(junit_xml_report)
+def test_category_in_junit_xml(tmp_path: Path):
+    junit_xml_report = tmp_path / "junit-report.xml"
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/optional-error.yml")
+        ),
+        "--junit-xml",
+        str(junit_xml_report),
+    ]
+    run_with_mock_cwl_runner(args)
+    tree = ET.parse(junit_xml_report)
+    root = tree.getroot()
+    category = root.find("testsuite").find("testcase").attrib["class"]
+    assert category == "js, init_work_dir"
diff --git a/cwltest/tests/test_compare.py b/cwltest/tests/test_compare.py
index 5a20cae..15003ed 100644
--- a/cwltest/tests/test_compare.py
+++ b/cwltest/tests/test_compare.py
@@ -1,64 +1,63 @@
-import unittest
 from .util import get_data
 from cwltest import CompareFail
 from cwltest.utils import compare_file, compare
 
+import pytest
 
-class TestCompareFile(unittest.TestCase):
-    def test_compare_file(self):
-        expected = {
-            "location": "cores.txt",
-            "size": 2,
-            "class": "File",
-            "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
-        }
 
-        actual = {
-            "basename": "cores.txt",
-            "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
-            "class": "File",
-            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-            "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-            "size": 2,
-        }
-        try:
-            compare_file(expected, actual)
-        except CompareFail:
-            self.fail("File comparison failed unexpectedly")
+def test_compare_file():
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+    }
 
-    def test_compare_contents_success(self):
-        expected = {
-            "location": "cores.txt",
-            "size": 2,
-            "class": "File",
-            "contents": "2\n",
-        }
+    actual = {
+        "basename": "cores.txt",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+        "class": "File",
+        "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "size": 2,
+    }
+    compare_file(expected, actual)
 
-        actual = {
-            "basename": "cores.txt",
-            "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
-            "class": "File",
-            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-            "path": get_data("tests/test-data/cores.txt"),
-            "size": 2,
-        }
-        compare(expected, actual)
 
-    def test_compare_contents_failure(self):
-        expected = {
-            "location": "cores.txt",
-            "size": 2,
-            "class": "File",
-            "contents": "2",
-        }
+def test_compare_contents_success():
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+        "contents": "2\n",
+    }
 
-        actual = {
-            "basename": "cores.txt",
-            "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
-            "class": "File",
-            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-            "path": get_data("tests/test-data/cores.txt"),
-            "size": 2,
-        }
-        with self.assertRaises(CompareFail):
-            compare_file(expected, actual)
+    actual = {
+        "basename": "cores.txt",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+        "class": "File",
+        "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": get_data("tests/test-data/cores.txt"),
+        "size": 2,
+    }
+    compare(expected, actual)
+
+
+def test_compare_contents_failure():
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+        "contents": "2",
+    }
+
+    actual = {
+        "basename": "cores.txt",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+        "class": "File",
+        "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": get_data("tests/test-data/cores.txt"),
+        "size": 2,
+    }
+    with pytest.raises(CompareFail):
+        compare_file(expected, actual)
diff --git a/cwltest/tests/test_prepare.py b/cwltest/tests/test_prepare.py
index d09f039..3c2ff6f 100644
--- a/cwltest/tests/test_prepare.py
+++ b/cwltest/tests/test_prepare.py
@@ -1,29 +1,26 @@
+"""Test prepare_test_command()"""
 import os
-import unittest
 from cwltest import prepare_test_command
 
 
-class TestPrepareCommand(unittest.TestCase):
-    """Test prepare_test_command()"""
-
-    def test_unix_relative_path(self):
-        """Confirm unix style to windows style path corrections."""
-        command = prepare_test_command(
-            tool="cwl-runner",
-            args=[],
-            testargs=None,
-            test={
-                "doc": "General test of command line generation",
-                "output": {"args": ["echo"]},
-                "tool": "v1.0/bwa-mem-tool.cwl",
-                "job": "v1.0/bwa-mem-job.json",
-                "tags": ["required"],
-            },
-            cwd=os.getcwd(),
-        )
-        if os.name == "nt":
-            self.assertEqual(command[3], "v1.0\\bwa-mem-tool.cwl")
-            self.assertEqual(command[4], "v1.0\\bwa-mem-job.json")
-        else:
-            self.assertEqual(command[3], "v1.0/bwa-mem-tool.cwl")
-            self.assertEqual(command[4], "v1.0/bwa-mem-job.json")
+def test_unix_relative_path():
+    """Confirm unix style to windows style path corrections."""
+    command = prepare_test_command(
+        tool="cwl-runner",
+        args=[],
+        testargs=None,
+        test={
+            "doc": "General test of command line generation",
+            "output": {"args": ["echo"]},
+            "tool": "v1.0/bwa-mem-tool.cwl",
+            "job": "v1.0/bwa-mem-job.json",
+            "tags": ["required"],
+        },
+        cwd=os.getcwd(),
+    )
+    if os.name == "nt":
+        assert command[3] == "v1.0\\bwa-mem-tool.cwl"
+        assert command[4] == "v1.0\\bwa-mem-job.json"
+    else:
+        assert command[3] == "v1.0/bwa-mem-tool.cwl"
+        assert command[4] == "v1.0/bwa-mem-job.json"
diff --git a/cwltest/tests/test_short_names.py b/cwltest/tests/test_short_names.py
index 6efda7f..84a594c 100644
--- a/cwltest/tests/test_short_names.py
+++ b/cwltest/tests/test_short_names.py
@@ -1,56 +1,52 @@
-import unittest
-
 import os
 from os import linesep as n
+from pathlib import Path
 
 from .util import run_with_mock_cwl_runner, get_data
 import defusedxml.ElementTree as ET
 
 
-class TestShortNames(unittest.TestCase):
-    def test_stderr_output(self):
-        args = ["--test", get_data("tests/test-data/short-names.yml")]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        self.assertIn(
-            "Test [1/1] opt-error: Test with a short name{n}".format(n=n), stderr
-        )
-
-    def test_run_by_short_name(self):
-        short_name = "opt-error"
-        args = [
-            "--test",
-            get_data("tests/test-data/with-and-without-short-names.yml"),
-            "-s",
-            short_name,
-        ]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        self.assertIn("Test [2/2] opt-error: Test with a short name", stderr)
-        self.assertNotIn("Test [1/2]", stderr)
-
-    def test_list_tests(self):
-        args = [
-            "--test",
-            get_data("tests/test-data/with-and-without-short-names.yml"),
-            "-l",
-        ]
-        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
-        self.assertEqual(
-            "[1] Test without a short name{n}"
-            "[2] opt-error: Test with a short name{n}".format(n=n),
-            stdout,
-        )
-
-    def test_short_name_in_junit_xml(self):
-        junit_xml_report = get_data("tests/test-data/junit-report.xml")
-        args = [
-            "--test",
-            get_data("tests/test-data/short-names.yml"),
-            "--junit-xml",
-            junit_xml_report,
-        ]
-        run_with_mock_cwl_runner(args)
-        tree = ET.parse(junit_xml_report)
-        root = tree.getroot()
-        category = root.find("testsuite").find("testcase").attrib["file"]
-        self.assertEqual(category, "opt-error")
-        os.remove(junit_xml_report)
+def test_stderr_output():
+    args = ["--test", get_data("tests/test-data/short-names.yml")]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"Test [1/1] opt-error: Test with a short name{n}" in stderr
+
+
+def test_run_by_short_name():
+    short_name = "opt-error"
+    args = [
+        "--test",
+        get_data("tests/test-data/with-and-without-short-names.yml"),
+        "-s",
+        short_name,
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert "Test [2/2] opt-error: Test with a short name" in stderr
+    assert "Test [1/2]" not in stderr
+
+
+def test_list_tests():
+    args = [
+        "--test",
+        get_data("tests/test-data/with-and-without-short-names.yml"),
+        "-l",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert (
+        f"[1] Test without a short name{n}" f"[2] opt-error: Test with a short name{n}"
+    ) in stdout
+
+
+def test_short_name_in_junit_xml(tmp_path: Path):
+    junit_xml_report = tmp_path / "junit-report.xml"
+    args = [
+        "--test",
+        get_data("tests/test-data/short-names.yml"),
+        "--junit-xml",
+        str(junit_xml_report),
+    ]
+    run_with_mock_cwl_runner(args)
+    tree = ET.parse(junit_xml_report)
+    root = tree.getroot()
+    category = root.find("testsuite").find("testcase").attrib["file"]
+    assert category == "opt-error"

From 202b77a56ceb192a060f651ec2e4a826c25be217 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 15 Nov 2021 19:23:56 +0100
Subject: [PATCH 018/165] test timeout feature

---
 .coveragerc                             | 14 +++++++++
 Makefile                                |  2 +-
 cwltest/tests/mock_cwl_runner.py        | 10 +++++-
 cwltest/tests/test-data/timeout.cwl     |  5 +++
 cwltest/tests/test-data/timeout.yml     |  9 ++++++
 cwltest/tests/test-data/v1.0/empty.json |  1 +
 cwltest/tests/test_timeout.py           | 42 +++++++++++++++++++++++++
 cwltest/tests/util.py                   |  7 ++---
 test-requirements.txt                   |  1 -
 tox.ini                                 |  2 +-
 10 files changed, 85 insertions(+), 8 deletions(-)
 create mode 100644 .coveragerc
 create mode 100644 cwltest/tests/test-data/timeout.cwl
 create mode 100644 cwltest/tests/test-data/timeout.yml
 create mode 100644 cwltest/tests/test-data/v1.0/empty.json
 create mode 100644 cwltest/tests/test_timeout.py

diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..4a89de0
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,14 @@
+[run]
+branch = True
+source = cwltest
+omit = cwltest/tests/*
+
+[report]
+exclude_lines =
+    if self.debug:
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True
+omit =
+    cwltest/tests/*
diff --git a/Makefile b/Makefile
index e67f0e1..abda48e 100644
--- a/Makefile
+++ b/Makefile
@@ -112,7 +112,7 @@ diff_pylint_report: pylint_report.txt
 	diff-quality --violations=pylint pylint_report.txt
 
 .coverage: $(PYSOURCES) all
-	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= -n auto ${PYTEST_EXTRA}"
+	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}"
 
 coverage.xml: .coverage
 	coverage xml
diff --git a/cwltest/tests/mock_cwl_runner.py b/cwltest/tests/mock_cwl_runner.py
index a352f7d..478e504 100644
--- a/cwltest/tests/mock_cwl_runner.py
+++ b/cwltest/tests/mock_cwl_runner.py
@@ -1,12 +1,15 @@
 import argparse
+import sys
+from time import sleep
 
 from cwltest import UNSUPPORTED_FEATURE
 
 UNSUPPORTED_FEATURE_TOOL = "return-unsupported.cwl"
 ERROR_TOOL = "return-1.cwl"
+TIMEOUT_TOOL = "timeout.cwl"
 
 
-def main():  # type: ()->int
+def main() -> int:
     parser = argparse.ArgumentParser()
     parser.add_argument("processfile")
     parser.add_argument("jobfile")
@@ -20,6 +23,11 @@ def main():  # type: ()->int
         exit(UNSUPPORTED_FEATURE)
     elif args.processfile.endswith(ERROR_TOOL):
         exit(1)
+    elif args.processfile.endswith(TIMEOUT_TOOL):
+        print("timeout stderr", file=sys.stderr)
+        sys.stderr.flush()
+        sleep(100000)
+        exit(1)
 
     exit(0)
 
diff --git a/cwltest/tests/test-data/timeout.cwl b/cwltest/tests/test-data/timeout.cwl
new file mode 100644
index 0000000..a487298
--- /dev/null
+++ b/cwltest/tests/test-data/timeout.cwl
@@ -0,0 +1,5 @@
+class: CommandLineTool
+cwlVersion: v1.0
+inputs: []
+outputs: []
+baseCommand: [sleep, "15"]
diff --git a/cwltest/tests/test-data/timeout.yml b/cwltest/tests/test-data/timeout.yml
new file mode 100644
index 0000000..30231d6
--- /dev/null
+++ b/cwltest/tests/test-data/timeout.yml
@@ -0,0 +1,9 @@
+- job: v1.0/empty.json
+  output:
+    output_txt:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      location: output.txt
+      size: 13
+  tool: timeout.cwl
+  doc: Test of timeout stdout and stderr capture
diff --git a/cwltest/tests/test-data/v1.0/empty.json b/cwltest/tests/test-data/v1.0/empty.json
new file mode 100644
index 0000000..0967ef4
--- /dev/null
+++ b/cwltest/tests/test-data/v1.0/empty.json
@@ -0,0 +1 @@
+{}
diff --git a/cwltest/tests/test_timeout.py b/cwltest/tests/test_timeout.py
new file mode 100644
index 0000000..431e665
--- /dev/null
+++ b/cwltest/tests/test_timeout.py
@@ -0,0 +1,42 @@
+import re
+import os
+from os import linesep as n
+from os import sep as p
+from pathlib import Path
+
+import defusedxml.ElementTree as ET
+
+from .util import run_with_mock_cwl_runner, get_data
+import schema_salad.ref_resolver
+
+
+def test_timeout_stderr_stdout(tmp_path):
+    junit_xml_report = tmp_path / "junit-report.xml"
+
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(get_data("tests/test-data/timeout.yml")),
+        "--timeout",
+        "5",
+        "--junit-xml",
+        str(junit_xml_report),
+    ]
+    try:
+        cwd = os.getcwd()
+        os.chdir(get_data("tests/test-data/"))
+        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    finally:
+        os.chdir(cwd)
+
+    assert error_code == 1
+    assert "Test 1 timed out" in stderr
+    tree = ET.parse(junit_xml_report)
+    try:
+        root = tree.getroot()
+        timeout_text = root.find("testsuite").find("testcase").find("failure").text
+        timeout_stderr = root.find("testsuite").find("testcase").find("system-err").text
+        assert "Test timed out" in timeout_text
+        assert "timeout stderr" in timeout_stderr
+    except AttributeError as e:
+        print(junit_xml_report.read_text())
+        raise e
diff --git a/cwltest/tests/util.py b/cwltest/tests/util.py
index 414db00..25879bc 100644
--- a/cwltest/tests/util.py
+++ b/cwltest/tests/util.py
@@ -1,5 +1,4 @@
 import os
-import sys
 
 import subprocess  # nosec
 
@@ -11,9 +10,9 @@
 
 
 def get_data(filename):
-    filename = os.path.normpath(
-        filename
-    )  # normalizing path depending on OS or else it will cause problem when joining path
+    filename = os.path.normpath(filename)
+    # normalizing path depending on OS or else it will cause problem when
+    # joining path
     filepath = None
     try:
         filepath = resource_filename(Requirement.parse("cwltest"), filename)
diff --git a/test-requirements.txt b/test-requirements.txt
index fb43315..eb7dc7f 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,3 +1,2 @@
 pytest >= 6.2, < 6.3
 pytest-cov
-pytest-xdist
diff --git a/tox.ini b/tox.ini
index c0f3f1a..52e21a3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -12,7 +12,7 @@ skipsdist = True
 skip_missing_interpreters = True
 
 [pytest]
-addopts=-n auto --pyargs cwltest
+addopts = --pyargs cwltest
 testpaths = cwltest/tests
 
 [gh-actions]

From 8958ba01f77b4b64c94cc9a3fa8ea89d77183ab3 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 15 Nov 2021 19:44:51 +0100
Subject: [PATCH 019/165] support Python 3.10

---
 .flake8                                       |  4 ++
 .github/workflows/ci-tests.yml                | 16 +++--
 MANIFEST.in                                   |  2 +-
 Makefile                                      |  2 +-
 cwltest/utils.py                              |  8 +--
 ..._requirements.txt => mypy-requirements.txt |  0
 release-test.sh                               | 16 +++--
 setup.py                                      |  1 +
 tox.ini                                       | 64 +++++++++++--------
 9 files changed, 66 insertions(+), 47 deletions(-)
 create mode 100644 .flake8
 rename mypy_requirements.txt => mypy-requirements.txt (100%)

diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000..35967ff
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,4 @@
+[flake8]
+ignore = E203, E266, E501, W503, E211, E731
+max-line-length = 88
+select = B,C,E,F,W,T4,B9
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index cf34d1d..573fb61 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -6,6 +6,10 @@ on:
   pull_request:
     branches: [ main ]
 
+concurrency:
+  group: build-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
 
   tox:
@@ -16,7 +20,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [6, 7, 8, 9]
+        py-ver-minor: [6, 7, 8, 9, 10]
         step: [lint, unit, mypy]
 
     env:
@@ -54,7 +58,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ matrix.step == 'unit' }}
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2.1.0
         with:
           fail_ci_if_error: true
 
@@ -65,11 +69,11 @@ jobs:
 
     strategy:
       matrix:
-        step: [lint-readme, pydocstyle]
+        step: [lintreadme, pydocstyle]
 
     env:
-      py-semver: 3.9
-      TOXENV: ${{ format('py39-{0}', matrix.step) }}
+      py-semver: "3.10"
+      TOXENV: ${{ format('py310-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v2
@@ -110,7 +114,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.9
+          python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
 
       - name: Cache for pip
         uses: actions/cache@v2
diff --git a/MANIFEST.in b/MANIFEST.in
index 6e775fd..74643c8 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-include Makefile gittaggers.py test-requirements.txt mypy_requirements.txt requirements.txt
+include Makefile gittaggers.py test-requirements.txt mypy-requirements.txt requirements.txt
 include cwltest/cwltest-schema.yml
 include cwltest/tests/*
 include cwltest/tests/test-data/*
diff --git a/Makefile b/Makefile
index abda48e..ea7110e 100644
--- a/Makefile
+++ b/Makefile
@@ -28,7 +28,7 @@ PACKAGE=cwltest
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
 DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
 	isort wheel autoflake flake8-bugbear pyupgrade bandit \
-	-rtest-requirements.txt -rmypy_requirements.txt
+	-rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 VERSION=2.2.$(shell TZ=UTC git log --first-parent --max-count=1 \
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 984d8a8..50e1cb5 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -111,7 +111,7 @@ def check_keys(keys, expected, actual):
         except CompareFail as e:
             raise CompareFail.format(
                 expected, actual, f"field '{k}' failed comparison: {str(e)}"
-            )
+            ) from e
 
 
 def compare_file(expected, actual):
@@ -159,7 +159,7 @@ def compare_dict(expected, actual):
         except CompareFail as e:
             raise CompareFail.format(
                 expected, actual, f"failed comparison for key '{c}': {e}"
-            )
+            ) from e
     extra_keys = set(actual.keys()).difference(list(expected.keys()))
     for k in extra_keys:
         if actual[k] is not None:
@@ -194,13 +194,13 @@ def compare(expected, actual):  # type: (Any, Any) -> None
                 try:
                     compare(expected[c], actual[c])
                 except CompareFail as e:
-                    raise CompareFail.format(expected, actual, e)
+                    raise CompareFail.format(expected, actual, e) from e
         else:
             if expected != actual:
                 raise CompareFail.format(expected, actual)
 
     except Exception as e:
-        raise CompareFail(str(e))
+        raise CompareFail(str(e)) from e
 
 
 def get_test_number_by_key(tests, key, value):
diff --git a/mypy_requirements.txt b/mypy-requirements.txt
similarity index 100%
rename from mypy_requirements.txt
rename to mypy-requirements.txt
diff --git a/release-test.sh b/release-test.sh
index dcb6d90..e840392 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -7,6 +7,8 @@ export LC_ALL=C
 
 package=cwltest
 module=cwltest
+extras=""
+
 if [ "$GITHUB_ACTIONS" = "true" ]; then
     # We are running as a GH Action
     repo=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}.git
@@ -16,8 +18,8 @@ else
     HEAD=$(git rev-parse HEAD)
 fi
 run_tests="bin/py.test --pyargs ${module}"
-pipver=20.3b1 # minimum required version of pip for Python 3.9
-setuptoolsver=41.1.0 # required for Python 3.9
+pipver=20.3.3  # minimum required version of pip for Python 3.10
+setuptoolsver=50.0.0  # required for Python 3.10
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
 rm -Rf testenv? || /bin/true
@@ -33,7 +35,7 @@ then
 	rm -f testenv1/lib/python-wheels/setuptools* \
 		&& pip install --force-reinstall -U pip==${pipver} \
 		&& pip install setuptools==${setuptoolsver} wheel
-	pip install -rtest-requirements.txt
+	pip install -rtest-requirements.txt ".${extras}"
 	make test
 	pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 	mkdir testenv1/not-${module}
@@ -59,7 +61,7 @@ rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
 # The following can fail if you haven't pushed your commits to ${repo}
-pip install -e "git+${repo}@${HEAD}#egg=${package}"
+pip install -e "git+${repo}@${HEAD}#egg=${package}${extras}"
 pushd src/${package}
 pip install -rtest-requirements.txt
 make dist
@@ -83,13 +85,13 @@ rm -f lib/python-wheels/setuptools* \
         && pip install setuptools==${setuptoolsver} wheel
 package_tar=$(find . -name "${package}*tar.gz")
 pip install "-r${DIR}/test-requirements.txt"
-pip install "${package_tar}"
+pip install "${package_tar}${extras}"
 mkdir out
 tar --extract --directory=out -z -f ${package}*.tar.gz
 pushd out/${package}*
 make dist
 make test
-pip install "-r${DIR}/mypy_requirements.txt"
+pip install "-r${DIR}/mypy-requirements.txt"
 make mypy
 pip uninstall -y ${package} || true; pip uninstall -y ${package} || true; make install
 mkdir ../not-${module}
@@ -107,7 +109,7 @@ source bin/activate
 rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
-pip install ${module}*.whl
+pip install "$(ls ${module}*.whl)${extras}"
 pip install "-r${DIR}/test-requirements.txt"
 mkdir not-${module}
 pushd not-${module}
diff --git a/setup.py b/setup.py
index bb098fb..9c1d31b 100644
--- a/setup.py
+++ b/setup.py
@@ -61,6 +61,7 @@
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Typing :: Typed",
     ],
 )
diff --git a/tox.ini b/tox.ini
index 52e21a3..82b219b 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,14 +1,13 @@
 [tox]
 envlist =
-  py{36,37,38,39}-lint,
-  py{36,37,38,39}-unit,
-  py{36,37,38,39}-bandit,
-  py{36,37,38,39}-mypy,
+  py{36,37,38,39,310}-lint,
+  py{36,37,38,39,310}-unit,
+  py{36,37,38,39,310}-bandit,
+  py{36,37,38,39,310}-mypy,
   py39-pipconflictchecker,
-  py39-lint-readme,
+  py39-lintreadme,
   py39-pydocstyle
 
-skipsdist = True
 skip_missing_interpreters = True
 
 [pytest]
@@ -21,42 +20,48 @@ python =
   3.7: py37
   3.8: py38
   3.9: py39
+  3.10: py310
 
 [testenv]
 description =
-  py{36,37,38,39}-unit: Run the unit tests
-  py{36,37,38,39}-lint: Lint the Python code
-  py{36,37,38,39}-bandit: Search for common security issues
-  py{36,37,38,39}-mypy: Check for type safety
+  py{36,37,38,39,310}-unit: Run the unit tests
+  py{36,37,38,39,310}-lint: Lint the Python code
+  py{36,37,38,39,310}-bandit: Search for common security issues
+  py{36,37,38,39,310}-mypy: Check for type safety
   py39-pydocstyle: docstring style checker
-  py39-lint-readme: Lint the README.rst->.md conversion
+  py39-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 deps =
-  py{36,37,38,39}-{unit,lint,bandit,mypy}: -rrequirements.txt
-  py{36,37,38,39}-{unit,mypy}: -rtest-requirements.txt
-  py{36,37,38,39}-lint: flake8-bugbear
-  py{36,37,38,39}-lint: black
-  py{36,37,38,39}-bandit: bandit
-  py{36,37,38,39}-mypy: -rmypy_requirements.txt
+  py{36,37,38,39,310}-{unit,mypy}: -rrequirements.txt
+  py{36,37,38,39,310}-{unit,mypy}: -rtest-requirements.txt
+  py{36,37,38,39,310}-lint: flake8-bugbear
+  py{36,37,38,39,310}-lint: black
+  py{36,37,38,39,310}-bandit: bandit
+  py{36,37,38,39,310}-mypy: -rmypy-requirements.txt
 
 setenv =
-  py{36,37,38,39}-unit: LC_ALL = C.UTF-8
+  py{36,37,38,39,310}-unit: LC_ALL = C.UTF-8
 
 commands =
-  py{36,37,38,39}-unit: python -m pip install -U pip setuptools wheel
-  py{36,37,38,39}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
-  py{36,37,38,39}-bandit: bandit --recursive cwltest
-  py{36,37,38,39}-lint: make flake8
-  py{36,37,38,39}-lint: make format-check
-  py{36,37,38,39}-mypy: make mypy
+  py{36,37,38,39,310}-unit: python -m pip install -U pip setuptools wheel
+  py{36,37,38,39,310}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py{36,37,38,39,310}-bandit: bandit --recursive cwltest --exclude cwltest/tests/*
+  py{36,37,38,39,310}-lint: make flake8
+  py{36,37,38,39,310}-lint: make format-check
+  py{36,37,38,39,310}-mypy: make mypy
 
 whitelist_externals =
-  py{36,37,38,39}-lint: flake8
-  py{36,37,38,39}-lint: black
-  py{36,37,38,39}-{mypy,shellcheck,lint,unit}: make
+  py{36,37,38,39,310}-lint: flake8
+  py{36,37,38,39,310}-lint: black
+  py{36,37,38,39,310}-{mypy,shellcheck,lint,unit}: make
+
+skip_install =
+  py{36,37,38,39,310}-lint: true
+  py{36,37,38,39,310}-bandit: true
+
 
 [testenv:py39-pydocstyle]
 whitelist_externals = make
@@ -64,6 +69,7 @@ commands = make diff_pydocstyle_report
 deps =
     pydocstyle
     diff-cover
+skip_install = true
 
 [testenv:py39-pipconflictchecker]
 commands = pipconflictchecker
@@ -72,7 +78,8 @@ deps =
   pip-conflict-checker
   pip==9.0.3
 
-[testenv:py39-lint-readme]
+[testenv:py39-lintreadme]
+description = Lint the README.rst->.md conversion
 commands =
   python setup.py sdist
   python setup.py bdist_wheel
@@ -81,3 +88,4 @@ deps =
     twine
     wheel
     readme_renderer[md]
+skip_install = true

From 91e655b8ef98f96d81be47f94e9ebc075b4470ae Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 16 Dec 2021 00:31:17 +0000
Subject: [PATCH 020/165] Bump mypy from 0.910 to 0.920

Bumps [mypy](https://github.com/python/mypy) from 0.910 to 0.920.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.910...v0.920)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index e33b163..88051cf 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.910
+mypy==0.920
 types-setuptools
 types-requests

From 4c567337ce5bbe78f28e92e2d2fb6dc3c445c94f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 22 Dec 2021 00:24:45 +0000
Subject: [PATCH 021/165] Bump mypy from 0.920 to 0.921

Bumps [mypy](https://github.com/python/mypy) from 0.920 to 0.921.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.920...v0.921)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 88051cf..b84679c 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.920
+mypy==0.921
 types-setuptools
 types-requests

From ad0089ff08ec6ae03f23c51234422ad23d713894 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 23 Dec 2021 00:18:39 +0000
Subject: [PATCH 022/165] Bump mypy from 0.921 to 0.930

Bumps [mypy](https://github.com/python/mypy) from 0.921 to 0.930.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.921...v0.930)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index b84679c..f2b31ba 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.921
+mypy==0.930
 types-setuptools
 types-requests

From d331e526e4e8c69b6d44b59309c38dfe1efe98fe Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 10 Jan 2022 00:53:36 +0000
Subject: [PATCH 023/165] Bump mypy from 0.930 to 0.931

Bumps [mypy](https://github.com/python/mypy) from 0.930 to 0.931.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.930...v0.931)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f2b31ba..9ea607e 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.930
+mypy==0.931
 types-setuptools
 types-requests

From 6ad17026863eccf1f1a57858e54f95e436e222a3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Feb 2022 00:49:06 +0000
Subject: [PATCH 024/165] Update pytest requirement from <6.3,>=6.2 to
 >=6.2,<7.1

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/6.2.0...7.0.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt      | 2 +-
 setup.py              | 2 +-
 test-requirements.txt | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 9eadc1f..a51fd20 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
-pytest < 7
+pytest < 8
 defusedxml
diff --git a/setup.py b/setup.py
index 9c1d31b..4716d04 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@
 ]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
-pytest_runner = ["pytest < 7", "pytest-runner"] if needs_pytest else []
+pytest_runner = ["pytest < 8", "pytest-runner"] if needs_pytest else []
 
 setup(
     name="cwltest",
diff --git a/test-requirements.txt b/test-requirements.txt
index eb7dc7f..70724d7 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,2 +1,2 @@
-pytest >= 6.2, < 6.3
+pytest >= 6.2, < 7.1
 pytest-cov

From d4fd5efb82250824c92c47290631522fc93dd0ab Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 8 Feb 2022 00:17:18 +0000
Subject: [PATCH 025/165] Update pytest requirement from <7 to <8

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/6.2.0...7.0.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 4716d04..445d543 100644
--- a/setup.py
+++ b/setup.py
@@ -42,7 +42,7 @@
     include_package_data=True,
     install_requires=install_requires,
     test_suite="tests",
-    tests_require=["pytest<7"],
+    tests_require=["pytest<8"],
     entry_points={
         "console_scripts": [
             "cwltest=cwltest:main",

From f016448aeb3ae9b395d8631d8ef112edb17b8e8b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Mar 2022 00:44:40 +0000
Subject: [PATCH 026/165] Bump mypy from 0.931 to 0.940

Bumps [mypy](https://github.com/python/mypy) from 0.931 to 0.940.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.931...v0.940)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 9ea607e..6aace86 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.931
+mypy==0.940
 types-setuptools
 types-requests

From 29ad114bd54e34a22f18e313e1793409620bd18a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Mar 2022 07:30:29 +0000
Subject: [PATCH 027/165] Update pytest requirement from <7.1,>=6.2 to
 >=6.2,<7.2

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/6.2.0...7.1.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 test-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test-requirements.txt b/test-requirements.txt
index 70724d7..072f0cc 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,2 +1,2 @@
-pytest >= 6.2, < 7.1
+pytest >= 6.2, < 7.2
 pytest-cov

From 12485839c8ff83af9e0e7c6f77c07f9a5975a3dc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 15 Mar 2022 00:18:49 +0000
Subject: [PATCH 028/165] Bump mypy from 0.940 to 0.941

Bumps [mypy](https://github.com/python/mypy) from 0.940 to 0.941.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.940...v0.941)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 6aace86..4d047ad 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.940
+mypy==0.941
 types-setuptools
 types-requests

From f7a635832d640507d38585fa853c00d8b1047c82 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 25 Mar 2022 00:19:45 +0000
Subject: [PATCH 029/165] Bump mypy from 0.941 to 0.942

Bumps [mypy](https://github.com/python/mypy) from 0.941 to 0.942.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.941...v0.942)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 4d047ad..990114f 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.941
+mypy==0.942
 types-setuptools
 types-requests

From b5f5b96c5ebd27128f942dcda05d3be3cb7709a6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 28 Apr 2022 00:09:50 +0000
Subject: [PATCH 030/165] Bump mypy from 0.942 to 0.950

Bumps [mypy](https://github.com/python/mypy) from 0.942 to 0.950.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.942...v0.950)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 990114f..ef46782 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.942
+mypy==0.950
 types-setuptools
 types-requests

From c2f9c45223c67f953ecfc0d944dc68914b677f20 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 14 May 2022 08:59:52 +0000
Subject: [PATCH 031/165] Add `sould_fail.default` to the schema

---
 cwltest/cwltest-schema.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/cwltest/cwltest-schema.yml b/cwltest/cwltest-schema.yml
index e084a75..3d40c7c 100644
--- a/cwltest/cwltest-schema.yml
+++ b/cwltest/cwltest-schema.yml
@@ -21,6 +21,8 @@ $graph:
         type: string?
         jsonldPredicate:
           _type: "@id"
-      should_fail: boolean?
+      should_fail:
+        type: boolean?
+        default: false
       output:
         type: Any?

From 9dac068b7c163b26be1686981e2125bf8eb1955d Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 21 May 2022 19:30:21 +0900
Subject: [PATCH 032/165] Print `doc` field in one line (#136)

---
 cwltest/__init__.py                         | 27 +++++++++++++++------
 cwltest/tests/test-data/multi-lined-doc.yml | 15 ++++++++++++
 cwltest/tests/test_multi_lined_doc.py       | 20 +++++++++++++++
 3 files changed, 54 insertions(+), 8 deletions(-)
 create mode 100644 cwltest/tests/test-data/multi-lined-doc.yml
 create mode 100644 cwltest/tests/test_multi_lined_doc.py

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 9e0ec7a..b400af4 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -127,14 +127,20 @@ def run_test(
                     test_number,
                     total_tests,
                     test.get("short_name"),
-                    test.get("doc"),
+                    test.get("doc", "").replace("\n", " ").strip(),
                     suffix,
                 )
             )
         else:
             sys.stderr.write(
                 "%sTest [%i/%i] %s%s\n"
-                % (prefix, test_number, total_tests, test.get("doc"), suffix)
+                % (
+                    prefix,
+                    test_number,
+                    total_tests,
+                    test.get("doc", "").replace("\n", " ").strip(),
+                    suffix,
+                )
             )
         if verbose:
             sys.stderr.write(f"Running: {' '.join(test_command)}\n")
@@ -174,7 +180,7 @@ def run_test(
             test_number,
             " ".join([quote(tc) for tc in test_command]),
         )
-        _logger.error(test.get("doc"))
+        _logger.error(test.get("doc", "").replace("\n", " ").strip())
         if err.returncode == UNSUPPORTED_FEATURE:
             _logger.error("Does not support required feature")
         else:
@@ -203,7 +209,7 @@ def run_test(
             test_number,
             " ".join([quote(tc) for tc in test_command]),
         )
-        _logger.error(test.get("doc"))
+        _logger.error(test.get("doc", "").replace("\n", " ").strip())
         # Kill and re-communicate to get the logs and reap the child, as
         # instructed in the subprocess docs.
         if process:
@@ -229,7 +235,7 @@ def run_test(
             test_number,
             " ".join([quote(tc) for tc in test_command]),
         )
-        _logger.warning(test.get("doc"))
+        _logger.warning(test.get("doc", "").replace("\n", " ").strip())
         _logger.warning("Returned zero but it should be non-zero")
         return TestResult(1, outstr, outerr, duration, args.classname)
 
@@ -241,7 +247,7 @@ def run_test(
             test_number,
             " ".join([quote(tc) for tc in test_command]),
         )
-        _logger.warning(test.get("doc"))
+        _logger.warning(test.get("doc", "").replace("\n", " ").strip())
         _logger.warning("Compare failure %s", ex)
         fail_message = str(ex)
 
@@ -456,10 +462,15 @@ def main():  # type: () -> int
         for i, t in enumerate(tests):
             if t.get("short_name"):
                 print(
-                    "[%i] %s: %s" % (i + 1, t["short_name"], t.get("doc", "").strip())
+                    "[%i] %s: %s"
+                    % (
+                        i + 1,
+                        t["short_name"],
+                        t.get("doc", "").replace("\n", " ").strip(),
+                    )
                 )
             else:
-                print("[%i] %s" % (i + 1, t.get("doc", "").strip()))
+                print("[%i] %s" % (i + 1, t.get("doc", "").replace("\n", " ").strip()))
 
         return 0
 
diff --git a/cwltest/tests/test-data/multi-lined-doc.yml b/cwltest/tests/test-data/multi-lined-doc.yml
new file mode 100644
index 0000000..af21928
--- /dev/null
+++ b/cwltest/tests/test-data/multi-lined-doc.yml
@@ -0,0 +1,15 @@
+- job: v1.0/cat-job.json
+  output: {}
+  tool: return-0.cwl
+  doc: |
+    Test with
+    label
+  label: opt-error
+  tags: [ js, init_work_dir ]
+- job: v1.0/cat-job.json
+  output: {}
+  tool: return-0.cwl
+  doc: |
+    Test without
+    label
+  tags: [ js, init_work_dir ]
diff --git a/cwltest/tests/test_multi_lined_doc.py b/cwltest/tests/test_multi_lined_doc.py
new file mode 100644
index 0000000..1fa1501
--- /dev/null
+++ b/cwltest/tests/test_multi_lined_doc.py
@@ -0,0 +1,20 @@
+import os
+from os import linesep as n
+from pathlib import Path
+
+from .util import run_with_mock_cwl_runner, get_data
+import defusedxml.ElementTree as ET
+
+
+def test_run():
+    args = ["--test", get_data("tests/test-data/multi-lined-doc.yml")]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"Test [1/2] opt-error: Test with label{n}" in stderr
+    assert f"Test [2/2] Test without label{n}" in stderr
+
+
+def test_list():
+    args = ["--test", get_data("tests/test-data/multi-lined-doc.yml"), "-l"]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"[1] opt-error: Test with label{n}" in stdout
+    assert f"[2] Test without label{n}" in stdout

From 4e842e80fff29f23a69572bcfbe08ebacbb37cbd Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 21 May 2022 22:18:28 +0900
Subject: [PATCH 033/165] Support string `id` field (#137)

---
 cwltest/__init__.py                   | 13 +++++++++++++
 cwltest/tests/test-data/string-id.yml |  5 +++++
 cwltest/tests/test_string_id.py       | 12 ++++++++++++
 3 files changed, 30 insertions(+)
 create mode 100644 cwltest/tests/test-data/string-id.yml
 create mode 100644 cwltest/tests/test_string_id.py

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index b400af4..f5e61f9 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -4,6 +4,7 @@
 import json
 import logging
 import os
+import re
 import shutil
 import subprocess  # nosec
 import sys
@@ -41,6 +42,16 @@
 templock = threading.Lock()
 
 
+def shortname(
+    name,  # type: str
+):  # type: (...) -> str
+    """
+    Return the short name of a given name.
+    It is a workaround of https://github.com/common-workflow-language/schema_salad/issues/511.
+    """
+    return [n for n in re.split("[/#]", name) if len(n)][-1]
+
+
 def prepare_test_command(
     tool,  # type: str
     args,  # type: List[str]
@@ -448,6 +459,8 @@ def main():  # type: () -> int
     for t in tests:
         if t.get("label"):
             t["short_name"] = t["label"]
+        elif t.get("id") and isinstance(t.get("id"), str):
+            t["short_name"] = shortname(t["id"])
 
     if args.show_tags:
         alltags = set()  # type: Set[str]
diff --git a/cwltest/tests/test-data/string-id.yml b/cwltest/tests/test-data/string-id.yml
new file mode 100644
index 0000000..0fd21eb
--- /dev/null
+++ b/cwltest/tests/test-data/string-id.yml
@@ -0,0 +1,5 @@
+- job: v1.0/cat1-job.json
+  output: {}
+  tool: return-0.cwl
+  doc: Test with a string label
+  id: test-string-id
diff --git a/cwltest/tests/test_string_id.py b/cwltest/tests/test_string_id.py
new file mode 100644
index 0000000..77180ae
--- /dev/null
+++ b/cwltest/tests/test_string_id.py
@@ -0,0 +1,12 @@
+import os
+from os import linesep as n
+from pathlib import Path
+
+from .util import run_with_mock_cwl_runner, get_data
+import defusedxml.ElementTree as ET
+
+
+def test_list():
+    args = ["--test", get_data("tests/test-data/string-id.yml"), "-l"]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"[1] test-string-id: Test with a string label{n}" in stdout

From 0c8e5ab13310a9984a1386d65534f7dce0b1a7e4 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 21 May 2022 15:00:03 +0000
Subject: [PATCH 034/165] Add `--exclude-tags` option

---
 cwltest/__init__.py                      | 12 +++++++++
 cwltest/tests/test-data/exclude-tags.yml | 24 +++++++++++++++++
 cwltest/tests/test_exclude_tags.py       | 33 ++++++++++++++++++++++++
 3 files changed, 69 insertions(+)
 create mode 100644 cwltest/tests/test-data/exclude-tags.yml
 create mode 100644 cwltest/tests/test_exclude_tags.py

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index f5e61f9..f89f413 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -317,6 +317,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
         "--only-tools", action="https://github.com/store_true", help="Only test CommandLineTools"
     )
     parser.add_argument("--tags", type=str, default=None, help="Tags to be tested")
+    parser.add_argument(
+        "--exclude-tags", type=str, default=None, help="Tags not to be tested"
+    )
     parser.add_argument("--show-tags", action="https://github.com/store_true", help="Show all Tags.")
     parser.add_argument(
         "--junit-xml", type=str, default=None, help="Path to JUnit xml file"
@@ -456,6 +459,15 @@ def main():  # type: () -> int
             if any(tag in ts for tag in tags):
                 tests.append(t)
 
+    if args.exclude_tags:
+        ex_tests = []
+        tags = args.exclude_tags.split(",")
+        for t in tests:
+            ts = t.get("tags", [])
+            if all(tag not in ts for tag in tags):
+                ex_tests.append(t)
+        tests = ex_tests
+
     for t in tests:
         if t.get("label"):
             t["short_name"] = t["label"]
diff --git a/cwltest/tests/test-data/exclude-tags.yml b/cwltest/tests/test-data/exclude-tags.yml
new file mode 100644
index 0000000..106d5c2
--- /dev/null
+++ b/cwltest/tests/test-data/exclude-tags.yml
@@ -0,0 +1,24 @@
+- job: v1.0/cat-job.json
+  output: {}
+  tool: return-0.cwl
+  doc: |
+    Test with
+    label
+  id: opt-error1
+  tags: [ command_line_tool ]
+- job: v1.0/cat-job.json
+  id: opt-error2
+  output: {}
+  tool: return-0.cwl
+  doc: |
+    Test without
+    label
+  tags: [ command_line_tool, workflow ]
+- job: v1.0/cat-job.json
+  id: opt-error3
+  output: {}
+  tool: return-0.cwl
+  doc: |
+    Test without
+    label
+  tags: [ workflow ]
diff --git a/cwltest/tests/test_exclude_tags.py b/cwltest/tests/test_exclude_tags.py
new file mode 100644
index 0000000..db01989
--- /dev/null
+++ b/cwltest/tests/test_exclude_tags.py
@@ -0,0 +1,33 @@
+import os
+from os import linesep as n
+from pathlib import Path
+
+from .util import run_with_mock_cwl_runner, get_data
+import defusedxml.ElementTree as ET
+
+
+def test_list_only_exclude():
+    args = [
+        "--test",
+        get_data("tests/test-data/exclude-tags.yml"),
+        "-l",
+        "--exclude-tags=workflow",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"[1] opt-error1: Test with label{n}" in stdout
+    assert "opt-error2" not in stdout
+    assert "opt-error3" not in stdout
+
+
+def test_list_include_and_exclude():
+    args = [
+        "--test",
+        get_data("tests/test-data/exclude-tags.yml"),
+        "-l",
+        "--tags=command_line_tool",
+        "--exclude-tags=workflow",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"[1] opt-error1: Test with label{n}" in stdout
+    assert "opt-error2" not in stdout
+    assert "opt-error3" not in stdout

From f78337498db51bf1ac806147a9e811940fda9c89 Mon Sep 17 00:00:00 2001
From: "Bruno P. Kinoshita" <kinow@users.noreply.github.com>
Date: Sun, 22 May 2022 22:03:29 +1200
Subject: [PATCH 035/165] Update Python versions tested on README

---
 .github/workflows/ci-tests.yml | 1 +
 README.rst                     | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 573fb61..97fab80 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -19,6 +19,7 @@ jobs:
 
     strategy:
       matrix:
+        # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
         py-ver-minor: [6, 7, 8, 9, 10]
         step: [lint, unit, mypy]
diff --git a/README.rst b/README.rst
index bd0df40..e93d862 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.6, 3.7, 3.8, and 3.9
+This is written and tested for Python 3.6, 3.7, 3.8, 3.9, and 3.10.
 
 Install
 -------

From b65f9b79d714c51547b1dd5e56b8e1affa0e1dd3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 26 May 2022 01:02:59 +0000
Subject: [PATCH 036/165] Bump mypy from 0.950 to 0.960

Bumps [mypy](https://github.com/python/mypy) from 0.950 to 0.960.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.950...v0.960)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index ef46782..3ee89b2 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.950
+mypy==0.960
 types-setuptools
 types-requests

From 9672fa57bafa375994ab78bd77b492c636eec257 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Mon, 30 May 2022 16:44:42 +0900
Subject: [PATCH 037/165] Add strict schema (#138)

---
 cwltest/cwltest-schema-strict.yml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 cwltest/cwltest-schema-strict.yml

diff --git a/cwltest/cwltest-schema-strict.yml b/cwltest/cwltest-schema-strict.yml
new file mode 100644
index 0000000..3ce52dd
--- /dev/null
+++ b/cwltest/cwltest-schema-strict.yml
@@ -0,0 +1,27 @@
+$base: "https://w3id.org/cwl/cwltest#"
+$graph:
+  - name: TestCase
+    type: record
+    documentRoot: true
+    fields:
+      id:
+        type: string
+        jsonldPredicate:
+          _type: "@id"
+          identity: true
+      short_name: string?
+      doc: string?
+      tags: string[]
+      tool:
+        type: string
+        jsonldPredicate:
+          _type: "@id"
+      job:
+        type: string?
+        jsonldPredicate:
+          _type: "@id"
+      should_fail:
+        type: boolean?
+        default: false
+      output:
+        type: Any?

From 7fc2297b23246e981acfbab54ed01f4a8c55d6f1 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Mon, 30 May 2022 23:20:12 +0900
Subject: [PATCH 038/165] Add deprecation messages (#141)

---
 cwltest/__init__.py                    | 12 ++++++++++--
 cwltest/tests/test-data/integer-id.yml |  5 +++++
 cwltest/tests/test_categories.py       |  3 +++
 cwltest/tests/test_integer_id.py       | 19 +++++++++++++++++++
 cwltest/tests/test_multi_lined_doc.py  |  1 +
 5 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100644 cwltest/tests/test-data/integer-id.yml
 create mode 100644 cwltest/tests/test_integer_id.py

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index f89f413..5a63b77 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -470,9 +470,17 @@ def main():  # type: () -> int
 
     for t in tests:
         if t.get("label"):
+            _logger.warning("The `label` field is deprecated. Use `id` field instead.")
             t["short_name"] = t["label"]
-        elif t.get("id") and isinstance(t.get("id"), str):
-            t["short_name"] = shortname(t["id"])
+        elif t.get("id"):
+            if isinstance(t.get("id"), str):
+                t["short_name"] = shortname(t["id"])
+            else:
+                _logger.warning(
+                    "The `id` field with integer is deprecated. Use string identifier instead."
+                )
+        else:
+            _logger.warning("The `id` field is missing.")
 
     if args.show_tags:
         alltags = set()  # type: Set[str]
diff --git a/cwltest/tests/test-data/integer-id.yml b/cwltest/tests/test-data/integer-id.yml
new file mode 100644
index 0000000..8223cef
--- /dev/null
+++ b/cwltest/tests/test-data/integer-id.yml
@@ -0,0 +1,5 @@
+- job: v1.0/cat1-job.json
+  output: {}
+  tool: return-0.cwl
+  doc: Test with an integer id
+  id: 1
diff --git a/cwltest/tests/test_categories.py b/cwltest/tests/test_categories.py
index 77e8711..9da4e30 100644
--- a/cwltest/tests/test_categories.py
+++ b/cwltest/tests/test_categories.py
@@ -31,6 +31,8 @@ def test_unsupported_with_required_tests():
     else:
         q = ""
     assert (
+        "The `id` field is missing.{n}"
+        "The `id` field is missing.{n}"
         "Test [1/2] Required test that is unsupported (without tags){n}"
         "{n}"
         "Test 1 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
@@ -57,6 +59,7 @@ def test_unsupported_with_optional_tests():
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     assert error_code == 0
     assert (
+        "The `id` field is missing.{n}"
         "Test [1/1] Optional test that is unsupported{n}{n}"
         "0 tests passed, 1 unsupported "
         "features{n}".format(n=n)
diff --git a/cwltest/tests/test_integer_id.py b/cwltest/tests/test_integer_id.py
new file mode 100644
index 0000000..7993111
--- /dev/null
+++ b/cwltest/tests/test_integer_id.py
@@ -0,0 +1,19 @@
+import os
+from os import linesep as n
+from pathlib import Path
+
+from .util import run_with_mock_cwl_runner, get_data
+import defusedxml.ElementTree as ET
+
+
+def test_warning_with_integer_id():
+    args = [
+        "--test",
+        get_data("tests/test-data/integer-id.yml"),
+        "-l",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert (
+        "The `id` field with integer is deprecated. Use string identifier instead."
+        in stderr
+    )
diff --git a/cwltest/tests/test_multi_lined_doc.py b/cwltest/tests/test_multi_lined_doc.py
index 1fa1501..9b6f4b3 100644
--- a/cwltest/tests/test_multi_lined_doc.py
+++ b/cwltest/tests/test_multi_lined_doc.py
@@ -9,6 +9,7 @@
 def test_run():
     args = ["--test", get_data("tests/test-data/multi-lined-doc.yml")]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert "The `label` field is deprecated. Use `id` field instead." in stderr
     assert f"Test [1/2] opt-error: Test with label{n}" in stderr
     assert f"Test [2/2] Test without label{n}" in stderr
 

From 4d60453ace928624bc2a241d8d32919cffa180f6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 27 Sep 2022 00:11:20 +0000
Subject: [PATCH 039/165] Bump mypy from 0.960 to 0.981

Bumps [mypy](https://github.com/python/mypy) from 0.960 to 0.981.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.960...v0.981)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 3ee89b2..7678736 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.960
+mypy==0.981
 types-setuptools
 types-requests

From 678b401b4b155c5f5bc0bd3767c39fed3895021f Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 27 Sep 2022 11:06:45 +0200
Subject: [PATCH 040/165] make mypy_3.6: Still check the types in a Python 3.6
 context, but using Py 3.7+

---
 .github/workflows/ci-tests.yml | 4 ++++
 Makefile                       | 9 +++++++++
 tox.ini                        | 9 +++++----
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 97fab80..9ea22be 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -23,6 +23,10 @@ jobs:
         py-ver-major: [3]
         py-ver-minor: [6, 7, 8, 9, 10]
         step: [lint, unit, mypy]
+        exclude:
+          - py-ver-major: 3
+            py-ver-minor: 6
+            step: mypy
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
diff --git a/Makefile b/Makefile
index ea7110e..a807129 100644
--- a/Makefile
+++ b/Makefile
@@ -161,6 +161,15 @@ mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:typeshed mypy $^
 
+mypy_3.6: $(filter-out setup.py gittagger.py,$(PYSOURCES))
+	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
+	then \
+		rm -Rf typeshed/ruamel/yaml ; \
+		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
+			typeshed/ruamel/ ; \
+	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
+	MYPYPATH=$$MYPYPATH:typeshed mypy --python-version 3.6 $^
+
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
diff --git a/tox.ini b/tox.ini
index 82b219b..430d084 100644
--- a/tox.ini
+++ b/tox.ini
@@ -3,7 +3,7 @@ envlist =
   py{36,37,38,39,310}-lint,
   py{36,37,38,39,310}-unit,
   py{36,37,38,39,310}-bandit,
-  py{36,37,38,39,310}-mypy,
+  py{37,38,39,310}-mypy,
   py39-pipconflictchecker,
   py39-lintreadme,
   py39-pydocstyle
@@ -27,7 +27,7 @@ description =
   py{36,37,38,39,310}-unit: Run the unit tests
   py{36,37,38,39,310}-lint: Lint the Python code
   py{36,37,38,39,310}-bandit: Search for common security issues
-  py{36,37,38,39,310}-mypy: Check for type safety
+  py{37,38,39,310}-mypy: Check for type safety
   py39-pydocstyle: docstring style checker
   py39-lintreadme: Lint the README.rst->.md conversion
 
@@ -40,7 +40,7 @@ deps =
   py{36,37,38,39,310}-lint: flake8-bugbear
   py{36,37,38,39,310}-lint: black
   py{36,37,38,39,310}-bandit: bandit
-  py{36,37,38,39,310}-mypy: -rmypy-requirements.txt
+  py{37,38,39,310}-mypy: -rmypy-requirements.txt
 
 setenv =
   py{36,37,38,39,310}-unit: LC_ALL = C.UTF-8
@@ -51,7 +51,8 @@ commands =
   py{36,37,38,39,310}-bandit: bandit --recursive cwltest --exclude cwltest/tests/*
   py{36,37,38,39,310}-lint: make flake8
   py{36,37,38,39,310}-lint: make format-check
-  py{36,37,38,39,310}-mypy: make mypy
+  py{37,38,39,310}-mypy: make mypy
+  py37-mypy: make mypy_3.6
 
 whitelist_externals =
   py{36,37,38,39,310}-lint: flake8

From 733b6a71b695d039e9c9738654392a8b21775ece Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 27 Sep 2022 11:22:35 +0200
Subject: [PATCH 041/165] move type stubs out of protected name

---
 MANIFEST.in                                   |    2 +-
 Makefile                                      |   12 +-
 cwltest/__init__.py                           |    2 +-
 .../cachecontrol/__init__.pyi                 |    3 +-
 mypy-stubs/cachecontrol/cache.pyi             |    5 +
 .../cachecontrol/caches/__init__.pyi          |    4 +-
 mypy-stubs/cachecontrol/caches/file_cache.pyi |   31 +
 .../cachecontrol/compat.pyi                   |    2 +-
 mypy-stubs/cachecontrol/controller.pyi        |   18 +
 mypy-stubs/cachecontrol/wrapper.pyi           |   18 +
 mypy-stubs/junit_xml.pyi                      |   93 +
 mypy-stubs/rdflib/__init__.pyi                |   32 +
 mypy-stubs/rdflib/collection.pyi              |   19 +
 mypy-stubs/rdflib/compare.pyi                 |   10 +
 mypy-stubs/rdflib/graph.pyi                   |  252 +++
 mypy-stubs/rdflib/namespace/_CSVW.pyi         |   88 +
 mypy-stubs/rdflib/namespace/_DC.pyi           |   20 +
 mypy-stubs/rdflib/namespace/_DCAT.pyi         |   41 +
 mypy-stubs/rdflib/namespace/_DCTERMS.pyi      |  101 +
 mypy-stubs/rdflib/namespace/_DOAP.pyi         |   47 +
 mypy-stubs/rdflib/namespace/_FOAF.pyi         |   80 +
 mypy-stubs/rdflib/namespace/_ODRL2.pyi        |  209 +++
 mypy-stubs/rdflib/namespace/_ORG.pyi          |   50 +
 mypy-stubs/rdflib/namespace/_OWL.pyi          |   82 +
 mypy-stubs/rdflib/namespace/_PROF.pyi         |   15 +
 mypy-stubs/rdflib/namespace/_PROV.pyi         |  175 ++
 mypy-stubs/rdflib/namespace/_QB.pyi           |   41 +
 mypy-stubs/rdflib/namespace/_RDF.pyi          |   27 +
 mypy-stubs/rdflib/namespace/_RDFS.pyi         |   20 +
 mypy-stubs/rdflib/namespace/_SDO.pyi          | 1645 +++++++++++++++++
 mypy-stubs/rdflib/namespace/_SH.pyi           |  183 ++
 mypy-stubs/rdflib/namespace/_SKOS.pyi         |   37 +
 mypy-stubs/rdflib/namespace/_SOSA.pyi         |   41 +
 mypy-stubs/rdflib/namespace/_SSN.pyi          |   26 +
 mypy-stubs/rdflib/namespace/_TIME.pyi         |  100 +
 mypy-stubs/rdflib/namespace/_VOID.pyi         |   35 +
 mypy-stubs/rdflib/namespace/_XSD.pyi          |   77 +
 mypy-stubs/rdflib/namespace/__init__.pyi      |   85 +
 mypy-stubs/rdflib/parser.pyi                  |    5 +
 mypy-stubs/rdflib/paths.pyi                   |   24 +
 mypy-stubs/rdflib/plugin.pyi                  |    8 +
 .../rdflib/plugins/__init__.pyi               |    1 -
 .../rdflib/plugins/parsers/__init__.pyi       |    1 -
 .../rdflib/plugins/parsers/notation3.pyi      |    1 +
 mypy-stubs/rdflib/query.pyi                   |   42 +
 mypy-stubs/rdflib/resource.pyi                |   33 +
 mypy-stubs/rdflib/term.pyi                    |   43 +
 {typeshed => mypy-stubs}/ruamel/__init__.py   |    0
 typeshed/avro/__init__.pyi                    |   10 -
 typeshed/avro/schema.pyi                      |  117 --
 typeshed/cachecontrol/adapter.pyi             |   19 -
 typeshed/cachecontrol/cache.pyi               |   19 -
 typeshed/cachecontrol/caches/file_cache.pyi   |   22 -
 typeshed/cachecontrol/controller.pyi          |   25 -
 typeshed/cachecontrol/filewrapper.pyi         |    8 -
 typeshed/cachecontrol/serialize.pyi           |   10 -
 typeshed/cachecontrol/wrapper.pyi             |   14 -
 typeshed/future/__init__.pyi                  |    0
 typeshed/future/utils/__init__.pyi            |   61 -
 typeshed/galaxy/__init__.pyi                  |   13 -
 typeshed/galaxy/exceptions/__init__.pyi       |  143 --
 typeshed/galaxy/exceptions/error_codes.pyi    |   17 -
 typeshed/galaxy/jobs/__init__.pyi             |    4 -
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 typeshed/select.pyi                           |  137 --
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 typeshed/shellescape/main.pyi                 |    5 -
 typeshed/urllib/__init__.py                   |    0
 typeshed/urllib/parse.pyi                     |  152 --
 typeshed/urllib/subprocess.pyi                | 1208 ------------
 208 files changed, 3872 insertions(+), 6139 deletions(-)
 rename {typeshed => mypy-stubs}/cachecontrol/__init__.pyi (63%)
 create mode 100644 mypy-stubs/cachecontrol/cache.pyi
 rename {typeshed => mypy-stubs}/cachecontrol/caches/__init__.pyi (80%)
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 create mode 100644 mypy-stubs/cachecontrol/controller.pyi
 create mode 100644 mypy-stubs/cachecontrol/wrapper.pyi
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 create mode 100644 mypy-stubs/rdflib/plugins/parsers/notation3.pyi
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diff --git a/MANIFEST.in b/MANIFEST.in
index 74643c8..f902163 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -3,6 +3,6 @@ include cwltest/cwltest-schema.yml
 include cwltest/tests/*
 include cwltest/tests/test-data/*
 include cwltest/tests/test-data/v1.0/*
-recursive-include typeshed *.py?
+recursive-include mypy-stubs *.py?
 global-exclude *~
 global-exclude *.pyc
diff --git a/Makefile b/Makefile
index a807129..b655cd9 100644
--- a/Makefile
+++ b/Makefile
@@ -155,20 +155,20 @@ mypy3: mypy
 mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
-		rm -Rf typeshed/ruamel/yaml ; \
+		rm -Rf mypy-stubs/ruamel/yaml ; \
 		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			typeshed/ruamel/ ; \
+			mypy-stubs/ruamel/ ; \
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
-	MYPYPATH=$$MYPYPATH:typeshed mypy $^
+	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 mypy_3.6: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
-		rm -Rf typeshed/ruamel/yaml ; \
+		rm -Rf mypy-stubs/ruamel/yaml ; \
 		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			typeshed/ruamel/ ; \
+			mypy-stubs/ruamel/ ; \
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
-	MYPYPATH=$$MYPYPATH:typeshed mypy --python-version 3.6 $^
+	MYPYPATH=$$MYPYPATH:mypy-stubs mypy --python-version 3.6 $^
 
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 5a63b77..e16c828 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -595,7 +595,7 @@ def main():  # type: () -> int
 
     if args.junit_xml:
         with open(args.junit_xml, "w") as xml:
-            junit_xml.TestSuite.to_file(xml, [report])
+            junit_xml.to_xml_report_file(xml, [report])
 
     if args.badgedir:
         os.mkdir(args.badgedir)
diff --git a/typeshed/cachecontrol/__init__.pyi b/mypy-stubs/cachecontrol/__init__.pyi
similarity index 63%
rename from typeshed/cachecontrol/__init__.pyi
rename to mypy-stubs/cachecontrol/__init__.pyi
index dba67bc..d8c9745 100644
--- a/typeshed/cachecontrol/__init__.pyi
+++ b/mypy-stubs/cachecontrol/__init__.pyi
@@ -3,8 +3,7 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any
+
 from .wrapper import CacheControl as CacheControl
-#from .adapter import CacheControlAdapter as CacheControlAdapter
-#from .controller import CacheController as CacheController
 
 __email__ = ...  # type: Any
diff --git a/mypy-stubs/cachecontrol/cache.pyi b/mypy-stubs/cachecontrol/cache.pyi
new file mode 100644
index 0000000..f738f6f
--- /dev/null
+++ b/mypy-stubs/cachecontrol/cache.pyi
@@ -0,0 +1,5 @@
+class BaseCache:
+    def get(self, key: str) -> bytes | None: ...
+    def set(self, key: str, value: bytes, expires: int | None = None) -> None: ...
+    def delete(self, key: str) -> None: ...
+    def close(self) -> None: ...
diff --git a/typeshed/cachecontrol/caches/__init__.pyi b/mypy-stubs/cachecontrol/caches/__init__.pyi
similarity index 80%
rename from typeshed/cachecontrol/caches/__init__.pyi
rename to mypy-stubs/cachecontrol/caches/__init__.pyi
index b7784c2..42c0ad6 100644
--- a/typeshed/cachecontrol/caches/__init__.pyi
+++ b/mypy-stubs/cachecontrol/caches/__init__.pyi
@@ -3,7 +3,9 @@
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
 
 from typing import Any
+
 from .file_cache import FileCache as FileCache
-#from .redis_cache import RedisCache as RedisCache
+
+# from .redis_cache import RedisCache as RedisCache
 
 notice = ...  # type: Any
diff --git a/mypy-stubs/cachecontrol/caches/file_cache.pyi b/mypy-stubs/cachecontrol/caches/file_cache.pyi
new file mode 100644
index 0000000..a89d758
--- /dev/null
+++ b/mypy-stubs/cachecontrol/caches/file_cache.pyi
@@ -0,0 +1,31 @@
+from os import PathLike
+from typing import ContextManager
+
+from ..cache import BaseCache as BaseCache
+from ..controller import CacheController as CacheController
+
+class _LockClass:
+    path: str
+
+_lock_class = ContextManager[_LockClass]
+
+class FileCache(BaseCache):
+    directory: str
+    forever: bool
+    filemode: int
+    dirmode: int
+    lock_class: _lock_class | None = None
+    def __init__(
+        self,
+        directory: str | PathLike[str],
+        forever: bool = ...,
+        filemode: int = ...,
+        dirmode: int = ...,
+        use_dir_lock: bool | None = ...,
+        lock_class: _lock_class | None = ...,
+    ) -> None: ...
+    @staticmethod
+    def encode(x: str) -> str: ...
+    def get(self, key: str) -> None | bytes: ...
+    def set(self, key: str, value: bytes, expires: int | None = None) -> None: ...
+    def delete(self, key: str) -> None: ...
diff --git a/typeshed/cachecontrol/compat.pyi b/mypy-stubs/cachecontrol/compat.pyi
similarity index 83%
rename from typeshed/cachecontrol/compat.pyi
rename to mypy-stubs/cachecontrol/compat.pyi
index 0926ecc..fabfae3 100644
--- a/typeshed/cachecontrol/compat.pyi
+++ b/mypy-stubs/cachecontrol/compat.pyi
@@ -4,4 +4,4 @@
 
 from typing import Any
 
-text_type = ...  # type: Any
+str = ...  # type: Any
diff --git a/mypy-stubs/cachecontrol/controller.pyi b/mypy-stubs/cachecontrol/controller.pyi
new file mode 100644
index 0000000..e8a06aa
--- /dev/null
+++ b/mypy-stubs/cachecontrol/controller.pyi
@@ -0,0 +1,18 @@
+from typing import Collection
+
+from _typeshed import Incomplete
+
+from .cache import BaseCache
+
+class CacheController:
+    cache: BaseCache
+    cache_etags: bool
+    serializer: Incomplete
+    cacheable_status_codes: Collection[int] | None = None
+    def __init__(
+        self,
+        cache: BaseCache | None = None,
+        cache_etags: bool = True,
+        serializer: Incomplete | None = None,
+        status_codes: Collection[int] | None = None,
+    ) -> None: ...
diff --git a/mypy-stubs/cachecontrol/wrapper.pyi b/mypy-stubs/cachecontrol/wrapper.pyi
new file mode 100644
index 0000000..6244687
--- /dev/null
+++ b/mypy-stubs/cachecontrol/wrapper.pyi
@@ -0,0 +1,18 @@
+from typing import Collection, Type
+
+from _typeshed import Incomplete
+from requests import Session
+
+from .cache import BaseCache
+from .controller import CacheController
+
+def CacheControl(
+    sess: Session,
+    cache: BaseCache | None = None,
+    cache_etags: bool = True,
+    serializer: Incomplete | None = None,
+    heuristic: Incomplete | None = None,
+    controller_class: Type[CacheController] | None = None,
+    adapter_class: Incomplete | None = None,
+    cacheable_methods: Collection[str] | None = None,
+) -> Session: ...
diff --git a/mypy-stubs/junit_xml.pyi b/mypy-stubs/junit_xml.pyi
new file mode 100644
index 0000000..e305ce4
--- /dev/null
+++ b/mypy-stubs/junit_xml.pyi
@@ -0,0 +1,93 @@
+# Stubs for junit_xml (Python 3.5)
+#
+# NOTE: This dynamically typed stub was automatically generated by stubgen.
+
+from typing import IO, Any, List, Optional
+
+unichr = chr
+
+class TestSuite:
+    name: Any = ...
+    test_cases: Any = ...
+    timestamp: Any = ...
+    hostname: Any = ...
+    id: Any = ...
+    package: Any = ...
+    file: Any = ...
+    log: Any = ...
+    url: Any = ...
+    stdout: Any = ...
+    stderr: Any = ...
+    properties: Any = ...
+    def __init__(
+        self,
+        name: str,
+        test_cases: Optional[Any] = ...,
+        hostname: Optional[Any] = ...,
+        id: Optional[Any] = ...,
+        package: Optional[Any] = ...,
+        timestamp: Optional[Any] = ...,
+        properties: Optional[Any] = ...,
+        file: Optional[Any] = ...,
+        log: Optional[Any] = ...,
+        url: Optional[Any] = ...,
+        stdout: Optional[Any] = ...,
+        stderr: Optional[Any] = ...,
+    ) -> None: ...
+
+class TestCase:
+    name: Any = ...
+    assertions: Any = ...
+    elapsed_sec: Any = ...
+    timestamp: Any = ...
+    classname: Any = ...
+    status: Any = ...
+    category: Any = ...
+    file: Any = ...
+    line: Any = ...
+    log: Any = ...
+    url: Any = ...
+    stdout: Any = ...
+    stderr: Any = ...
+    is_enabled: bool = ...
+    error_message: Any = ...
+    error_output: Any = ...
+    error_type: Any = ...
+    failure_message: Any = ...
+    failure_output: Any = ...
+    failure_type: Any = ...
+    skipped_message: Any = ...
+    skipped_output: Any = ...
+    def __init__(
+        self,
+        name: str,
+        classname: Optional[Any] = ...,
+        elapsed_sec: Optional[Any] = ...,
+        stdout: Optional[Any] = ...,
+        stderr: Optional[Any] = ...,
+        assertions: Optional[Any] = ...,
+        timestamp: Optional[Any] = ...,
+        status: Optional[Any] = ...,
+        category: Optional[Any] = ...,
+        file: Optional[Any] = ...,
+        line: Optional[Any] = ...,
+        log: Optional[Any] = ...,
+        group: Optional[Any] = ...,
+        url: Optional[Any] = ...,
+    ) -> None: ...
+    def add_failure_info(
+        self,
+        message: Optional[Any] = ...,
+        output: Optional[Any] = ...,
+        failure_type: Optional[Any] = ...,
+    ) -> None: ...
+    def add_skipped_info(
+        self, message: Optional[Any] = ..., output: Optional[Any] = ...
+    ) -> None: ...
+
+def to_xml_report_file(
+    file_descriptor: IO[Any],
+    test_suites: List[TestSuite],
+    prettyprint: bool = True,
+    encoding: Optional[str] = None,
+) -> None: ...
diff --git a/mypy-stubs/rdflib/__init__.pyi b/mypy-stubs/rdflib/__init__.pyi
new file mode 100644
index 0000000..03d8e90
--- /dev/null
+++ b/mypy-stubs/rdflib/__init__.pyi
@@ -0,0 +1,32 @@
+from rdflib.graph import ConjunctiveGraph as ConjunctiveGraph
+from rdflib.graph import Graph as Graph
+from rdflib.namespace import CSVW as CSVW
+from rdflib.namespace import DC as DC
+from rdflib.namespace import DCAT as DCAT
+from rdflib.namespace import DCTERMS as DCTERMS
+from rdflib.namespace import DOAP as DOAP
+from rdflib.namespace import FOAF as FOAF
+from rdflib.namespace import ODRL2 as ODRL2
+from rdflib.namespace import ORG as ORG
+from rdflib.namespace import OWL as OWL
+from rdflib.namespace import PROF as PROF
+from rdflib.namespace import PROV as PROV
+from rdflib.namespace import QB as QB
+from rdflib.namespace import RDF as RDF
+from rdflib.namespace import RDFS as RDFS
+from rdflib.namespace import SDO as SDO
+from rdflib.namespace import SH as SH
+from rdflib.namespace import SKOS as SKOS
+from rdflib.namespace import SOSA as SOSA
+from rdflib.namespace import SSN as SSN
+from rdflib.namespace import TIME as TIME
+from rdflib.namespace import VOID as VOID
+from rdflib.namespace import XMLNS as XMLNS
+from rdflib.namespace import XSD as XSD
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import BNode as BNode
+from rdflib.term import Literal as Literal
+from rdflib.term import URIRef as URIRef
+from rdflib.term import Variable as Variable
+
+__version__: str
diff --git a/mypy-stubs/rdflib/collection.pyi b/mypy-stubs/rdflib/collection.pyi
new file mode 100644
index 0000000..0bee984
--- /dev/null
+++ b/mypy-stubs/rdflib/collection.pyi
@@ -0,0 +1,19 @@
+from typing import Any, Iterator
+
+from rdflib.graph import Graph
+from rdflib.term import Node
+
+class Collection:
+    graph: Graph
+    uri: Node
+    def __init__(self, graph: Graph, uri: Node, seq: Any = ...) -> None: ...
+    def n3(self) -> str: ...
+    def __len__(self) -> int: ...
+    def index(self, item: Any) -> int: ...
+    def __getitem__(self, key: str) -> Any: ...
+    def __setitem__(self, key: str, value: Any) -> None: ...
+    def __delitem__(self, key: str) -> None: ...
+    def __iter__(self) -> Iterator[Any]: ...
+    def append(self, item: Any) -> Collection: ...
+    def __iadd__(self, other: Any) -> Collection: ...
+    def clear(self) -> Collection: ...
diff --git a/mypy-stubs/rdflib/compare.pyi b/mypy-stubs/rdflib/compare.pyi
new file mode 100644
index 0000000..6451292
--- /dev/null
+++ b/mypy-stubs/rdflib/compare.pyi
@@ -0,0 +1,10 @@
+from typing import Dict, Union
+
+from rdflib.graph import ConjunctiveGraph, Graph
+
+Stats = Dict[str, Union[int, str]]
+
+class IsomorphicGraph(ConjunctiveGraph):
+    pass
+
+def to_isomorphic(graph: Graph = ...) -> IsomorphicGraph: ...
diff --git a/mypy-stubs/rdflib/graph.pyi b/mypy-stubs/rdflib/graph.pyi
new file mode 100644
index 0000000..23c2e6e
--- /dev/null
+++ b/mypy-stubs/rdflib/graph.pyi
@@ -0,0 +1,252 @@
+import pathlib
+from typing import (
+    IO,
+    Any,
+    Iterable,
+    Iterator,
+    List,
+    Optional,
+    Set,
+    Tuple,
+    Union,
+    overload,
+)
+
+from rdflib import query
+from rdflib.collection import Collection
+from rdflib.paths import Path
+from rdflib.resource import Resource
+from rdflib.term import BNode, Identifier, Node
+
+class Graph(Node):
+    base: Any = ...
+    context_aware: bool = ...
+    formula_aware: bool = ...
+    default_union: bool = ...
+    def __init__(
+        self,
+        store: str = ...,
+        identifier: Optional[Any] = ...,
+        namespace_manager: Optional[Any] = ...,
+        base: Optional[Any] = ...,
+    ) -> None: ...
+    store: Any = ...
+    identifier: Any = ...
+    namespace_manager: Any = ...
+    def toPython(self) -> str: ...
+    def destroy(self, configuration: Any) -> None: ...
+    def commit(self) -> None: ...
+    def rollback(self) -> None: ...
+    def open(self, configuration: Any, create: bool = ...) -> Any: ...
+    def close(self, commit_pending_transaction: bool = ...) -> None: ...
+    def add(self, triple: Any) -> None: ...
+    def addN(self, quads: Any) -> None: ...
+    def remove(self, triple: Any) -> None: ...
+    def triples(
+        self,
+        triple: Tuple[
+            Optional[Union[str, Identifier]],
+            Optional[Union[str, Identifier]],
+            Optional[Identifier],
+        ],
+    ) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ...
+    def __getitem__(
+        self, item: slice | Path | Node
+    ) -> Iterator[
+        Tuple[Identifier, Identifier, Identifier] | Tuple[Identifier, identifier] | Node
+    ]: ...
+    def __contains__(self, triple: Any) -> bool: ...
+    def __add__(self, other: Any) -> Graph: ...
+    def set(self, triple: Any) -> None: ...
+    def subjects(
+        self, predicate: Optional[Any] = ..., object: Optional[Any] = ...
+    ) -> Iterable[Node]: ...
+    def predicates(
+        self, subject: Optional[Any] = ..., object: Optional[Any] = ...
+    ) -> Iterable[Node]: ...
+    def objects(
+        self, subject: Optional[Any] = ..., predicate: Optional[Any] = ...
+    ) -> Iterable[Identifier]: ...
+    def subject_predicates(self, object: Optional[Any] = ...) -> None: ...
+    def subject_objects(self, predicate: Optional[Any] = ...) -> None: ...
+    def predicate_objects(self, subject: Optional[Any] = ...) -> None: ...
+    def triples_choices(self, triple: Any, context: Optional[Any] = ...) -> None: ...
+    def value(
+        self,
+        subject: Optional[Any] = ...,
+        predicate: Any = ...,
+        object: Optional[Any] = ...,
+        default: Optional[Any] = ...,
+        any: bool = ...,
+    ) -> Any: ...
+    def label(self, subject: Any, default: str = ...) -> Any: ...
+    def preferredLabel(
+        self,
+        subject: Any,
+        lang: Optional[Any] = ...,
+        default: Optional[Any] = ...,
+        labelProperties: Any = ...,
+    ) -> List[Tuple[Any, Any]]: ...
+    def comment(self, subject: Any, default: str = ...) -> Any: ...
+    def items(self, list: Any) -> Iterator[Any]: ...
+    def transitiveClosure(
+        self, func: Any, arg: Any, seen: Optional[Any] = ...
+    ) -> Iterator[Any]: ...
+    def transitive_objects(
+        self, subject: Any, property: Any, remember: Optional[Any] = ...
+    ) -> Iterator[Any]: ...
+    def transitive_subjects(
+        self, predicate: Any, object: Any, remember: Optional[Any] = ...
+    ) -> Iterator[Any]: ...
+    def seq(self, subject: Any) -> Seq | None: ...
+    def qname(self, uri: Any) -> Any: ...
+    def compute_qname(self, uri: Any, generate: bool = ...) -> Any: ...
+    def bind(
+        self, prefix: Any, namespace: Any, override: bool = ..., replace: bool = ...
+    ) -> Any: ...
+    def namespaces(self) -> Iterator[Tuple[Any, Any]]: ...
+    def absolutize(self, uri: Any, defrag: int = ...) -> Any: ...
+
+    # no destination and non-None positional encoding
+    @overload
+    def serialize(
+        self,
+        destination: None,
+        format: str,
+        base: Optional[str],
+        encoding: str,
+        **args: Any,
+    ) -> bytes: ...
+
+    # no destination and non-None keyword encoding
+    @overload
+    def serialize(
+        self,
+        destination: None = ...,
+        format: str = ...,
+        base: Optional[str] = ...,
+        *,
+        encoding: str,
+        **args: Any,
+    ) -> bytes: ...
+
+    # no destination and None encoding
+    @overload
+    def serialize(
+        self,
+        destination: None = ...,
+        format: str = ...,
+        base: Optional[str] = ...,
+        encoding: None = ...,
+        **args: Any,
+    ) -> str: ...
+
+    # non-None destination
+    @overload
+    def serialize(
+        self,
+        destination: Union[str, pathlib.PurePath, IO[bytes]],
+        format: str = ...,
+        base: Optional[str] = ...,
+        encoding: Optional[str] = ...,
+        **args: Any,
+    ) -> "Graph": ...
+
+    # fallback
+    @overload
+    def serialize(
+        self,
+        destination: Optional[Union[str, pathlib.PurePath, IO[bytes]]] = ...,
+        format: str = ...,
+        base: Optional[str] = ...,
+        encoding: Optional[str] = ...,
+        **args: Any,
+    ) -> Union[bytes, str, "Graph"]: ...
+    def parse(
+        self,
+        source: Optional[Any] = ...,
+        publicID: Optional[Any] = ...,
+        format: Optional[str] = ...,
+        location: Optional[Any] = ...,
+        file: Optional[Any] = ...,
+        data: Optional[Any] = ...,
+        **args: Any,
+    ) -> "Graph": ...
+    def load(
+        self, source: Any, publicID: Optional[Any] = ..., format: str = ...
+    ) -> "Graph": ...
+    def query(
+        self,
+        query_object: Any,
+        processor: str = ...,
+        result: str = ...,
+        initNs: Optional[Any] = ...,
+        initBindings: Optional[Any] = ...,
+        use_store_provided: bool = ...,
+        **kwargs: Any,
+    ) -> query.Result: ...
+    def update(
+        self,
+        update_object: Any,
+        processor: str = ...,
+        initNs: Optional[Any] = ...,
+        initBindings: Optional[Any] = ...,
+        use_store_provided: bool = ...,
+        **kwargs: Any,
+    ) -> Any: ...
+    def n3(self) -> str: ...
+    def isomorphic(self, other: Any) -> bool: ...
+    def connected(self) -> bool: ...
+    def all_nodes(self) -> Set[Any]: ...
+    def collection(self, identifier: Any) -> Collection: ...
+    def resource(self, identifier: Any) -> Resource: ...
+    def skolemize(
+        self,
+        new_graph: Optional[Any] = ...,
+        bnode: Optional[Any] = ...,
+        authority: Optional[Any] = ...,
+        basepath: Optional[Any] = ...,
+    ) -> Graph: ...
+    def de_skolemize(
+        self, new_graph: Optional[Any] = ..., uriref: Optional[Any] = ...
+    ) -> Graph: ...
+
+class ConjunctiveGraph(Graph):
+    context_aware: bool = ...
+    default_union: bool = ...
+    default_context: Any = ...
+    def __init__(
+        self,
+        store: str = ...,
+        identifier: Optional[Any] = ...,
+        default_graph_base: Optional[Any] = ...,
+    ) -> None: ...
+    def add(self, triple_or_quad: Any) -> None: ...
+    def addN(self, quads: Any) -> None: ...
+    def remove(self, triple_or_quad: Any) -> None: ...
+    # def triples(self, triple_or_quad: Tuple[Optional[Union[str, BNode]], Optional[Union[str, BNode]], Optional[BNode]], context: Tuple[Optional[Union[str, BNode]], Optional[Union[str, BNode]], Optional[BNode]]) -> Iterator[Tuple[Identifier, Identifier, Identifier]]: ...
+    def quads(self, triple_or_quad: Optional[Any] = ...) -> None: ...
+    def triples_choices(self, triple: Any, context: Optional[Any] = ...) -> None: ...
+    def contexts(self, triple: Optional[Any] = ...) -> None: ...
+    def get_context(
+        self,
+        identifier: Node | str | None,
+        quoted: bool = ...,
+        base: Optional[str] = ...,
+    ) -> Graph: ...
+    def remove_context(self, context: Any) -> None: ...
+    def context_id(self, uri: Any, context_id: Optional[Any] = ...) -> Any: ...
+    def parse(
+        self,
+        source: Optional[Any] = ...,
+        publicID: Optional[Any] = ...,
+        format: Optional[str] = ...,
+        location: Optional[Any] = ...,
+        file: Optional[Any] = ...,
+        data: Optional[Any] = ...,
+        **args: Any,
+    ) -> Graph: ...
+
+class Seq:
+    def __init__(self, graph: Graph, subject: Any) -> None: ...
+    def toPython(self) -> Seq: ...
diff --git a/mypy-stubs/rdflib/namespace/_CSVW.pyi b/mypy-stubs/rdflib/namespace/_CSVW.pyi
new file mode 100644
index 0000000..aa1b137
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_CSVW.pyi
@@ -0,0 +1,88 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class CSVW(DefinedNamespace):
+    aboutUrl: URIRef
+    base: URIRef
+    column: URIRef
+    columnReference: URIRef
+    commentPrefix: URIRef
+    datatype: URIRef
+    decimalChar: URIRef
+    default: URIRef
+    delimiter: URIRef
+    describes: URIRef
+    dialect: URIRef
+    doubleQuote: URIRef
+    encoding: URIRef
+    foreignKey: URIRef
+    format: URIRef
+    groupChar: URIRef
+    header: URIRef
+    headerRowCount: URIRef
+    lang: URIRef
+    length: URIRef
+    lineTerminators: URIRef
+    maxExclusive: URIRef
+    maxInclusive: URIRef
+    maxLength: URIRef
+    minExclusive: URIRef
+    minInclusive: URIRef
+    minLength: URIRef
+    name: URIRef
+    note: URIRef
+    null: URIRef
+    ordered: URIRef
+    pattern: URIRef
+    primaryKey: URIRef
+    propertyUrl: URIRef
+    quoteChar: URIRef
+    reference: URIRef
+    referencedRow: URIRef
+    required: URIRef
+    resource: URIRef
+    row: URIRef
+    rowTitle: URIRef
+    rownum: URIRef
+    schemaReference: URIRef
+    scriptFormat: URIRef
+    separator: URIRef
+    skipBlankRows: URIRef
+    skipColumns: URIRef
+    skipInitialSpace: URIRef
+    skipRows: URIRef
+    source: URIRef
+    suppressOutput: URIRef
+    table: URIRef
+    tableDirection: URIRef
+    tableSchema: URIRef
+    targetFormat: URIRef
+    textDirection: URIRef
+    title: URIRef
+    transformations: URIRef
+    trim: URIRef
+    url: URIRef
+    valueUrl: URIRef
+    virtual: URIRef
+    Cell: URIRef
+    Column: URIRef
+    Datatype: URIRef
+    Dialect: URIRef
+    Direction: URIRef
+    ForeignKey: URIRef
+    NumericFormat: URIRef
+    Row: URIRef
+    Schema: URIRef
+    Table: URIRef
+    TableGroup: URIRef
+    TableReference: URIRef
+    Transformation: URIRef
+    JSON: URIRef
+    uriTemplate: URIRef
+    auto: URIRef
+    inherit: URIRef
+    ltr: URIRef
+    rtl: URIRef
+    csvEncodedTabularData: URIRef
+    tabularMetadata: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_DC.pyi b/mypy-stubs/rdflib/namespace/_DC.pyi
new file mode 100644
index 0000000..25d75e8
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_DC.pyi
@@ -0,0 +1,20 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class DC(DefinedNamespace):
+    contributor: URIRef
+    coverage: URIRef
+    creator: URIRef
+    date: URIRef
+    description: URIRef
+    format: URIRef
+    identifier: URIRef
+    language: URIRef
+    publisher: URIRef
+    relation: URIRef
+    rights: URIRef
+    source: URIRef
+    subject: URIRef
+    title: URIRef
+    type: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_DCAT.pyi b/mypy-stubs/rdflib/namespace/_DCAT.pyi
new file mode 100644
index 0000000..c920687
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_DCAT.pyi
@@ -0,0 +1,41 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class DCAT(DefinedNamespace):
+    accessURL: URIRef
+    bbox: URIRef
+    byteSize: URIRef
+    centroid: URIRef
+    compressFormat: URIRef
+    contactPoint: URIRef
+    dataset: URIRef
+    distribution: URIRef
+    downloadURL: URIRef
+    endDate: URIRef
+    keyword: URIRef
+    landingPage: URIRef
+    mediaType: URIRef
+    packageFormat: URIRef
+    record: URIRef
+    startDate: URIRef
+    theme: URIRef
+    themeTaxonomy: URIRef
+    Catalog: URIRef
+    CatalogRecord: URIRef
+    Dataset: URIRef
+    Distribution: URIRef
+    DataService: URIRef
+    Relationship: URIRef
+    Resource: URIRef
+    Role: URIRef
+    spatialResolutionInMeters: URIRef
+    temporalResolution: URIRef
+    accessService: URIRef
+    catalog: URIRef
+    endpointDescription: URIRef
+    endpointURL: URIRef
+    hadRole: URIRef
+    qualifiedRelation: URIRef
+    servesDataset: URIRef
+    service: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_DCTERMS.pyi b/mypy-stubs/rdflib/namespace/_DCTERMS.pyi
new file mode 100644
index 0000000..3c5d77f
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_DCTERMS.pyi
@@ -0,0 +1,101 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class DCTERMS(DefinedNamespace):
+    DCMIType: URIRef
+    DDC: URIRef
+    IMT: URIRef
+    LCC: URIRef
+    LCSH: URIRef
+    MESH: URIRef
+    NLM: URIRef
+    TGN: URIRef
+    UDC: URIRef
+    abstract: URIRef
+    accessRights: URIRef
+    accrualMethod: URIRef
+    accrualPeriodicity: URIRef
+    accrualPolicy: URIRef
+    alternative: URIRef
+    audience: URIRef
+    available: URIRef
+    bibliographicCitation: URIRef
+    conformsTo: URIRef
+    contributor: URIRef
+    coverage: URIRef
+    created: URIRef
+    creator: URIRef
+    date: URIRef
+    dateAccepted: URIRef
+    dateCopyrighted: URIRef
+    dateSubmitted: URIRef
+    description: URIRef
+    educationLevel: URIRef
+    extent: URIRef
+    format: URIRef
+    hasFormat: URIRef
+    hasPart: URIRef
+    hasVersion: URIRef
+    identifier: URIRef
+    instructionalMethod: URIRef
+    isFormatOf: URIRef
+    isPartOf: URIRef
+    isReferencedBy: URIRef
+    isReplacedBy: URIRef
+    isRequiredBy: URIRef
+    isVersionOf: URIRef
+    issued: URIRef
+    language: URIRef
+    license: URIRef
+    mediator: URIRef
+    medium: URIRef
+    modified: URIRef
+    provenance: URIRef
+    publisher: URIRef
+    references: URIRef
+    relation: URIRef
+    replaces: URIRef
+    requires: URIRef
+    rights: URIRef
+    rightsHolder: URIRef
+    source: URIRef
+    spatial: URIRef
+    subject: URIRef
+    tableOfContents: URIRef
+    temporal: URIRef
+    title: URIRef
+    type: URIRef
+    valid: URIRef
+    Agent: URIRef
+    AgentClass: URIRef
+    BibliographicResource: URIRef
+    FileFormat: URIRef
+    Frequency: URIRef
+    Jurisdiction: URIRef
+    LicenseDocument: URIRef
+    LinguisticSystem: URIRef
+    Location: URIRef
+    LocationPeriodOrJurisdiction: URIRef
+    MediaType: URIRef
+    MediaTypeOrExtent: URIRef
+    MethodOfAccrual: URIRef
+    MethodOfInstruction: URIRef
+    PeriodOfTime: URIRef
+    PhysicalMedium: URIRef
+    PhysicalResource: URIRef
+    Policy: URIRef
+    ProvenanceStatement: URIRef
+    RightsStatement: URIRef
+    SizeOrDuration: URIRef
+    Standard: URIRef
+    Box: URIRef
+    ISO3166: URIRef
+    Period: URIRef
+    Point: URIRef
+    RFC1766: URIRef
+    RFC3066: URIRef
+    RFC4646: URIRef
+    RFC5646: URIRef
+    URI: URIRef
+    W3CDTF: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_DOAP.pyi b/mypy-stubs/rdflib/namespace/_DOAP.pyi
new file mode 100644
index 0000000..846f8be
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_DOAP.pyi
@@ -0,0 +1,47 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class DOAP(DefinedNamespace):
+    audience: URIRef
+    blog: URIRef
+    browse: URIRef
+    category: URIRef
+    created: URIRef
+    description: URIRef
+    developer: URIRef
+    documenter: URIRef
+    helper: URIRef
+    implements: URIRef
+    language: URIRef
+    license: URIRef
+    location: URIRef
+    maintainer: URIRef
+    module: URIRef
+    name: URIRef
+    os: URIRef
+    platform: URIRef
+    release: URIRef
+    repository: URIRef
+    repositoryOf: URIRef
+    revision: URIRef
+    screenshots: URIRef
+    shortdesc: URIRef
+    tester: URIRef
+    translator: URIRef
+    vendor: URIRef
+    wiki: URIRef
+    ArchRepository: URIRef
+    BKRepository: URIRef
+    BazaarBranch: URIRef
+    CVSRepository: URIRef
+    DarcsRepository: URIRef
+    GitBranch: URIRef
+    GitRepository: URIRef
+    HgRepository: URIRef
+    Project: URIRef
+    Repository: URIRef
+    SVNRepository: URIRef
+    Specification: URIRef
+    Version: URIRef
+    homepage: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_FOAF.pyi b/mypy-stubs/rdflib/namespace/_FOAF.pyi
new file mode 100644
index 0000000..50923a1
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_FOAF.pyi
@@ -0,0 +1,80 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class FOAF(DefinedNamespace):
+    account: URIRef
+    accountName: URIRef
+    accountServiceHomepage: URIRef
+    age: URIRef
+    based_near: URIRef
+    birthday: URIRef
+    currentProject: URIRef
+    depiction: URIRef
+    depicts: URIRef
+    dnaChecksum: URIRef
+    familyName: URIRef
+    family_name: URIRef
+    firstName: URIRef
+    focus: URIRef
+    fundedBy: URIRef
+    geekcode: URIRef
+    gender: URIRef
+    givenName: URIRef
+    givenname: URIRef
+    holdsAccount: URIRef
+    img: URIRef
+    interest: URIRef
+    knows: URIRef
+    lastName: URIRef
+    made: URIRef
+    maker: URIRef
+    member: URIRef
+    membershipClass: URIRef
+    myersBriggs: URIRef
+    name: URIRef
+    nick: URIRef
+    page: URIRef
+    pastProject: URIRef
+    phone: URIRef
+    plan: URIRef
+    primaryTopic: URIRef
+    publications: URIRef
+    schoolHomepage: URIRef
+    sha1: URIRef
+    skypeID: URIRef
+    status: URIRef
+    surname: URIRef
+    theme: URIRef
+    thumbnail: URIRef
+    tipjar: URIRef
+    title: URIRef
+    topic: URIRef
+    topic_interest: URIRef
+    workInfoHomepage: URIRef
+    workplaceHomepage: URIRef
+    Agent: URIRef
+    Document: URIRef
+    Group: URIRef
+    Image: URIRef
+    LabelProperty: URIRef
+    OnlineAccount: URIRef
+    OnlineChatAccount: URIRef
+    OnlineEcommerceAccount: URIRef
+    OnlineGamingAccount: URIRef
+    Organization: URIRef
+    Person: URIRef
+    PersonalProfileDocument: URIRef
+    Project: URIRef
+    aimChatID: URIRef
+    homepage: URIRef
+    icqChatID: URIRef
+    isPrimaryTopicOf: URIRef
+    jabberID: URIRef
+    logo: URIRef
+    mbox: URIRef
+    mbox_sha1sum: URIRef
+    msnChatID: URIRef
+    openid: URIRef
+    weblog: URIRef
+    yahooChatID: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_ODRL2.pyi b/mypy-stubs/rdflib/namespace/_ODRL2.pyi
new file mode 100644
index 0000000..37e7556
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_ODRL2.pyi
@@ -0,0 +1,209 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class ODRL2(DefinedNamespace):
+    action: URIRef
+    andSequence: URIRef
+    assignee: URIRef
+    assigneeOf: URIRef
+    assigner: URIRef
+    assignerOf: URIRef
+    attributedParty: URIRef
+    attributingParty: URIRef
+    compensatedParty: URIRef
+    compensatingParty: URIRef
+    conflict: URIRef
+    consentedParty: URIRef
+    consentingParty: URIRef
+    consequence: URIRef
+    constraint: URIRef
+    contractedParty: URIRef
+    contractingParty: URIRef
+    dataType: URIRef
+    duty: URIRef
+    failure: URIRef
+    function: URIRef
+    hasPolicy: URIRef
+    implies: URIRef
+    includedIn: URIRef
+    informedParty: URIRef
+    informingParty: URIRef
+    inheritAllowed: URIRef
+    inheritFrom: URIRef
+    inheritRelation: URIRef
+    leftOperand: URIRef
+    obligation: URIRef
+    operand: URIRef
+    operator: URIRef
+    output: URIRef
+    partOf: URIRef
+    payeeParty: URIRef
+    permission: URIRef
+    profile: URIRef
+    prohibition: URIRef
+    proximity: URIRef
+    refinement: URIRef
+    relation: URIRef
+    remedy: URIRef
+    rightOperand: URIRef
+    rightOperandReference: URIRef
+    scope: URIRef
+    source: URIRef
+    status: URIRef
+    target: URIRef
+    timedCount: URIRef
+    trackedParty: URIRef
+    trackingParty: URIRef
+    uid: URIRef
+    undefined: URIRef
+    unit: URIRef
+    xone: URIRef
+    All: URIRef
+    All2ndConnections: URIRef
+    AllConnections: URIRef
+    AllGroups: URIRef
+    Group: URIRef
+    Individual: URIRef
+    absolutePosition: URIRef
+    absoluteSize: URIRef
+    absoluteSpatialPosition: URIRef
+    absoluteTemporalPosition: URIRef
+    count: URIRef
+    dateTime: URIRef
+    delayPeriod: URIRef
+    deliveryChannel: URIRef
+    device: URIRef
+    elapsedTime: URIRef
+    eq: URIRef
+    event: URIRef
+    fileFormat: URIRef
+    gt: URIRef
+    gteq: URIRef
+    hasPart: URIRef
+    ignore: URIRef
+    industry: URIRef
+    invalid: URIRef
+    isA: URIRef
+    isAllOf: URIRef
+    isAnyOf: URIRef
+    isNoneOf: URIRef
+    isPartOf: URIRef
+    language: URIRef
+    lt: URIRef
+    lteq: URIRef
+    media: URIRef
+    meteredTime: URIRef
+    neq: URIRef
+    payAmount: URIRef
+    percentage: URIRef
+    perm: URIRef
+    policyUsage: URIRef
+    product: URIRef
+    prohibit: URIRef
+    purpose: URIRef
+    recipient: URIRef
+    relativePosition: URIRef
+    relativeSize: URIRef
+    relativeSpatialPosition: URIRef
+    relativeTemporalPosition: URIRef
+    resolution: URIRef
+    spatial: URIRef
+    spatialCoordinates: URIRef
+    support: URIRef
+    system: URIRef
+    systemDevice: URIRef
+    timeInterval: URIRef
+    unitOfCount: URIRef
+    version: URIRef
+    virtualLocation: URIRef
+    Action: URIRef
+    Agreement: URIRef
+    Assertion: URIRef
+    Asset: URIRef
+    AssetCollection: URIRef
+    AssetScope: URIRef
+    ConflictTerm: URIRef
+    Constraint: URIRef
+    Duty: URIRef
+    LeftOperand: URIRef
+    LogicalConstraint: URIRef
+    Offer: URIRef
+    Operator: URIRef
+    Party: URIRef
+    PartyCollection: URIRef
+    PartyScope: URIRef
+    Permission: URIRef
+    Policy: URIRef
+    Privacy: URIRef
+    Prohibition: URIRef
+    Request: URIRef
+    RightOperand: URIRef
+    Rule: URIRef
+    Set: URIRef
+    Ticket: URIRef
+    UndefinedTerm: URIRef
+    acceptTracking: URIRef
+    adHocShare: URIRef
+    aggregate: URIRef
+    annotate: URIRef
+    anonymize: URIRef
+    append: URIRef
+    appendTo: URIRef
+    archive: URIRef
+    attachPolicy: URIRef
+    attachSource: URIRef
+    attribute: URIRef
+    commercialize: URIRef
+    compensate: URIRef
+    concurrentUse: URIRef
+    copy: URIRef
+    core: URIRef
+    delete: URIRef
+    derive: URIRef
+    digitize: URIRef
+    display: URIRef
+    distribute: URIRef
+    ensureExclusivity: URIRef
+    execute: URIRef
+    export: URIRef
+    extract: URIRef
+    extractChar: URIRef
+    extractPage: URIRef
+    extractWord: URIRef
+    give: URIRef
+    grantUse: URIRef
+    include: URIRef
+    index: URIRef
+    inform: URIRef
+    install: URIRef
+    lease: URIRef
+    lend: URIRef
+    license: URIRef
+    modify: URIRef
+    move: URIRef
+    nextPolicy: URIRef
+    obtainConsent: URIRef
+    pay: URIRef
+    play: URIRef
+    present: URIRef
+    preview: URIRef
+    print: URIRef
+    read: URIRef
+    reproduce: URIRef
+    reviewPolicy: URIRef
+    secondaryUse: URIRef
+    sell: URIRef
+    share: URIRef
+    shareAlike: URIRef
+    stream: URIRef
+    synchronize: URIRef
+    textToSpeech: URIRef
+    transfer: URIRef
+    transform: URIRef
+    translate: URIRef
+    uninstall: URIRef
+    use: URIRef
+    watermark: URIRef
+    write: URIRef
+    writeTo: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_ORG.pyi b/mypy-stubs/rdflib/namespace/_ORG.pyi
new file mode 100644
index 0000000..e7cd07f
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_ORG.pyi
@@ -0,0 +1,50 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class ORG(DefinedNamespace):
+    basedAt: URIRef
+    changedBy: URIRef
+    classification: URIRef
+    hasMember: URIRef
+    hasMembership: URIRef
+    hasPost: URIRef
+    hasPrimarySite: URIRef
+    hasRegisteredSite: URIRef
+    hasSite: URIRef
+    hasSubOrganization: URIRef
+    hasUnit: URIRef
+    headOf: URIRef
+    heldBy: URIRef
+    holds: URIRef
+    identifier: URIRef
+    linkedTo: URIRef
+    location: URIRef
+    member: URIRef
+    memberDuring: URIRef
+    memberOf: URIRef
+    organization: URIRef
+    originalOrganization: URIRef
+    postIn: URIRef
+    purpose: URIRef
+    remuneration: URIRef
+    reportsTo: URIRef
+    resultedFrom: URIRef
+    resultingOrganization: URIRef
+    role: URIRef
+    roleProperty: URIRef
+    siteAddress: URIRef
+    siteOf: URIRef
+    subOrganizationOf: URIRef
+    transitiveSubOrganizationOf: URIRef
+    unitOf: URIRef
+    ChangeEvent: URIRef
+    FormalOrganization: URIRef
+    Membership: URIRef
+    Organization: URIRef
+    OrganizationalCollaboration: URIRef
+    OrganizationalUnit: URIRef
+    Post: URIRef
+    Role: URIRef
+    Site: URIRef
+    Head: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_OWL.pyi b/mypy-stubs/rdflib/namespace/_OWL.pyi
new file mode 100644
index 0000000..e789663
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_OWL.pyi
@@ -0,0 +1,82 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class OWL(DefinedNamespace):
+    allValuesFrom: URIRef
+    annotatedProperty: URIRef
+    annotatedSource: URIRef
+    annotatedTarget: URIRef
+    assertionProperty: URIRef
+    cardinality: URIRef
+    complementOf: URIRef
+    datatypeComplementOf: URIRef
+    differentFrom: URIRef
+    disjointUnionOf: URIRef
+    disjointWith: URIRef
+    distinctMembers: URIRef
+    equivalentClass: URIRef
+    equivalentProperty: URIRef
+    hasKey: URIRef
+    hasSelf: URIRef
+    hasValue: URIRef
+    intersectionOf: URIRef
+    inverseOf: URIRef
+    maxCardinality: URIRef
+    maxQualifiedCardinality: URIRef
+    members: URIRef
+    minCardinality: URIRef
+    minQualifiedCardinality: URIRef
+    onClass: URIRef
+    onDataRange: URIRef
+    onDatatype: URIRef
+    onProperties: URIRef
+    onProperty: URIRef
+    oneOf: URIRef
+    propertyChainAxiom: URIRef
+    propertyDisjointWith: URIRef
+    qualifiedCardinality: URIRef
+    sameAs: URIRef
+    someValuesFrom: URIRef
+    sourceIndividual: URIRef
+    targetIndividual: URIRef
+    targetValue: URIRef
+    unionOf: URIRef
+    withRestrictions: URIRef
+    AllDifferent: URIRef
+    AllDisjointClasses: URIRef
+    AllDisjointProperties: URIRef
+    Annotation: URIRef
+    AnnotationProperty: URIRef
+    AsymmetricProperty: URIRef
+    Axiom: URIRef
+    Class: URIRef
+    DataRange: URIRef
+    DatatypeProperty: URIRef
+    DeprecatedClass: URIRef
+    DeprecatedProperty: URIRef
+    FunctionalProperty: URIRef
+    InverseFunctionalProperty: URIRef
+    IrreflexiveProperty: URIRef
+    NamedIndividual: URIRef
+    NegativePropertyAssertion: URIRef
+    ObjectProperty: URIRef
+    Ontology: URIRef
+    OntologyProperty: URIRef
+    ReflexiveProperty: URIRef
+    Restriction: URIRef
+    SymmetricProperty: URIRef
+    TransitiveProperty: URIRef
+    backwardCompatibleWith: URIRef
+    deprecated: URIRef
+    incompatibleWith: URIRef
+    priorVersion: URIRef
+    versionInfo: URIRef
+    Nothing: URIRef
+    Thing: URIRef
+    bottomDataProperty: URIRef
+    topDataProperty: URIRef
+    bottomObjectProperty: URIRef
+    topObjectProperty: URIRef
+    imports: URIRef
+    versionIRI: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_PROF.pyi b/mypy-stubs/rdflib/namespace/_PROF.pyi
new file mode 100644
index 0000000..69df238
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_PROF.pyi
@@ -0,0 +1,15 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class PROF(DefinedNamespace):
+    Profile: URIRef
+    ResourceDescriptor: URIRef
+    ResourceRole: URIRef
+    hasToken: URIRef
+    hasArtifact: URIRef
+    hasResource: URIRef
+    hasRole: URIRef
+    isInheritedFrom: URIRef
+    isProfileOf: URIRef
+    isTransitiveProfileOf: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_PROV.pyi b/mypy-stubs/rdflib/namespace/_PROV.pyi
new file mode 100644
index 0000000..bfe1ad9
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_PROV.pyi
@@ -0,0 +1,175 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class PROV(DefinedNamespace):
+    activityOfInfluence: URIRef
+    agentOfInfluence: URIRef
+    contributed: URIRef
+    ended: URIRef
+    entityOfInfluence: URIRef
+    generalizationOf: URIRef
+    generatedAsDerivation: URIRef
+    hadDelegate: URIRef
+    hadDerivation: URIRef
+    hadInfluence: URIRef
+    hadRevision: URIRef
+    informed: URIRef
+    locationOf: URIRef
+    qualifiedAssociationOf: URIRef
+    qualifiedAttributionOf: URIRef
+    qualifiedCommunicationOf: URIRef
+    qualifiedDelegationOf: URIRef
+    qualifiedDerivationOf: URIRef
+    qualifiedEndOf: URIRef
+    qualifiedGenerationOf: URIRef
+    qualifiedInfluenceOf: URIRef
+    qualifiedInvalidationOf: URIRef
+    qualifiedQuotationOf: URIRef
+    qualifiedSourceOf: URIRef
+    qualifiedStartOf: URIRef
+    qualifiedUsingActivity: URIRef
+    quotedAs: URIRef
+    revisedEntity: URIRef
+    started: URIRef
+    wasActivityOfInfluence: URIRef
+    wasAssociateFor: URIRef
+    wasMemberOf: URIRef
+    wasPlanOf: URIRef
+    wasPrimarySourceOf: URIRef
+    wasRoleIn: URIRef
+    wasUsedBy: URIRef
+    wasUsedInDerivation: URIRef
+    aq: URIRef
+    category: URIRef
+    component: URIRef
+    constraints: URIRef
+    definition: URIRef
+    dm: URIRef
+    editorialNote: URIRef
+    editorsDefinition: URIRef
+    inverse: URIRef
+    n: URIRef
+    order: URIRef
+    qualifiedForm: URIRef
+    sharesDefinitionWith: URIRef
+    specializationOf: URIRef
+    todo: URIRef
+    unqualifiedForm: URIRef
+    wasRevisionOf: URIRef
+    Accept: URIRef
+    Activity: URIRef
+    ActivityInfluence: URIRef
+    Agent: URIRef
+    AgentInfluence: URIRef
+    Association: URIRef
+    Attribution: URIRef
+    Bundle: URIRef
+    Collection: URIRef
+    Communication: URIRef
+    Contribute: URIRef
+    Contributor: URIRef
+    Copyright: URIRef
+    Create: URIRef
+    Creator: URIRef
+    Delegation: URIRef
+    Derivation: URIRef
+    Dictionary: URIRef
+    DirectQueryService: URIRef
+    EmptyDictionary: URIRef
+    End: URIRef
+    Entity: URIRef
+    EntityInfluence: URIRef
+    Generation: URIRef
+    Influence: URIRef
+    Insertion: URIRef
+    InstantaneousEvent: URIRef
+    Invalidation: URIRef
+    KeyEntityPair: URIRef
+    Location: URIRef
+    Modify: URIRef
+    Organization: URIRef
+    Person: URIRef
+    Plan: URIRef
+    PrimarySource: URIRef
+    Publish: URIRef
+    Publisher: URIRef
+    Quotation: URIRef
+    Removal: URIRef
+    Replace: URIRef
+    Revision: URIRef
+    RightsAssignment: URIRef
+    RightsHolder: URIRef
+    Role: URIRef
+    ServiceDescription: URIRef
+    SoftwareAgent: URIRef
+    Start: URIRef
+    Submit: URIRef
+    Usage: URIRef
+    atTime: URIRef
+    endedAtTime: URIRef
+    generatedAtTime: URIRef
+    invalidatedAtTime: URIRef
+    provenanceUriTemplate: URIRef
+    removedKey: URIRef
+    startedAtTime: URIRef
+    value: URIRef
+    pairEntity: URIRef
+    pairKey: URIRef
+    EmptyCollection: URIRef
+    actedOnBehalfOf: URIRef
+    activity: URIRef
+    agent: URIRef
+    alternateOf: URIRef
+    asInBundle: URIRef
+    atLocation: URIRef
+    derivedByInsertionFrom: URIRef
+    derivedByRemovalFrom: URIRef
+    describesService: URIRef
+    dictionary: URIRef
+    entity: URIRef
+    generated: URIRef
+    hadActivity: URIRef
+    hadDictionaryMember: URIRef
+    hadGeneration: URIRef
+    hadMember: URIRef
+    hadPlan: URIRef
+    hadPrimarySource: URIRef
+    hadRole: URIRef
+    hadUsage: URIRef
+    has_anchor: URIRef
+    has_provenance: URIRef
+    has_query_service: URIRef
+    influenced: URIRef
+    influencer: URIRef
+    insertedKeyEntityPair: URIRef
+    invalidated: URIRef
+    mentionOf: URIRef
+    pingback: URIRef
+    qualifiedAssociation: URIRef
+    qualifiedAttribution: URIRef
+    qualifiedCommunication: URIRef
+    qualifiedDelegation: URIRef
+    qualifiedDerivation: URIRef
+    qualifiedEnd: URIRef
+    qualifiedGeneration: URIRef
+    qualifiedInfluence: URIRef
+    qualifiedInsertion: URIRef
+    qualifiedInvalidation: URIRef
+    qualifiedPrimarySource: URIRef
+    qualifiedQuotation: URIRef
+    qualifiedRemoval: URIRef
+    qualifiedRevision: URIRef
+    qualifiedStart: URIRef
+    qualifiedUsage: URIRef
+    used: URIRef
+    wasAssociatedWith: URIRef
+    wasAttributedTo: URIRef
+    wasDerivedFrom: URIRef
+    wasEndedBy: URIRef
+    wasGeneratedBy: URIRef
+    wasInfluencedBy: URIRef
+    wasInformedBy: URIRef
+    wasInvalidatedBy: URIRef
+    wasQuotedFrom: URIRef
+    wasStartedBy: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_QB.pyi b/mypy-stubs/rdflib/namespace/_QB.pyi
new file mode 100644
index 0000000..4b90460
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_QB.pyi
@@ -0,0 +1,41 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class QB(DefinedNamespace):
+    attribute: URIRef
+    codeList: URIRef
+    component: URIRef
+    componentAttachment: URIRef
+    componentProperty: URIRef
+    componentRequired: URIRef
+    concept: URIRef
+    dataSet: URIRef
+    dimension: URIRef
+    hierarchyRoot: URIRef
+    measure: URIRef
+    measureDimension: URIRef
+    measureType: URIRef
+    observation: URIRef
+    observationGroup: URIRef
+    order: URIRef
+    parentChildProperty: URIRef
+    slice: URIRef
+    sliceKey: URIRef
+    sliceStructure: URIRef
+    structure: URIRef
+    Attachable: URIRef
+    AttributeProperty: URIRef
+    CodedProperty: URIRef
+    ComponentProperty: URIRef
+    ComponentSet: URIRef
+    ComponentSpecification: URIRef
+    DataSet: URIRef
+    DataStructureDefinition: URIRef
+    DimensionProperty: URIRef
+    HierarchicalCodeList: URIRef
+    MeasureProperty: URIRef
+    Observation: URIRef
+    ObservationGroup: URIRef
+    Slice: URIRef
+    SliceKey: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_RDF.pyi b/mypy-stubs/rdflib/namespace/_RDF.pyi
new file mode 100644
index 0000000..e613019
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_RDF.pyi
@@ -0,0 +1,27 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class RDF(DefinedNamespace):
+    nil: URIRef
+    direction: URIRef
+    first: URIRef
+    language: URIRef
+    object: URIRef
+    predicate: URIRef
+    rest: URIRef
+    subject: URIRef
+    type: URIRef
+    value: URIRef
+    Alt: URIRef
+    Bag: URIRef
+    CompoundLiteral: URIRef
+    List: URIRef
+    Property: URIRef
+    Seq: URIRef
+    Statement: URIRef
+    HTML: URIRef
+    JSON: URIRef
+    PlainLiteral: URIRef
+    XMLLiteral: URIRef
+    langString: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_RDFS.pyi b/mypy-stubs/rdflib/namespace/_RDFS.pyi
new file mode 100644
index 0000000..e28d084
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_RDFS.pyi
@@ -0,0 +1,20 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class RDFS(DefinedNamespace):
+    comment: URIRef
+    domain: URIRef
+    isDefinedBy: URIRef
+    label: URIRef
+    member: URIRef
+    range: URIRef
+    seeAlso: URIRef
+    subClassOf: URIRef
+    subPropertyOf: URIRef
+    Class: URIRef
+    Container: URIRef
+    ContainerMembershipProperty: URIRef
+    Datatype: URIRef
+    Literal: URIRef
+    Resource: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_SDO.pyi b/mypy-stubs/rdflib/namespace/_SDO.pyi
new file mode 100644
index 0000000..b974b4d
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_SDO.pyi
@@ -0,0 +1,1645 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class SDO(DefinedNamespace):
+    ActiveActionStatus: URIRef
+    CompletedActionStatus: URIRef
+    FailedActionStatus: URIRef
+    PotentialActionStatus: URIRef
+    Researcher: URIRef
+    GroupBoardingPolicy: URIRef
+    ZoneBoardingPolicy: URIRef
+    AudiobookFormat: URIRef
+    EBook: URIRef
+    Hardcover: URIRef
+    Paperback: URIRef
+    HearingImpairedSupported: URIRef
+    TollFree: URIRef
+    Friday: URIRef
+    Monday: URIRef
+    PublicHolidays: URIRef
+    Saturday: URIRef
+    Sunday: URIRef
+    Thursday: URIRef
+    Tuesday: URIRef
+    Wednesday: URIRef
+    OnSitePickup: URIRef
+    CommentPermission: URIRef
+    ReadPermission: URIRef
+    WritePermission: URIRef
+    AllWheelDriveConfiguration: URIRef
+    FourWheelDriveConfiguration: URIRef
+    FrontWheelDriveConfiguration: URIRef
+    RearWheelDriveConfiguration: URIRef
+    EventCancelled: URIRef
+    EventMovedOnline: URIRef
+    EventPostponed: URIRef
+    EventRescheduled: URIRef
+    EventScheduled: URIRef
+    CoOp: URIRef
+    MultiPlayer: URIRef
+    SinglePlayer: URIRef
+    OfflinePermanently: URIRef
+    OfflineTemporarily: URIRef
+    Online: URIRef
+    OnlineFull: URIRef
+    Female: URIRef
+    Male: URIRef
+    Discontinued: URIRef
+    InStock: URIRef
+    InStoreOnly: URIRef
+    LimitedAvailability: URIRef
+    OnlineOnly: URIRef
+    OutOfStock: URIRef
+    PreOrder: URIRef
+    PreSale: URIRef
+    SoldOut: URIRef
+    ItemListOrderAscending: URIRef
+    ItemListOrderDescending: URIRef
+    ItemListUnordered: URIRef
+    ParkingMap: URIRef
+    SeatingMap: URIRef
+    TransitMap: URIRef
+    VenueMap: URIRef
+    CompilationAlbum: URIRef
+    DJMixAlbum: URIRef
+    DemoAlbum: URIRef
+    LiveAlbum: URIRef
+    MixtapeAlbum: URIRef
+    RemixAlbum: URIRef
+    SoundtrackAlbum: URIRef
+    SpokenWordAlbum: URIRef
+    StudioAlbum: URIRef
+    AlbumRelease: URIRef
+    BroadcastRelease: URIRef
+    EPRelease: URIRef
+    SingleRelease: URIRef
+    CDFormat: URIRef
+    CassetteFormat: URIRef
+    DVDFormat: URIRef
+    DigitalAudioTapeFormat: URIRef
+    DigitalFormat: URIRef
+    LaserDiscFormat: URIRef
+    VinylFormat: URIRef
+    DamagedCondition: URIRef
+    NewCondition: URIRef
+    RefurbishedCondition: URIRef
+    UsedCondition: URIRef
+    OrderCancelled: URIRef
+    OrderDelivered: URIRef
+    OrderInTransit: URIRef
+    OrderPaymentDue: URIRef
+    OrderPickupAvailable: URIRef
+    OrderProblem: URIRef
+    OrderProcessing: URIRef
+    OrderReturned: URIRef
+    PaymentAutomaticallyApplied: URIRef
+    PaymentComplete: URIRef
+    PaymentDeclined: URIRef
+    PaymentDue: URIRef
+    PaymentPastDue: URIRef
+    ReservationCancelled: URIRef
+    ReservationConfirmed: URIRef
+    ReservationHold: URIRef
+    ReservationPending: URIRef
+    DiabeticDiet: URIRef
+    GlutenFreeDiet: URIRef
+    HalalDiet: URIRef
+    HinduDiet: URIRef
+    KosherDiet: URIRef
+    LowCalorieDiet: URIRef
+    LowFatDiet: URIRef
+    LowLactoseDiet: URIRef
+    LowSaltDiet: URIRef
+    VeganDiet: URIRef
+    VegetarianDiet: URIRef
+    RsvpResponseMaybe: URIRef
+    RsvpResponseNo: URIRef
+    RsvpResponseYes: URIRef
+    LeftHandDriving: URIRef
+    RightHandDriving: URIRef
+    about: URIRef
+    acceptedAnswer: URIRef
+    acceptedOffer: URIRef
+    acceptedPaymentMethod: URIRef
+    acceptsReservations: URIRef
+    accessCode: URIRef
+    accessMode: URIRef
+    accessModeSufficient: URIRef
+    accessibilityAPI: URIRef
+    accessibilityControl: URIRef
+    accessibilityFeature: URIRef
+    accessibilityHazard: URIRef
+    accessibilitySummary: URIRef
+    accountId: URIRef
+    accountablePerson: URIRef
+    acquiredFrom: URIRef
+    actionAccessibilityRequirement: URIRef
+    actionApplication: URIRef
+    actionOption: URIRef
+    actionPlatform: URIRef
+    actionStatus: URIRef
+    actor: URIRef
+    actors: URIRef
+    addOn: URIRef
+    additionalName: URIRef
+    additionalNumberOfGuests: URIRef
+    additionalProperty: URIRef
+    additionalType: URIRef
+    address: URIRef
+    addressCountry: URIRef
+    addressLocality: URIRef
+    addressRegion: URIRef
+    advanceBookingRequirement: URIRef
+    affiliation: URIRef
+    afterMedia: URIRef
+    agent: URIRef
+    aggregateRating: URIRef
+    aircraft: URIRef
+    album: URIRef
+    albumProductionType: URIRef
+    albumRelease: URIRef
+    albumReleaseType: URIRef
+    albums: URIRef
+    alignmentType: URIRef
+    alternateName: URIRef
+    alternativeHeadline: URIRef
+    alumni: URIRef
+    alumniOf: URIRef
+    amenityFeature: URIRef
+    amount: URIRef
+    amountOfThisGood: URIRef
+    annualPercentageRate: URIRef
+    answerCount: URIRef
+    application: URIRef
+    applicationCategory: URIRef
+    applicationSubCategory: URIRef
+    applicationSuite: URIRef
+    appliesToDeliveryMethod: URIRef
+    appliesToPaymentMethod: URIRef
+    area: URIRef
+    areaServed: URIRef
+    arrivalAirport: URIRef
+    arrivalBusStop: URIRef
+    arrivalGate: URIRef
+    arrivalPlatform: URIRef
+    arrivalStation: URIRef
+    arrivalTerminal: URIRef
+    arrivalTime: URIRef
+    artEdition: URIRef
+    artMedium: URIRef
+    artform: URIRef
+    articleBody: URIRef
+    articleSection: URIRef
+    artworkSurface: URIRef
+    assembly: URIRef
+    assemblyVersion: URIRef
+    associatedArticle: URIRef
+    associatedMedia: URIRef
+    athlete: URIRef
+    attendee: URIRef
+    attendees: URIRef
+    audience: URIRef
+    audienceType: URIRef
+    audio: URIRef
+    authenticator: URIRef
+    author: URIRef
+    availability: URIRef
+    availabilityEnds: URIRef
+    availabilityStarts: URIRef
+    availableAtOrFrom: URIRef
+    availableChannel: URIRef
+    availableDeliveryMethod: URIRef
+    availableFrom: URIRef
+    availableLanguage: URIRef
+    availableOnDevice: URIRef
+    availableThrough: URIRef
+    award: URIRef
+    awards: URIRef
+    awayTeam: URIRef
+    baseSalary: URIRef
+    bccRecipient: URIRef
+    bed: URIRef
+    beforeMedia: URIRef
+    benefits: URIRef
+    bestRating: URIRef
+    billingAddress: URIRef
+    billingIncrement: URIRef
+    billingPeriod: URIRef
+    birthDate: URIRef
+    birthPlace: URIRef
+    bitrate: URIRef
+    blogPost: URIRef
+    blogPosts: URIRef
+    boardingGroup: URIRef
+    boardingPolicy: URIRef
+    bookEdition: URIRef
+    bookFormat: URIRef
+    bookingAgent: URIRef
+    bookingTime: URIRef
+    borrower: URIRef
+    box: URIRef
+    branchCode: URIRef
+    branchOf: URIRef
+    brand: URIRef
+    breadcrumb: URIRef
+    broadcastAffiliateOf: URIRef
+    broadcastChannelId: URIRef
+    broadcastDisplayName: URIRef
+    broadcastFrequency: URIRef
+    broadcastFrequencyValue: URIRef
+    broadcastOfEvent: URIRef
+    broadcastServiceTier: URIRef
+    broadcastTimezone: URIRef
+    broadcaster: URIRef
+    broker: URIRef
+    browserRequirements: URIRef
+    busName: URIRef
+    busNumber: URIRef
+    businessFunction: URIRef
+    buyer: URIRef
+    byArtist: URIRef
+    calories: URIRef
+    candidate: URIRef
+    caption: URIRef
+    carbohydrateContent: URIRef
+    cargoVolume: URIRef
+    carrier: URIRef
+    carrierRequirements: URIRef
+    catalog: URIRef
+    catalogNumber: URIRef
+    category: URIRef
+    ccRecipient: URIRef
+    character: URIRef
+    characterAttribute: URIRef
+    characterName: URIRef
+    cheatCode: URIRef
+    checkinTime: URIRef
+    checkoutTime: URIRef
+    childMaxAge: URIRef
+    childMinAge: URIRef
+    children: URIRef
+    cholesterolContent: URIRef
+    circle: URIRef
+    citation: URIRef
+    claimReviewed: URIRef
+    clipNumber: URIRef
+    closes: URIRef
+    coach: URIRef
+    codeRepository: URIRef
+    codeSampleType: URIRef
+    colleague: URIRef
+    colleagues: URIRef
+    collection: URIRef
+    color: URIRef
+    comment: URIRef
+    commentCount: URIRef
+    commentText: URIRef
+    commentTime: URIRef
+    competitor: URIRef
+    composer: URIRef
+    confirmationNumber: URIRef
+    contactOption: URIRef
+    contactPoint: URIRef
+    contactPoints: URIRef
+    contactType: URIRef
+    containedIn: URIRef
+    containedInPlace: URIRef
+    containsPlace: URIRef
+    containsSeason: URIRef
+    contentLocation: URIRef
+    contentRating: URIRef
+    contentSize: URIRef
+    contentType: URIRef
+    contentUrl: URIRef
+    contributor: URIRef
+    cookTime: URIRef
+    cookingMethod: URIRef
+    copyrightHolder: URIRef
+    copyrightYear: URIRef
+    countriesNotSupported: URIRef
+    countriesSupported: URIRef
+    countryOfOrigin: URIRef
+    course: URIRef
+    courseCode: URIRef
+    courseMode: URIRef
+    coursePrerequisites: URIRef
+    coverageEndTime: URIRef
+    coverageStartTime: URIRef
+    creator: URIRef
+    creditedTo: URIRef
+    cssSelector: URIRef
+    currenciesAccepted: URIRef
+    currency: URIRef
+    customer: URIRef
+    dataFeedElement: URIRef
+    dataset: URIRef
+    datasetTimeInterval: URIRef
+    dateCreated: URIRef
+    dateDeleted: URIRef
+    dateIssued: URIRef
+    dateModified: URIRef
+    datePosted: URIRef
+    datePublished: URIRef
+    dateRead: URIRef
+    dateReceived: URIRef
+    dateSent: URIRef
+    dateVehicleFirstRegistered: URIRef
+    dateline: URIRef
+    dayOfWeek: URIRef
+    deathDate: URIRef
+    deathPlace: URIRef
+    defaultValue: URIRef
+    deliveryAddress: URIRef
+    deliveryLeadTime: URIRef
+    deliveryMethod: URIRef
+    deliveryStatus: URIRef
+    department: URIRef
+    departureAirport: URIRef
+    departureBusStop: URIRef
+    departureGate: URIRef
+    departurePlatform: URIRef
+    departureStation: URIRef
+    departureTerminal: URIRef
+    departureTime: URIRef
+    dependencies: URIRef
+    depth: URIRef
+    description: URIRef
+    device: URIRef
+    director: URIRef
+    directors: URIRef
+    disambiguatingDescription: URIRef
+    discount: URIRef
+    discountCode: URIRef
+    discountCurrency: URIRef
+    discusses: URIRef
+    discussionUrl: URIRef
+    dissolutionDate: URIRef
+    distance: URIRef
+    distribution: URIRef
+    doorTime: URIRef
+    downloadUrl: URIRef
+    downvoteCount: URIRef
+    driveWheelConfiguration: URIRef
+    dropoffLocation: URIRef
+    dropoffTime: URIRef
+    duns: URIRef
+    duration: URIRef
+    durationOfWarranty: URIRef
+    duringMedia: URIRef
+    editor: URIRef
+    educationalAlignment: URIRef
+    educationalCredentialAwarded: URIRef
+    educationalFramework: URIRef
+    educationalRole: URIRef
+    educationalUse: URIRef
+    elevation: URIRef
+    eligibleCustomerType: URIRef
+    eligibleDuration: URIRef
+    eligibleQuantity: URIRef
+    eligibleRegion: URIRef
+    eligibleTransactionVolume: URIRef
+    email: URIRef
+    embedUrl: URIRef
+    employee: URIRef
+    employees: URIRef
+    employmentType: URIRef
+    encodesCreativeWork: URIRef
+    encoding: URIRef
+    encodingFormat: URIRef
+    encodingType: URIRef
+    encodings: URIRef
+    endDate: URIRef
+    endTime: URIRef
+    endorsee: URIRef
+    entertainmentBusiness: URIRef
+    episode: URIRef
+    episodeNumber: URIRef
+    episodes: URIRef
+    equal: URIRef
+    error: URIRef
+    estimatedCost: URIRef
+    estimatedFlightDuration: URIRef
+    estimatedSalary: URIRef
+    event: URIRef
+    eventStatus: URIRef
+    events: URIRef
+    exampleOfWork: URIRef
+    executableLibraryName: URIRef
+    exerciseCourse: URIRef
+    exifData: URIRef
+    expectedArrivalFrom: URIRef
+    expectedArrivalUntil: URIRef
+    expectsAcceptanceOf: URIRef
+    experienceRequirements: URIRef
+    expires: URIRef
+    familyName: URIRef
+    fatContent: URIRef
+    faxNumber: URIRef
+    featureList: URIRef
+    feesAndCommissionsSpecification: URIRef
+    fiberContent: URIRef
+    fileFormat: URIRef
+    fileSize: URIRef
+    firstPerformance: URIRef
+    flightDistance: URIRef
+    flightNumber: URIRef
+    floorSize: URIRef
+    followee: URIRef
+    follows: URIRef
+    foodEstablishment: URIRef
+    foodEvent: URIRef
+    founder: URIRef
+    founders: URIRef
+    foundingDate: URIRef
+    foundingLocation: URIRef
+    free: URIRef
+    fromLocation: URIRef
+    fuelConsumption: URIRef
+    fuelEfficiency: URIRef
+    fuelType: URIRef
+    funder: URIRef
+    game: URIRef
+    gameItem: URIRef
+    gameLocation: URIRef
+    gamePlatform: URIRef
+    gameServer: URIRef
+    gameTip: URIRef
+    genre: URIRef
+    geo: URIRef
+    geoContains: URIRef
+    geoCoveredBy: URIRef
+    geoCovers: URIRef
+    geoCrosses: URIRef
+    geoDisjoint: URIRef
+    geoEquals: URIRef
+    geoIntersects: URIRef
+    geoMidpoint: URIRef
+    geoOverlaps: URIRef
+    geoRadius: URIRef
+    geoTouches: URIRef
+    geoWithin: URIRef
+    geographicArea: URIRef
+    givenName: URIRef
+    globalLocationNumber: URIRef
+    grantee: URIRef
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+    GamePlayMode: URIRef
+    GameServer: URIRef
+    GameServerStatus: URIRef
+    GardenStore: URIRef
+    GasStation: URIRef
+    GatedResidenceCommunity: URIRef
+    GenderType: URIRef
+    GeneralContractor: URIRef
+    GeoCircle: URIRef
+    GeoCoordinates: URIRef
+    GeoShape: URIRef
+    GiveAction: URIRef
+    GolfCourse: URIRef
+    GovernmentBuilding: URIRef
+    GovernmentOffice: URIRef
+    GovernmentOrganization: URIRef
+    GovernmentPermit: URIRef
+    GovernmentService: URIRef
+    GroceryStore: URIRef
+    HVACBusiness: URIRef
+    HairSalon: URIRef
+    HardwareStore: URIRef
+    HealthAndBeautyBusiness: URIRef
+    HealthClub: URIRef
+    HighSchool: URIRef
+    HinduTemple: URIRef
+    HobbyShop: URIRef
+    HomeAndConstructionBusiness: URIRef
+    HomeGoodsStore: URIRef
+    Hospital: URIRef
+    Hostel: URIRef
+    Hotel: URIRef
+    HotelRoom: URIRef
+    House: URIRef
+    HousePainter: URIRef
+    HowTo: URIRef
+    HowToDirection: URIRef
+    HowToItem: URIRef
+    HowToSection: URIRef
+    HowToStep: URIRef
+    HowToSupply: URIRef
+    HowToTip: URIRef
+    HowToTool: URIRef
+    IceCreamShop: URIRef
+    IgnoreAction: URIRef
+    ImageGallery: URIRef
+    ImageObject: URIRef
+    IndividualProduct: URIRef
+    InformAction: URIRef
+    InsertAction: URIRef
+    InstallAction: URIRef
+    InsuranceAgency: URIRef
+    Intangible: URIRef
+    Integer: URIRef
+    InteractAction: URIRef
+    InteractionCounter: URIRef
+    InternetCafe: URIRef
+    InvestmentOrDeposit: URIRef
+    InviteAction: URIRef
+    Invoice: URIRef
+    ItemAvailability: URIRef
+    ItemList: URIRef
+    ItemListOrderType: URIRef
+    ItemPage: URIRef
+    JewelryStore: URIRef
+    JobPosting: URIRef
+    JoinAction: URIRef
+    LakeBodyOfWater: URIRef
+    Landform: URIRef
+    LandmarksOrHistoricalBuildings: URIRef
+    Language: URIRef
+    LeaveAction: URIRef
+    LegalService: URIRef
+    LegislativeBuilding: URIRef
+    LendAction: URIRef
+    Library: URIRef
+    LikeAction: URIRef
+    LiquorStore: URIRef
+    ListItem: URIRef
+    ListenAction: URIRef
+    LiteraryEvent: URIRef
+    LiveBlogPosting: URIRef
+    LoanOrCredit: URIRef
+    LocalBusiness: URIRef
+    LocationFeatureSpecification: URIRef
+    LockerDelivery: URIRef
+    Locksmith: URIRef
+    LodgingBusiness: URIRef
+    LodgingReservation: URIRef
+    LoseAction: URIRef
+    Map: URIRef
+    MapCategoryType: URIRef
+    MarryAction: URIRef
+    Mass: URIRef
+    MediaGallery: URIRef
+    MediaObject: URIRef
+    MediaSubscription: URIRef
+    MedicalOrganization: URIRef
+    MeetingRoom: URIRef
+    MensClothingStore: URIRef
+    Menu: URIRef
+    MenuItem: URIRef
+    MenuSection: URIRef
+    Message: URIRef
+    MiddleSchool: URIRef
+    MobileApplication: URIRef
+    MobilePhoneStore: URIRef
+    MonetaryAmount: URIRef
+    MonetaryAmountDistribution: URIRef
+    Mosque: URIRef
+    Motel: URIRef
+    MotorcycleDealer: URIRef
+    MotorcycleRepair: URIRef
+    Mountain: URIRef
+    MoveAction: URIRef
+    Movie: URIRef
+    MovieClip: URIRef
+    MovieRentalStore: URIRef
+    MovieSeries: URIRef
+    MovieTheater: URIRef
+    MovingCompany: URIRef
+    Museum: URIRef
+    MusicAlbum: URIRef
+    MusicAlbumProductionType: URIRef
+    MusicAlbumReleaseType: URIRef
+    MusicComposition: URIRef
+    MusicEvent: URIRef
+    MusicGroup: URIRef
+    MusicPlaylist: URIRef
+    MusicRecording: URIRef
+    MusicRelease: URIRef
+    MusicReleaseFormatType: URIRef
+    MusicStore: URIRef
+    MusicVenue: URIRef
+    MusicVideoObject: URIRef
+    NGO: URIRef
+    NailSalon: URIRef
+    NewsArticle: URIRef
+    NightClub: URIRef
+    Notary: URIRef
+    NoteDigitalDocument: URIRef
+    Number: URIRef
+    NutritionInformation: URIRef
+    Occupation: URIRef
+    OceanBodyOfWater: URIRef
+    Offer: URIRef
+    OfferCatalog: URIRef
+    OfferItemCondition: URIRef
+    OfficeEquipmentStore: URIRef
+    OnDemandEvent: URIRef
+    OpeningHoursSpecification: URIRef
+    Order: URIRef
+    OrderAction: URIRef
+    OrderItem: URIRef
+    OrderStatus: URIRef
+    Organization: URIRef
+    OrganizationRole: URIRef
+    OrganizeAction: URIRef
+    OutletStore: URIRef
+    OwnershipInfo: URIRef
+    PaintAction: URIRef
+    Painting: URIRef
+    ParcelDelivery: URIRef
+    ParcelService: URIRef
+    ParentAudience: URIRef
+    Park: URIRef
+    ParkingFacility: URIRef
+    PawnShop: URIRef
+    PayAction: URIRef
+    PaymentCard: URIRef
+    PaymentChargeSpecification: URIRef
+    PaymentMethod: URIRef
+    PaymentService: URIRef
+    PaymentStatusType: URIRef
+    PeopleAudience: URIRef
+    PerformAction: URIRef
+    PerformanceRole: URIRef
+    PerformingArtsTheater: URIRef
+    PerformingGroup: URIRef
+    Periodical: URIRef
+    Permit: URIRef
+    Person: URIRef
+    PetStore: URIRef
+    Pharmacy: URIRef
+    Photograph: URIRef
+    PhotographAction: URIRef
+    Physician: URIRef
+    Place: URIRef
+    PlaceOfWorship: URIRef
+    PlanAction: URIRef
+    PlayAction: URIRef
+    Playground: URIRef
+    Plumber: URIRef
+    PoliceStation: URIRef
+    Pond: URIRef
+    PostOffice: URIRef
+    PostalAddress: URIRef
+    PreOrderAction: URIRef
+    PrependAction: URIRef
+    Preschool: URIRef
+    PresentationDigitalDocument: URIRef
+    PriceSpecification: URIRef
+    Product: URIRef
+    ProductModel: URIRef
+    ProfessionalService: URIRef
+    ProfilePage: URIRef
+    ProgramMembership: URIRef
+    PropertyValue: URIRef
+    PropertyValueSpecification: URIRef
+    PublicSwimmingPool: URIRef
+    PublicationEvent: URIRef
+    PublicationIssue: URIRef
+    PublicationVolume: URIRef
+    QAPage: URIRef
+    QualitativeValue: URIRef
+    QuantitativeValue: URIRef
+    QuantitativeValueDistribution: URIRef
+    Quantity: URIRef
+    Question: URIRef
+    QuoteAction: URIRef
+    RVPark: URIRef
+    RadioChannel: URIRef
+    RadioClip: URIRef
+    RadioEpisode: URIRef
+    RadioSeason: URIRef
+    RadioSeries: URIRef
+    RadioStation: URIRef
+    Rating: URIRef
+    ReactAction: URIRef
+    ReadAction: URIRef
+    RealEstateAgent: URIRef
+    ReceiveAction: URIRef
+    Recipe: URIRef
+    RecyclingCenter: URIRef
+    RegisterAction: URIRef
+    RejectAction: URIRef
+    RentAction: URIRef
+    RentalCarReservation: URIRef
+    ReplaceAction: URIRef
+    ReplyAction: URIRef
+    Report: URIRef
+    Reservation: URIRef
+    ReservationPackage: URIRef
+    ReservationStatusType: URIRef
+    ReserveAction: URIRef
+    Reservoir: URIRef
+    Residence: URIRef
+    Resort: URIRef
+    Restaurant: URIRef
+    RestrictedDiet: URIRef
+    ResumeAction: URIRef
+    ReturnAction: URIRef
+    Review: URIRef
+    ReviewAction: URIRef
+    RiverBodyOfWater: URIRef
+    Role: URIRef
+    RoofingContractor: URIRef
+    Room: URIRef
+    RsvpAction: URIRef
+    RsvpResponseType: URIRef
+    SaleEvent: URIRef
+    ScheduleAction: URIRef
+    ScholarlyArticle: URIRef
+    School: URIRef
+    ScreeningEvent: URIRef
+    Sculpture: URIRef
+    SeaBodyOfWater: URIRef
+    SearchAction: URIRef
+    SearchResultsPage: URIRef
+    Season: URIRef
+    Seat: URIRef
+    SelfStorage: URIRef
+    SellAction: URIRef
+    SendAction: URIRef
+    Series: URIRef
+    Service: URIRef
+    ServiceChannel: URIRef
+    ShareAction: URIRef
+    ShoeStore: URIRef
+    ShoppingCenter: URIRef
+    SingleFamilyResidence: URIRef
+    SiteNavigationElement: URIRef
+    SkiResort: URIRef
+    SocialEvent: URIRef
+    SocialMediaPosting: URIRef
+    SoftwareApplication: URIRef
+    SoftwareSourceCode: URIRef
+    SomeProducts: URIRef
+    SpeakableSpecification: URIRef
+    Specialty: URIRef
+    SportingGoodsStore: URIRef
+    SportsActivityLocation: URIRef
+    SportsClub: URIRef
+    SportsEvent: URIRef
+    SportsOrganization: URIRef
+    SportsTeam: URIRef
+    SpreadsheetDigitalDocument: URIRef
+    StadiumOrArena: URIRef
+    State: URIRef
+    SteeringPositionValue: URIRef
+    Store: URIRef
+    StructuredValue: URIRef
+    SubscribeAction: URIRef
+    SubwayStation: URIRef
+    Suite: URIRef
+    SuspendAction: URIRef
+    Synagogue: URIRef
+    TVClip: URIRef
+    TVEpisode: URIRef
+    TVSeason: URIRef
+    TVSeries: URIRef
+    Table: URIRef
+    TakeAction: URIRef
+    TattooParlor: URIRef
+    Taxi: URIRef
+    TaxiReservation: URIRef
+    TaxiService: URIRef
+    TaxiStand: URIRef
+    TechArticle: URIRef
+    TelevisionChannel: URIRef
+    TelevisionStation: URIRef
+    TennisComplex: URIRef
+    Text: URIRef
+    TextDigitalDocument: URIRef
+    TheaterEvent: URIRef
+    TheaterGroup: URIRef
+    Thing: URIRef
+    Ticket: URIRef
+    TieAction: URIRef
+    Time: URIRef
+    TipAction: URIRef
+    TireShop: URIRef
+    TouristAttraction: URIRef
+    TouristInformationCenter: URIRef
+    ToyStore: URIRef
+    TrackAction: URIRef
+    TradeAction: URIRef
+    TrainReservation: URIRef
+    TrainStation: URIRef
+    TrainTrip: URIRef
+    TransferAction: URIRef
+    TravelAction: URIRef
+    TravelAgency: URIRef
+    Trip: URIRef
+    TypeAndQuantityNode: URIRef
+    URL: URIRef
+    UnRegisterAction: URIRef
+    UnitPriceSpecification: URIRef
+    UpdateAction: URIRef
+    UseAction: URIRef
+    UserBlocks: URIRef
+    UserCheckins: URIRef
+    UserComments: URIRef
+    UserDownloads: URIRef
+    UserInteraction: URIRef
+    UserLikes: URIRef
+    UserPageVisits: URIRef
+    UserPlays: URIRef
+    UserPlusOnes: URIRef
+    UserTweets: URIRef
+    Vehicle: URIRef
+    VideoGallery: URIRef
+    VideoGame: URIRef
+    VideoGameClip: URIRef
+    VideoGameSeries: URIRef
+    VideoObject: URIRef
+    ViewAction: URIRef
+    VisualArtsEvent: URIRef
+    VisualArtwork: URIRef
+    Volcano: URIRef
+    VoteAction: URIRef
+    WPAdBlock: URIRef
+    WPFooter: URIRef
+    WPHeader: URIRef
+    WPSideBar: URIRef
+    WantAction: URIRef
+    WarrantyPromise: URIRef
+    WarrantyScope: URIRef
+    WatchAction: URIRef
+    Waterfall: URIRef
+    WearAction: URIRef
+    WebApplication: URIRef
+    WebPage: URIRef
+    WebPageElement: URIRef
+    WebSite: URIRef
+    WholesaleStore: URIRef
+    WinAction: URIRef
+    Winery: URIRef
+    WorkersUnion: URIRef
+    WriteAction: URIRef
+    Zoo: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_SH.pyi b/mypy-stubs/rdflib/namespace/_SH.pyi
new file mode 100644
index 0000000..d755656
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_SH.pyi
@@ -0,0 +1,183 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class SH(DefinedNamespace):
+    alternativePath: URIRef
+    annotationProperty: URIRef
+    annotationValue: URIRef
+    annotationVarName: URIRef
+    ask: URIRef
+    closed: URIRef
+    condition: URIRef
+    conforms: URIRef
+    construct: URIRef
+    datatype: URIRef
+    deactivated: URIRef
+    declare: URIRef
+    defaultValue: URIRef
+    description: URIRef
+    detail: URIRef
+    disjoint: URIRef
+    entailment: URIRef
+    equals: URIRef
+    expression: URIRef
+    filterShape: URIRef
+    flags: URIRef
+    focusNode: URIRef
+    group: URIRef
+    hasValue: URIRef
+    ignoredProperties: URIRef
+    intersection: URIRef
+    inversePath: URIRef
+    js: URIRef
+    jsFunctionName: URIRef
+    jsLibrary: URIRef
+    jsLibraryURL: URIRef
+    labelTemplate: URIRef
+    languageIn: URIRef
+    lessThan: URIRef
+    lessThanOrEquals: URIRef
+    maxCount: URIRef
+    maxExclusive: URIRef
+    maxInclusive: URIRef
+    maxLength: URIRef
+    message: URIRef
+    minCount: URIRef
+    minExclusive: URIRef
+    minInclusive: URIRef
+    minLength: URIRef
+    name: URIRef
+    namespace: URIRef
+    node: URIRef
+    nodeKind: URIRef
+    nodeValidator: URIRef
+    nodes: URIRef
+    object: URIRef
+    oneOrMorePath: URIRef
+    optional: URIRef
+    order: URIRef
+    parameter: URIRef
+    path: URIRef
+    pattern: URIRef
+    predicate: URIRef
+    prefix: URIRef
+    prefixes: URIRef
+    property: URIRef
+    propertyValidator: URIRef
+    qualifiedMaxCount: URIRef
+    qualifiedMinCount: URIRef
+    qualifiedValueShape: URIRef
+    qualifiedValueShapesDisjoint: URIRef
+    result: URIRef
+    resultAnnotation: URIRef
+    resultMessage: URIRef
+    resultPath: URIRef
+    resultSeverity: URIRef
+    returnType: URIRef
+    rule: URIRef
+    select: URIRef
+    severity: URIRef
+    shapesGraph: URIRef
+    shapesGraphWellFormed: URIRef
+    sourceConstraint: URIRef
+    sourceConstraintComponent: URIRef
+    sourceShape: URIRef
+    sparql: URIRef
+    subject: URIRef
+    suggestedShapesGraph: URIRef
+    target: URIRef
+    targetClass: URIRef
+    targetNode: URIRef
+    targetObjectsOf: URIRef
+    targetSubjectsOf: URIRef
+    union: URIRef
+    uniqueLang: URIRef
+    update: URIRef
+    validator: URIRef
+    value: URIRef
+    xone: URIRef
+    zeroOrMorePath: URIRef
+    zeroOrOnePath: URIRef
+    AbstractResult: URIRef
+    ConstraintComponent: URIRef
+    Function: URIRef
+    JSConstraint: URIRef
+    JSExecutable: URIRef
+    JSFunction: URIRef
+    JSLibrary: URIRef
+    JSRule: URIRef
+    JSTarget: URIRef
+    JSTargetType: URIRef
+    JSValidator: URIRef
+    NodeKind: URIRef
+    NodeShape: URIRef
+    Parameter: URIRef
+    Parameterizable: URIRef
+    PrefixDeclaration: URIRef
+    PropertyGroup: URIRef
+    PropertyShape: URIRef
+    ResultAnnotation: URIRef
+    Rule: URIRef
+    SPARQLAskExecutable: URIRef
+    SPARQLAskValidator: URIRef
+    SPARQLConstraint: URIRef
+    SPARQLConstructExecutable: URIRef
+    SPARQLExecutable: URIRef
+    SPARQLFunction: URIRef
+    SPARQLRule: URIRef
+    SPARQLSelectExecutable: URIRef
+    SPARQLSelectValidator: URIRef
+    SPARQLTarget: URIRef
+    SPARQLTargetType: URIRef
+    SPARQLUpdateExecutable: URIRef
+    Severity: URIRef
+    Shape: URIRef
+    Target: URIRef
+    TargetType: URIRef
+    TripleRule: URIRef
+    ValidationReport: URIRef
+    ValidationResult: URIRef
+    Validator: URIRef
+    this: URIRef
+    AndConstraintComponent: URIRef
+    ClassConstraintComponent: URIRef
+    ClosedConstraintComponent: URIRef
+    DatatypeConstraintComponent: URIRef
+    DisjointConstraintComponent: URIRef
+    EqualsConstraintComponent: URIRef
+    ExpressionConstraintComponent: URIRef
+    HasValueConstraintComponent: URIRef
+    InConstraintComponent: URIRef
+    JSConstraintComponent: URIRef
+    LanguageInConstraintComponent: URIRef
+    LessThanConstraintComponent: URIRef
+    LessThanOrEqualsConstraintComponent: URIRef
+    MaxCountConstraintComponent: URIRef
+    MaxExclusiveConstraintComponent: URIRef
+    MaxInclusiveConstraintComponent: URIRef
+    MaxLengthConstraintComponent: URIRef
+    MinCountConstraintComponent: URIRef
+    MinExclusiveConstraintComponent: URIRef
+    MinInclusiveConstraintComponent: URIRef
+    MinLengthConstraintComponent: URIRef
+    NodeConstraintComponent: URIRef
+    NodeKindConstraintComponent: URIRef
+    NotConstraintComponent: URIRef
+    OrConstraintComponent: URIRef
+    PatternConstraintComponent: URIRef
+    PropertyConstraintComponent: URIRef
+    QualifiedMaxCountConstraintComponent: URIRef
+    QualifiedMinCountConstraintComponent: URIRef
+    SPARQLConstraintComponent: URIRef
+    UniqueLangConstraintComponent: URIRef
+    XoneConstraintComponent: URIRef
+    BlankNode: URIRef
+    BlankNodeOrIRI: URIRef
+    BlankNodeOrLiteral: URIRef
+    IRI: URIRef
+    IRIOrLiteral: URIRef
+    Literal: URIRef
+    Info: URIRef
+    Violation: URIRef
+    Warning: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_SKOS.pyi b/mypy-stubs/rdflib/namespace/_SKOS.pyi
new file mode 100644
index 0000000..a52fcc4
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_SKOS.pyi
@@ -0,0 +1,37 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class SKOS(DefinedNamespace):
+    altLabel: URIRef
+    broadMatch: URIRef
+    broader: URIRef
+    broaderTransitive: URIRef
+    changeNote: URIRef
+    closeMatch: URIRef
+    definition: URIRef
+    editorialNote: URIRef
+    exactMatch: URIRef
+    example: URIRef
+    hasTopConcept: URIRef
+    hiddenLabel: URIRef
+    historyNote: URIRef
+    inScheme: URIRef
+    mappingRelation: URIRef
+    member: URIRef
+    memberList: URIRef
+    narrowMatch: URIRef
+    narrower: URIRef
+    narrowerTransitive: URIRef
+    notation: URIRef
+    note: URIRef
+    prefLabel: URIRef
+    related: URIRef
+    relatedMatch: URIRef
+    scopeNote: URIRef
+    semanticRelation: URIRef
+    topConceptOf: URIRef
+    Collection: URIRef
+    Concept: URIRef
+    ConceptScheme: URIRef
+    OrderedCollection: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_SOSA.pyi b/mypy-stubs/rdflib/namespace/_SOSA.pyi
new file mode 100644
index 0000000..465a729
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_SOSA.pyi
@@ -0,0 +1,41 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class SOSA(DefinedNamespace):
+    ActuatableProperty: URIRef
+    Actuation: URIRef
+    Actuator: URIRef
+    FeatureOfInterest: URIRef
+    ObservableProperty: URIRef
+    Observation: URIRef
+    Platform: URIRef
+    Procedure: URIRef
+    Result: URIRef
+    Sample: URIRef
+    Sampler: URIRef
+    Sampling: URIRef
+    Sensor: URIRef
+    hasSimpleResult: URIRef
+    resultTime: URIRef
+    actsOnProperty: URIRef
+    hasFeatureOfInterest: URIRef
+    hasResult: URIRef
+    hasSample: URIRef
+    hosts: URIRef
+    isActedOnBy: URIRef
+    isFeatureOfInterestOf: URIRef
+    isHostedBy: URIRef
+    isObservedBy: URIRef
+    isResultOf: URIRef
+    isSampleOf: URIRef
+    madeActuation: URIRef
+    madeByActuator: URIRef
+    madeBySampler: URIRef
+    madeBySensor: URIRef
+    madeObservation: URIRef
+    madeSampling: URIRef
+    observedProperty: URIRef
+    observes: URIRef
+    phenomenonTime: URIRef
+    usedProcedure: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_SSN.pyi b/mypy-stubs/rdflib/namespace/_SSN.pyi
new file mode 100644
index 0000000..aa82b50
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_SSN.pyi
@@ -0,0 +1,26 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class SSN(DefinedNamespace):
+    Deployment: URIRef
+    Input: URIRef
+    Output: URIRef
+    Property: URIRef
+    Stimulus: URIRef
+    System: URIRef
+    wasOriginatedBy: URIRef
+    deployedOnPlatform: URIRef
+    deployedSystem: URIRef
+    detects: URIRef
+    forProperty: URIRef
+    hasDeployment: URIRef
+    hasInput: URIRef
+    hasOutput: URIRef
+    hasProperty: URIRef
+    hasSubSystem: URIRef
+    implementedBy: URIRef
+    implements: URIRef
+    inDeployment: URIRef
+    isPropertyOf: URIRef
+    isProxyFor: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_TIME.pyi b/mypy-stubs/rdflib/namespace/_TIME.pyi
new file mode 100644
index 0000000..2321ca3
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_TIME.pyi
@@ -0,0 +1,100 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class TIME(DefinedNamespace):
+    generalDay: URIRef
+    generalMonth: URIRef
+    generalYear: URIRef
+    DateTimeDescription: URIRef
+    DateTimeInterval: URIRef
+    DayOfWeek: URIRef
+    Duration: URIRef
+    DurationDescription: URIRef
+    GeneralDateTimeDescription: URIRef
+    GeneralDurationDescription: URIRef
+    Instant: URIRef
+    Interval: URIRef
+    MonthOfYear: URIRef
+    ProperInterval: URIRef
+    TRS: URIRef
+    TemporalDuration: URIRef
+    TemporalEntity: URIRef
+    TemporalPosition: URIRef
+    TemporalUnit: URIRef
+    TimePosition: URIRef
+    TimeZone: URIRef
+    day: URIRef
+    dayOfYear: URIRef
+    days: URIRef
+    hasXSDDuration: URIRef
+    hour: URIRef
+    hours: URIRef
+    inXSDDate: URIRef
+    inXSDDateTimeStamp: URIRef
+    inXSDgYear: URIRef
+    inXSDgYearMonth: URIRef
+    minute: URIRef
+    minutes: URIRef
+    month: URIRef
+    months: URIRef
+    nominalPosition: URIRef
+    numericDuration: URIRef
+    numericPosition: URIRef
+    second: URIRef
+    seconds: URIRef
+    week: URIRef
+    weeks: URIRef
+    year: URIRef
+    years: URIRef
+    January: URIRef
+    Year: URIRef
+    inXSDDateTime: URIRef
+    xsdDateTime: URIRef
+    hasTRS: URIRef
+    after: URIRef
+    dayOfWeek: URIRef
+    hasBeginning: URIRef
+    hasDateTimeDescription: URIRef
+    hasDuration: URIRef
+    hasDurationDescription: URIRef
+    hasEnd: URIRef
+    hasTemporalDuration: URIRef
+    hasTime: URIRef
+    inDateTime: URIRef
+    inTemporalPosition: URIRef
+    inTimePosition: URIRef
+    inside: URIRef
+    intervalAfter: URIRef
+    intervalBefore: URIRef
+    intervalContains: URIRef
+    intervalDisjoint: URIRef
+    intervalDuring: URIRef
+    intervalEquals: URIRef
+    intervalFinishedBy: URIRef
+    intervalFinishes: URIRef
+    intervalIn: URIRef
+    intervalMeets: URIRef
+    intervalMetBy: URIRef
+    intervalOverlappedBy: URIRef
+    intervalOverlaps: URIRef
+    intervalStartedBy: URIRef
+    intervalStarts: URIRef
+    monthOfYear: URIRef
+    timeZone: URIRef
+    unitType: URIRef
+    before: URIRef
+    Friday: URIRef
+    Monday: URIRef
+    Saturday: URIRef
+    Sunday: URIRef
+    Thursday: URIRef
+    Tuesday: URIRef
+    Wednesday: URIRef
+    unitDay: URIRef
+    unitHour: URIRef
+    unitMinute: URIRef
+    unitMonth: URIRef
+    unitSecond: URIRef
+    unitWeek: URIRef
+    unitYear: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_VOID.pyi b/mypy-stubs/rdflib/namespace/_VOID.pyi
new file mode 100644
index 0000000..90c00d8
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_VOID.pyi
@@ -0,0 +1,35 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class VOID(DefinedNamespace):
+    classPartition: URIRef
+    classes: URIRef
+    dataDump: URIRef
+    distinctObjects: URIRef
+    distinctSubjects: URIRef
+    documents: URIRef
+    entities: URIRef
+    exampleResource: URIRef
+    feature: URIRef
+    inDataset: URIRef
+    linkPredicate: URIRef
+    objectsTarget: URIRef
+    openSearchDescription: URIRef
+    properties: URIRef
+    property: URIRef
+    propertyPartition: URIRef
+    rootResource: URIRef
+    sparqlEndpoint: URIRef
+    subjectsTarget: URIRef
+    subset: URIRef
+    target: URIRef
+    triples: URIRef
+    uriLookupEndpoint: URIRef
+    uriRegexPattern: URIRef
+    uriSpace: URIRef
+    vocabulary: URIRef
+    Dataset: URIRef
+    DatasetDescription: URIRef
+    Linkset: URIRef
+    TechnicalFeature: URIRef
diff --git a/mypy-stubs/rdflib/namespace/_XSD.pyi b/mypy-stubs/rdflib/namespace/_XSD.pyi
new file mode 100644
index 0000000..d9f948f
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/_XSD.pyi
@@ -0,0 +1,77 @@
+from rdflib.namespace import DefinedNamespace as DefinedNamespace
+from rdflib.namespace import Namespace as Namespace
+from rdflib.term import URIRef as URIRef
+
+class XSD(DefinedNamespace):
+    ENTITIES: URIRef
+    ENTITY: URIRef
+    ID: URIRef
+    IDREF: URIRef
+    IDREFS: URIRef
+    NCName: URIRef
+    NMTOKEN: URIRef
+    NMTOKENS: URIRef
+    NOTATION: URIRef
+    Name: URIRef
+    QName: URIRef
+    anyURI: URIRef
+    base64Binary: URIRef
+    boolean: URIRef
+    byte: URIRef
+    date: URIRef
+    dateTime: URIRef
+    dateTimeStamp: URIRef
+    dayTimeDuration: URIRef
+    decimal: URIRef
+    double: URIRef
+    duration: URIRef
+    float: URIRef
+    gDay: URIRef
+    gMonth: URIRef
+    gMonthDay: URIRef
+    gYear: URIRef
+    gYearMonth: URIRef
+    hexBinary: URIRef
+    int: URIRef
+    integer: URIRef
+    language: URIRef
+    long: URIRef
+    negativeInteger: URIRef
+    nonNegativeInteger: URIRef
+    nonPositiveInteger: URIRef
+    normalizedString: URIRef
+    positiveInteger: URIRef
+    short: URIRef
+    string: URIRef
+    time: URIRef
+    token: URIRef
+    unsignedByte: URIRef
+    unsignedInt: URIRef
+    unsignedLong: URIRef
+    unsignedShort: URIRef
+    yearMonthDuration: URIRef
+    ordered: URIRef
+    bounded: URIRef
+    cardinality: URIRef
+    numeric: URIRef
+    length: URIRef
+    minLength: URIRef
+    maxLength: URIRef
+    pattern: URIRef
+    enumeration: URIRef
+    whiteSpace: URIRef
+    maxExclusive: URIRef
+    maxInclusive: URIRef
+    minExclusive: URIRef
+    minInclusive: URIRef
+    totalDigits: URIRef
+    fractionDigits: URIRef
+    Assertions: URIRef
+    explicitTimezone: URIRef
+    year: URIRef
+    month: URIRef
+    day: URIRef
+    hour: URIRef
+    minute: URIRef
+    second: URIRef
+    timezoneOffset: URIRef
diff --git a/mypy-stubs/rdflib/namespace/__init__.pyi b/mypy-stubs/rdflib/namespace/__init__.pyi
new file mode 100644
index 0000000..e5342fd
--- /dev/null
+++ b/mypy-stubs/rdflib/namespace/__init__.pyi
@@ -0,0 +1,85 @@
+from typing import Any, Tuple
+
+from rdflib.term import URIRef
+
+__all__ = [
+    "split_uri",
+    "Namespace",
+    "ClosedNamespace",
+    "RDF",
+    "RDFS",
+    "CSVW",
+    "DC",
+    "DCAT",
+    "DCTERMS",
+    "DOAP",
+    "FOAF",
+    "ODRL2",
+    "ORG",
+    "OWL",
+    "PROF",
+    "PROV",
+    "QB",
+    "SDO",
+    "SH",
+    "SKOS",
+    "SOSA",
+    "SSN",
+    "TIME",
+    "VOID",
+    "XSD",
+    "OWL",
+]
+
+class Namespace(str):
+    @property
+    def title(self) -> URIRef: ...
+    def term(self, name: Any) -> URIRef: ...
+    def __getitem__(self, key: Any) -> URIRef: ...
+    def __getattr__(self, name: str) -> URIRef: ...
+
+class URIPattern(str):
+    def format(self, *args: Any, **kwargs: Any) -> str: ...
+
+class DefinedNamespaceMeta(type):
+    def __getitem__(cls, name: Any, default: Any | None = ...) -> URIRef: ...
+    def __getattr__(cls, name: Any) -> URIRef: ...
+    def __contains__(cls, item: Any) -> bool: ...
+
+class DefinedNamespace(metaclass=DefinedNamespaceMeta):
+    def __init__(self) -> None: ...
+
+class ClosedNamespace(Namespace):
+    def __new__(cls, uri: Any, terms: Any) -> ClosedNamespace: ...
+    @property
+    def uri(self) -> str: ...
+
+NAME_START_CATEGORIES = ["Ll", "Lu", "Lo", "Lt", "Nl"]
+SPLIT_START_CATEGORIES = NAME_START_CATEGORIES + ["Nd"]
+
+XMLNS = "http://www.w3.org/XML/1998/namespace"
+
+def split_uri(uri: Any, split_start: Any = ...) -> Tuple[str, str]: ...
+
+from rdflib.namespace._CSVW import CSVW
+from rdflib.namespace._DC import DC
+from rdflib.namespace._DCAT import DCAT
+from rdflib.namespace._DCTERMS import DCTERMS
+from rdflib.namespace._DOAP import DOAP
+from rdflib.namespace._FOAF import FOAF
+from rdflib.namespace._ODRL2 import ODRL2
+from rdflib.namespace._ORG import ORG
+from rdflib.namespace._OWL import OWL
+from rdflib.namespace._PROF import PROF
+from rdflib.namespace._PROV import PROV
+from rdflib.namespace._QB import QB
+from rdflib.namespace._RDF import RDF
+from rdflib.namespace._RDFS import RDFS
+from rdflib.namespace._SDO import SDO
+from rdflib.namespace._SH import SH
+from rdflib.namespace._SKOS import SKOS
+from rdflib.namespace._SOSA import SOSA
+from rdflib.namespace._SSN import SSN
+from rdflib.namespace._TIME import TIME
+from rdflib.namespace._VOID import VOID
+from rdflib.namespace._XSD import XSD
diff --git a/mypy-stubs/rdflib/parser.pyi b/mypy-stubs/rdflib/parser.pyi
new file mode 100644
index 0000000..4c628be
--- /dev/null
+++ b/mypy-stubs/rdflib/parser.pyi
@@ -0,0 +1,5 @@
+from typing import Any
+
+class Parser:
+    def __init__(self) -> None: ...
+    def parse(self, source: Any, sink: Any) -> None: ...
diff --git a/mypy-stubs/rdflib/paths.pyi b/mypy-stubs/rdflib/paths.pyi
new file mode 100644
index 0000000..9bea179
--- /dev/null
+++ b/mypy-stubs/rdflib/paths.pyi
@@ -0,0 +1,24 @@
+from collections.abc import Generator
+from typing import Any, Callable, Union
+
+from rdflib.term import Node as Node
+from rdflib.term import URIRef as URIRef
+
+ZeroOrMore: str
+OneOrMore: str
+ZeroOrOne: str
+
+class Path:
+    __or__: Callable[[Path, Union["URIRef", "Path"]], "AlternativePath"]
+    __invert__: Callable[[Path], "InvPath"]
+    __neg__: Callable[[Path], "NegatedPath"]
+    __truediv__: Callable[[Path, Union["URIRef", "Path"]], "SequencePath"]
+    __mul__: Callable[[Path, str], "MulPath"]
+    def __hash__(self) -> int: ...
+    def __lt__(self, other: Any) -> bool: ...
+
+class InvPath(Path): ...
+class SequencePath(Path): ...
+class AlternativePath(Path): ...
+class MulPath(Path): ...
+class NegatedPath(Path): ...
diff --git a/mypy-stubs/rdflib/plugin.pyi b/mypy-stubs/rdflib/plugin.pyi
new file mode 100644
index 0000000..d6f840d
--- /dev/null
+++ b/mypy-stubs/rdflib/plugin.pyi
@@ -0,0 +1,8 @@
+from typing import Any, Type, TypeVar
+
+def register(name: str, kind: Any, module_path: str, class_name: str) -> None: ...
+
+PluginT = TypeVar("PluginT")
+
+def get(name: str, kind: Type[PluginT]) -> Type[PluginT]: ...
+def plugins(name: Any | None = ..., kind: Any | None = ...) -> None: ...
diff --git a/typeshed/rdflib/plugins/__init__.pyi b/mypy-stubs/rdflib/plugins/__init__.pyi
similarity index 99%
rename from typeshed/rdflib/plugins/__init__.pyi
rename to mypy-stubs/rdflib/plugins/__init__.pyi
index e856e17..fc4e2d1 100644
--- a/typeshed/rdflib/plugins/__init__.pyi
+++ b/mypy-stubs/rdflib/plugins/__init__.pyi
@@ -1,4 +1,3 @@
 # Stubs for rdflib.plugins (Python 3.5)
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/rdflib/plugins/parsers/__init__.pyi b/mypy-stubs/rdflib/plugins/parsers/__init__.pyi
similarity index 99%
rename from typeshed/rdflib/plugins/parsers/__init__.pyi
rename to mypy-stubs/rdflib/plugins/parsers/__init__.pyi
index 3f18710..589759a 100644
--- a/typeshed/rdflib/plugins/parsers/__init__.pyi
+++ b/mypy-stubs/rdflib/plugins/parsers/__init__.pyi
@@ -1,4 +1,3 @@
 # Stubs for rdflib.plugins.parsers (Python 3.5)
 #
 # NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/mypy-stubs/rdflib/plugins/parsers/notation3.pyi b/mypy-stubs/rdflib/plugins/parsers/notation3.pyi
new file mode 100644
index 0000000..40932a7
--- /dev/null
+++ b/mypy-stubs/rdflib/plugins/parsers/notation3.pyi
@@ -0,0 +1 @@
+class BadSyntax(SyntaxError): ...
diff --git a/mypy-stubs/rdflib/query.pyi b/mypy-stubs/rdflib/query.pyi
new file mode 100644
index 0000000..73f4008
--- /dev/null
+++ b/mypy-stubs/rdflib/query.pyi
@@ -0,0 +1,42 @@
+from typing import IO, Any, Dict, Iterator, List, Mapping, Optional, Tuple, overload
+
+from rdflib import URIRef, Variable
+from rdflib.term import Identifier
+from typing_extensions import SupportsIndex
+
+class ResultRow(Tuple["Identifier", ...]):
+    def __new__(
+        cls, values: Mapping[Variable, Identifier], labels: List[Variable]
+    ) -> ResultRow: ...
+    def __getattr__(self, name: str) -> Identifier: ...
+    @overload
+    def __getitem__(self, name: str) -> Identifier: ...
+    @overload
+    def __getitem__(self, __x: SupportsIndex) -> Identifier: ...
+    @overload
+    def __getitem__(self, __x: slice) -> Tuple[Identifier, ...]: ...
+    def get(self, name: str, default: Any | None = ...) -> Identifier: ...
+    def asdict(self) -> Dict[str, Identifier]: ...
+
+class Result:
+    type: Any
+    vars: Any
+    askAnswer: Any
+    graph: Any
+    def __init__(self, type_: str) -> None: ...
+    bindings: Any
+    def __iter__(self) -> Iterator[bool | ResultRow]: ...
+    @staticmethod
+    def parse(
+        source: IO[Any] | None = ...,
+        format: str | None = ...,
+        content_type: str | None = ...,
+        **kwargs: Any
+    ) -> Result: ...
+    def serialize(
+        self,
+        destination: str | IO[Any] | None = ...,
+        encoding: str = ...,
+        format: str = ...,
+        **args: Any
+    ) -> Optional[bytes]: ...
diff --git a/mypy-stubs/rdflib/resource.pyi b/mypy-stubs/rdflib/resource.pyi
new file mode 100644
index 0000000..e520dbe
--- /dev/null
+++ b/mypy-stubs/rdflib/resource.pyi
@@ -0,0 +1,33 @@
+from typing import Any, Iterable, Iterator, Tuple
+
+from _typeshed import Incomplete
+from rdflib.graph import Graph, Seq
+from rdflib.term import Node
+
+class Resource:
+    def __init__(self, graph: Graph, subject: Node) -> None: ...
+    graph: Incomplete
+    identifier: Incomplete
+    def add(self, p: Node, o: Node) -> None: ...
+    def remove(self, p: Node, o: Node | None = ...) -> None: ...
+    def set(self, p: Node, o: Node) -> None: ...
+    def subjects(self, predicate: Any | None = ...) -> Iterable[Node]: ...
+    def predicates(self, o: Incomplete | None = ...) -> Iterable[Node]: ...
+    def objects(self, predicate: Any | None = ...) -> Iterable[Node]: ...
+    def subject_predicates(self) -> Iterator[Tuple[Node, Node]]: ...
+    def subject_objects(self) -> Iterator[Tuple[Node, Node]]: ...
+    def predicate_objects(self) -> Iterator[Tuple[Node, Node]]: ...
+    def value(
+        self, p: Node, o: Node | None = ..., default: Any | None = ..., any: bool = ...
+    ) -> Any: ...
+    def label(self) -> Any: ...
+    def comment(self) -> Any: ...
+    def items(self) -> Iterator[Any]: ...
+    def transitive_objects(
+        self, predicate: Node, remember: Any | None = ...
+    ) -> Iterator[Any]: ...
+    def transitive_subjects(
+        self, predicate: Node, remember: Any | None = ...
+    ) -> Iterator[Any]: ...
+    def seq(self) -> Seq | None: ...
+    def qname(self) -> Any: ...
diff --git a/mypy-stubs/rdflib/term.pyi b/mypy-stubs/rdflib/term.pyi
new file mode 100644
index 0000000..0830bdc
--- /dev/null
+++ b/mypy-stubs/rdflib/term.pyi
@@ -0,0 +1,43 @@
+from typing import Any, Callable, Union
+
+class Node: ...
+
+class Identifier(Node, str):
+    def __new__(cls, value: Union[Any, str, None]) -> "Identifier": ...
+    def eq(self, other: Any) -> bool: ...
+    def neq(self, other: Any) -> bool: ...
+
+class IdentifiedNode(Identifier): ...
+
+class URIRef(IdentifiedNode):
+    def toPython(self) -> str: ...
+    def n3(self, namespace_manager: Any | None = ...) -> str: ...
+    def defrag(self) -> "URIRef": ...
+    def de_skolemize(self) -> "BNode": ...
+
+class Genid(URIRef): ...
+class RDFLibGenid(Genid): ...
+
+class BNode(IdentifiedNode):
+    def toPython(self) -> str: ...
+    def n3(self, namespace_manager: Any | None = ...) -> str: ...
+    def skolemize(
+        self, authority: Any | None = ..., basepath: Any | None = ...
+    ) -> "RDFLibGenid": ...
+
+class Literal(Identifier):
+    def normalize(self) -> "Literal": ...
+    @property
+    def value(self) -> Any: ...
+    @property
+    def language(self) -> str | None: ...
+    @property
+    def datatype(self) -> Any: ...
+    def eq(self, other: Any) -> bool: ...
+    def neq(self, other: Any) -> bool: ...
+    def n3(self, namespace_manager: Any | None = ...) -> str: ...
+    def toPython(self) -> str: ...
+
+class Variable(Identifier):
+    def toPython(self) -> str: ...
+    def n3(self, namespace_manager: Any | None = ...) -> str: ...
diff --git a/typeshed/ruamel/__init__.py b/mypy-stubs/ruamel/__init__.py
similarity index 100%
rename from typeshed/ruamel/__init__.py
rename to mypy-stubs/ruamel/__init__.py
diff --git a/typeshed/avro/__init__.pyi b/typeshed/avro/__init__.pyi
deleted file mode 100644
index 39efba5..0000000
--- a/typeshed/avro/__init__.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for avro (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-# Names in __all__ with no definition:
-#   datafile
-#   io
-#   ipc
-#   protocol
-#   schema
diff --git a/typeshed/avro/schema.pyi b/typeshed/avro/schema.pyi
deleted file mode 100644
index 05f48e5..0000000
--- a/typeshed/avro/schema.pyi
+++ /dev/null
@@ -1,117 +0,0 @@
-# Stubs for avro.schema (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Union, Dict, List, Text
-
-PRIMITIVE_TYPES = ... # type: Any
-NAMED_TYPES = ... # type: Any
-VALID_TYPES = ... # type: Any
-SCHEMA_RESERVED_PROPS = ... # type: Any
-FIELD_RESERVED_PROPS = ... # type: Any
-VALID_FIELD_SORT_ORDERS = ... # type: Any
-
-class AvroException(Exception): ...
-class SchemaParseException(AvroException): ...
-
-class Schema:
-    type = ... # type: Any
-    def __init__(self, type, other_props=None): ...
-    props = ... # type: Any
-    other_props = ... # type: Any
-    def get_prop(self, key): ...
-    def set_prop(self, key, value): ...
-    def to_json(self, names): ...
-
-class Name:
-    def __init__(self, name_attr, space_attr, default_space): ...
-    def __eq__(self, other): ...
-    fullname = ... # type: Any
-    def get_space(self): ...
-
-class Names:
-    names = ... # type: Any
-    default_namespace = ... # type: Any
-    def __init__(self, default_namespace: Union[str, Text] = None) -> None: ...
-    def has_name(self, name_attr: Union[str, Text], space_attr: Union[str, Text]) -> bool: ...
-    def get_name(self, name_attr: Union[str, Text], space_attr: Union[str, Text]) -> Schema: ...
-    def prune_namespace(self, properties): ...
-    def add_name(self, name_attr, space_attr, new_schema): ...
-
-class NamedSchema(Schema):
-    def __init__(self, type, name, namespace=None, names=None, other_props=None): ...
-    def name_ref(self, names): ...
-    name = ... # type: Any
-    namespace = ... # type: Any
-    fullname = ... # type: Any
-
-class Field:
-    type = ... # type: Any
-    name = ... # type: Any
-    def __init__(self, type, name, has_default, default=None, order=None, names=None, doc=None, other_props=None): ...
-    default = ... # type: Any
-    has_default = ... # type: Any
-    order = ... # type: Any
-    doc = ... # type: Any
-    props = ... # type: Any
-    other_props = ... # type: Any
-    def get_prop(self, key): ...
-    def set_prop(self, key, value): ...
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class PrimitiveSchema(Schema):
-    fullname = ... # type: Any
-    def __init__(self, type, other_props=None): ...
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class FixedSchema(NamedSchema):
-    def __init__(self, name, namespace, size, names=None, other_props=None): ...
-    size = ... # type: Any
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class EnumSchema(NamedSchema):
-    def __init__(self, name, namespace, symbols, names=None, doc=None, other_props=None): ...
-    symbols = ... # type: Any
-    doc = ... # type: Any
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class ArraySchema(Schema):
-    def __init__(self, items, names=None, other_props=None): ...
-    items = ... # type: Any
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class MapSchema(Schema):
-    def __init__(self, values, names=None, other_props=None): ...
-    values = ... # type: Any
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class UnionSchema(Schema):
-    def __init__(self, schemas, names=None): ...
-    schemas = ... # type: Any
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-class ErrorUnionSchema(UnionSchema):
-    def __init__(self, schemas, names=None): ...
-    def to_json(self, names=None): ...
-
-class RecordSchema(NamedSchema):
-    @staticmethod
-    def make_field_objects(field_data, names): ...
-    def __init__(self, name, namespace, fields, names=None, schema_type='', doc=None, other_props=None): ...
-    fields = ... # type: Any
-    doc = ... # type: Any
-    @property
-    def fields_dict(self): ...
-    def to_json(self, names=None): ...
-    def __eq__(self, that): ...
-
-def get_other_props(all_props, reserved_props): ...
-def make_avsc_object(json_data: Union[Dict, List, str], names: Names) -> Schema: ...
-def parse(json_string): ...
diff --git a/typeshed/cachecontrol/adapter.pyi b/typeshed/cachecontrol/adapter.pyi
deleted file mode 100644
index 734fe14..0000000
--- a/typeshed/cachecontrol/adapter.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for cachecontrol.adapter (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from requests.adapters import HTTPAdapter
-from .controller import CacheController as CacheController
-from .cache import DictCache as DictCache
-from .filewrapper import CallbackFileWrapper as CallbackFileWrapper
-
-class CacheControlAdapter(HTTPAdapter):
-    invalidating_methods = ...  # type: Any
-    cache = ...  # type: Any
-    heuristic = ...  # type: Any
-    controller = ...  # type: Any
-    def __init__(self, cache=None, cache_etags=True, controller_class=None, serializer=None, heuristic=None, *args, **kw): ...
-    def send(self, request, **kw): ...
-    def build_response(self, request, response, from_cache=False): ...
-    def close(self): ...
diff --git a/typeshed/cachecontrol/cache.pyi b/typeshed/cachecontrol/cache.pyi
deleted file mode 100644
index c4f507b..0000000
--- a/typeshed/cachecontrol/cache.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for cachecontrol.cache (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class BaseCache:
-    def get(self, key): ...
-    def set(self, key, value): ...
-    def delete(self, key): ...
-    def close(self): ...
-
-class DictCache(BaseCache):
-    lock = ...  # type: Any
-    data = ...  # type: Any
-    def __init__(self, init_dict=None): ...
-    def get(self, key): ...
-    def set(self, key, value): ...
-    def delete(self, key): ...
diff --git a/typeshed/cachecontrol/caches/file_cache.pyi b/typeshed/cachecontrol/caches/file_cache.pyi
deleted file mode 100644
index 2d6ca0c..0000000
--- a/typeshed/cachecontrol/caches/file_cache.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for cachecontrol.caches.file_cache (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Callable
-from ..cache import BaseCache as BaseCache
-from ..controller import CacheController as CacheController
-
-class FileCache(BaseCache):
-    directory = ...  # type: str
-    forever = ...  # type: bool
-    filemode = ...  # type: str
-    dirmode = ...  # type: str
-    lock_class = ...  # type: Callable
-    def __init__(self, directory: str, forever=False, filemode=384, dirmode=448, use_dir_lock=None, lock_class=None) -> None: ...
-    @staticmethod
-    def encode(x): ...
-    def get(self, key): ...
-    def set(self, key, value): ...
-    def delete(self, key): ...
-
-def url_to_file_path(url, filecache): ...
diff --git a/typeshed/cachecontrol/controller.pyi b/typeshed/cachecontrol/controller.pyi
deleted file mode 100644
index 1161e79..0000000
--- a/typeshed/cachecontrol/controller.pyi
+++ /dev/null
@@ -1,25 +0,0 @@
-# Stubs for cachecontrol.controller (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-#from .cache import DictCache as DictCache
-#from .serialize import Serializer as Serializer
-
-logger = ...  # type: Any
-URI = ...  # type: Any
-
-def parse_uri(uri): ...
-
-class CacheController:
-    cache = ...  # type: Any
-    cache_etags = ...  # type: Any
-    serializer = ...  # type: Any
-    def __init__(self, cache=None, cache_etags=True, serializer=None): ...
-    @classmethod
-    def cache_url(https://github.com/cls,%20uri): ...
-    def parse_cache_control(self, headers): ...
-    def cached_request(self, request): ...
-    def conditional_headers(self, request): ...
-    def cache_response(self, request, response, body=None): ...
-    def update_cached_response(self, request, response): ...
diff --git a/typeshed/cachecontrol/filewrapper.pyi b/typeshed/cachecontrol/filewrapper.pyi
deleted file mode 100644
index d21df15..0000000
--- a/typeshed/cachecontrol/filewrapper.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for cachecontrol.filewrapper (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-class CallbackFileWrapper:
-    def __init__(self, fp, callback): ...
-    def __getattr__(self, name): ...
-    def read(self, amt=None): ...
diff --git a/typeshed/cachecontrol/serialize.pyi b/typeshed/cachecontrol/serialize.pyi
deleted file mode 100644
index a0f9eec..0000000
--- a/typeshed/cachecontrol/serialize.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for cachecontrol.serialize (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .compat import HTTPResponse as HTTPResponse, pickle as pickle, text_type as text_type
-
-class Serializer:
-    def dumps(self, request, response, body=None): ...
-    def loads(self, request, data): ...
-    def prepare_response(self, request, cached): ...
diff --git a/typeshed/cachecontrol/wrapper.pyi b/typeshed/cachecontrol/wrapper.pyi
deleted file mode 100644
index 67ef6b4..0000000
--- a/typeshed/cachecontrol/wrapper.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for cachecontrol.wrapper (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Optional, Union
-from .adapter import CacheControlAdapter as CacheControlAdapter
-from .cache import DictCache, BaseCache
-import requests
-
-def CacheControl(sess: requests.sessions.Session,
-                 cache: Optional[Union[DictCache, BaseCache]] = None,
-                 cache_etags: bool = True,
-                 serializer=None,
-                 heuristic=None) -> requests.sessions.Session: ...
diff --git a/typeshed/future/__init__.pyi b/typeshed/future/__init__.pyi
deleted file mode 100644
index e69de29..0000000
diff --git a/typeshed/future/utils/__init__.pyi b/typeshed/future/utils/__init__.pyi
deleted file mode 100644
index a67c2a1..0000000
--- a/typeshed/future/utils/__init__.pyi
+++ /dev/null
@@ -1,61 +0,0 @@
-# Stubs for future.utils (Python 3)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-PY3: Any
-PY2: Any
-PY26: Any
-PYPY: Any
-
-def python_2_unicode_compatible(cls): ...
-def with_metaclass(meta: Any, *bases: Any): ...
-def bstr(s: Any): ...
-def bord(s: Any): ...
-
-def tobytes(s: Any): ...
-def native_str_to_bytes(s: Any, encoding: str = ...): ...
-def bytes_to_native_str(b: Any, encoding: str = ...): ...
-def text_to_native_str(t: Any, encoding: Optional[Any] = ...): ...
-def lrange(*args: Any, **kwargs: Any): ...
-def lzip(*args: Any, **kwargs: Any): ...
-def lmap(*args: Any, **kwargs: Any): ...
-def lfilter(*args: Any, **kwargs: Any): ...
-
-def isidentifier(s: Any, dotted: bool = ...): ...
-def viewitems(obj: Any, **kwargs: Any): ...
-def viewkeys(obj: Any, **kwargs: Any): ...
-def viewvalues(obj: Any, **kwargs: Any): ...
-def iteritems(obj: Any, **kwargs: Any): ...
-def iterkeys(obj: Any, **kwargs: Any): ...
-def itervalues(obj: Any, **kwargs: Any): ...
-def bind_method(cls, name: Any, func: Any) -> None: ...
-def getexception(): ...
-def raise_(tp: Any, value: Optional[Any] = ..., tb: Optional[Any] = ...) -> None: ...
-def raise_from(exc: Any, cause: Any) -> None: ...
-def raise_with_traceback(exc: Any, traceback: Any = ...) -> None: ...
-reraise = raise_
-
-def implements_iterator(cls): ...
-
-get_next: Any
-
-def encode_filename(filename: Any): ...
-def is_new_style(cls): ...
-native_str = str
-native_bytes = bytes
-
-def istext(obj: Any): ...
-def isbytes(obj: Any): ...
-def isnewbytes(obj: Any): ...
-def isint(obj: Any): ...
-def native(obj: Any): ...
-
-exec_: Any
-
-def old_div(a: Any, b: Any): ...
-def as_native_str(encoding: str = ...): ...
-def listvalues(d: Any): ...
-def listitems(d: Any): ...
-def ensure_new_type(obj: Any): ...
diff --git a/typeshed/galaxy/__init__.pyi b/typeshed/galaxy/__init__.pyi
deleted file mode 100644
index aa2f6e6..0000000
--- a/typeshed/galaxy/__init__.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-PROJECT_NAME = ...  # type: str
-PROJECT_OWNER = ...  # type: str
-PROJECT_USERAME = ...  # type: str
-PROJECT_URL = ...  # type: str
-PROJECT_AUTHOR = ...  # type: str
-PROJECT_EMAIL = ...  # type: str
-RAW_CONTENT_URL = ...  # type: Any
diff --git a/typeshed/galaxy/exceptions/__init__.pyi b/typeshed/galaxy/exceptions/__init__.pyi
deleted file mode 100644
index e59ac08..0000000
--- a/typeshed/galaxy/exceptions/__init__.pyi
+++ /dev/null
@@ -1,143 +0,0 @@
-# Stubs for galaxy.exceptions (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..exceptions import error_codes as error_codes
-
-class MessageException(Exception):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-    err_msg = ...  # type: Any
-    type = ...  # type: Any
-    extra_error_info = ...  # type: Any
-    def __init__(self, err_msg: Optional[Any] = ..., type: str = ..., **extra_error_info) -> None: ...
-
-class ItemDeletionException(MessageException): ...
-class ObjectInvalid(Exception): ...
-
-class ActionInputError(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-    def __init__(self, err_msg, type: str = ...) -> None: ...
-
-class DuplicatedSlugException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class DuplicatedIdentifierException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ObjectAttributeInvalidException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ObjectAttributeMissingException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class MalformedId(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class MalformedContents(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class UnknownContentsType(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class RequestParameterMissingException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ToolMetaParameterException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ToolMissingException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class RequestParameterInvalidException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class AuthenticationFailed(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class AuthenticationRequired(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ItemAccessibilityException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ItemOwnershipException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ConfigDoesNotAllowException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class InsufficientPermissionsException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class AdminRequiredException(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ObjectNotFound(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class DeprecatedMethod(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class Conflict(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ConfigurationError(Exception):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class InconsistentDatabase(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class InternalServerError(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class NotImplemented(MessageException):
-    status_code = ...  # type: int
-    err_code = ...  # type: Any
-
-class ContainerCLIError(Exception):
-    stdout = ...  # type: Any
-    stderr = ...  # type: Any
-    returncode = ...  # type: Any
-    command = ...  # type: Any
-    subprocess_command = ...  # type: Any
-    def __init__(self, msg: Optional[Any] = ..., stdout: Optional[Any] = ..., stderr: Optional[Any] = ..., returncode: Optional[Any] = ..., command: Optional[Any] = ..., subprocess_command: Optional[Any] = ..., **kwargs) -> None: ...
-
-class ContainerNotFound(Exception):
-    container_id = ...  # type: Any
-    def __init__(self, msg: Optional[Any] = ..., container_id: Optional[Any] = ..., **kwargs) -> None: ...
-
-class ContainerImageNotFound(Exception):
-    image = ...  # type: Any
-    def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., **kwargs) -> None: ...
-
-class ContainerRunError(Exception):
-    image = ...  # type: Any
-    command = ...  # type: Any
-    def __init__(self, msg: Optional[Any] = ..., image: Optional[Any] = ..., command: Optional[Any] = ..., **kwargs) -> None: ...
diff --git a/typeshed/galaxy/exceptions/error_codes.pyi b/typeshed/galaxy/exceptions/error_codes.pyi
deleted file mode 100644
index b25ca3e..0000000
--- a/typeshed/galaxy/exceptions/error_codes.pyi
+++ /dev/null
@@ -1,17 +0,0 @@
-# Stubs for galaxy.exceptions.error_codes (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-UNKNOWN_ERROR_MESSAGE = ...  # type: str
-
-class ErrorCode:
-    code = ...  # type: Any
-    default_error_message = ...  # type: Any
-    def __init__(self, code, default_error_message) -> None: ...
-    def __int__(self): ...
-
-error_codes_json = ...  # type: Any
-name = ...  # type: Any
-error_code_obj = ...  # type: Any
diff --git a/typeshed/galaxy/jobs/__init__.pyi b/typeshed/galaxy/jobs/__init__.pyi
deleted file mode 100644
index c65cfb4..0000000
--- a/typeshed/galaxy/jobs/__init__.pyi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Stubs for galaxy.jobs (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/galaxy/jobs/metrics/__init__.pyi b/typeshed/galaxy/jobs/metrics/__init__.pyi
deleted file mode 100644
index 758ddc6..0000000
--- a/typeshed/galaxy/jobs/metrics/__init__.pyi
+++ /dev/null
@@ -1,38 +0,0 @@
-# Stubs for galaxy.jobs.metrics (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..metrics import formatting as formatting
-
-log = ...  # type: Any
-DEFAULT_FORMATTER = ...  # type: Any
-
-class JobMetrics:
-    plugin_classes = ...  # type: Any
-    default_job_instrumenter = ...  # type: Any
-    job_instrumenters = ...  # type: Any
-    def __init__(self, conf_file: Optional[Any] = ..., **kwargs) -> None: ...
-    def format(self, plugin, key, value): ...
-    def set_destination_conf_file(self, destination_id, conf_file): ...
-    def set_destination_conf_element(self, destination_id, element): ...
-    def set_destination_instrumenter(self, destination_id, job_instrumenter: Optional[Any] = ...): ...
-    def collect_properties(self, destination_id, job_id, job_directory): ...
-
-class NullJobInstrumenter:
-    def pre_execute_commands(self, job_directory): ...
-    def post_execute_commands(self, job_directory): ...
-    def collect_properties(self, job_id, job_directory): ...
-
-NULL_JOB_INSTRUMENTER = ...  # type: Any
-
-class JobInstrumenter:
-    extra_kwargs = ...  # type: Any
-    plugin_classes = ...  # type: Any
-    plugins = ...  # type: Any
-    def __init__(self, plugin_classes, plugins_source, **kwargs) -> None: ...
-    def pre_execute_commands(self, job_directory): ...
-    def post_execute_commands(self, job_directory): ...
-    def collect_properties(self, job_id, job_directory): ...
-    @staticmethod
-    def from_file(plugin_classes, conf_file, **kwargs): ...
diff --git a/typeshed/galaxy/jobs/metrics/collectl/__init__.pyi b/typeshed/galaxy/jobs/metrics/collectl/__init__.pyi
deleted file mode 100644
index c58636e..0000000
--- a/typeshed/galaxy/jobs/metrics/collectl/__init__.pyi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Stubs for galaxy.jobs.metrics.collectl (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/galaxy/jobs/metrics/collectl/cli.pyi b/typeshed/galaxy/jobs/metrics/collectl/cli.pyi
deleted file mode 100644
index 88e3120..0000000
--- a/typeshed/galaxy/jobs/metrics/collectl/cli.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for galaxy.jobs.metrics.collectl.cli (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class CollectlCli:
-    mode = ...  # type: Any
-    command_args = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def build_command_line(self): ...
-    def run(self, stdout: Any = ..., stderr: Any = ...): ...
diff --git a/typeshed/galaxy/jobs/metrics/collectl/processes.pyi b/typeshed/galaxy/jobs/metrics/collectl/processes.pyi
deleted file mode 100644
index ad6fbd8..0000000
--- a/typeshed/galaxy/jobs/metrics/collectl/processes.pyi
+++ /dev/null
@@ -1,24 +0,0 @@
-# Stubs for galaxy.jobs.metrics.collectl.processes (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-def generate_process_statistics(collectl_playback_cli, pid, statistics: Any = ...): ...
-
-class CollectlProcessSummarizer:
-    pid = ...  # type: Any
-    statistics = ...  # type: Any
-    columns_of_interest = ...  # type: Any
-    tree_statistics = ...  # type: Any
-    process_accum_statistics = ...  # type: Any
-    interval_count = ...  # type: int
-    def __init__(self, pid, statistics) -> None: ...
-    def handle_interval(self, interval): ...
-    def get_statistics(self): ...
-
-class CollectlProcessInterval:
-    rows = ...  # type: Any
-    def __init__(self) -> None: ...
-    def row_is_in(self, row): ...
-    def add_row(self, row): ...
diff --git a/typeshed/galaxy/jobs/metrics/collectl/stats.pyi b/typeshed/galaxy/jobs/metrics/collectl/stats.pyi
deleted file mode 100644
index 39f0c8d..0000000
--- a/typeshed/galaxy/jobs/metrics/collectl/stats.pyi
+++ /dev/null
@@ -1,15 +0,0 @@
-# Stubs for galaxy.jobs.metrics.collectl.stats (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class StatisticsTracker:
-    min = ...  # type: Any
-    max = ...  # type: Any
-    count = ...  # type: int
-    sum = ...  # type: int
-    def __init__(self) -> None: ...
-    def track(self, value): ...
-    @property
-    def avg(self): ...
diff --git a/typeshed/galaxy/jobs/metrics/collectl/subsystems.pyi b/typeshed/galaxy/jobs/metrics/collectl/subsystems.pyi
deleted file mode 100644
index 1da48e6..0000000
--- a/typeshed/galaxy/jobs/metrics/collectl/subsystems.pyi
+++ /dev/null
@@ -1,35 +0,0 @@
-# Stubs for galaxy.jobs.metrics.collectl.subsystems (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-class CollectlSubsystem:
-    @property
-    def command_line_arg(self): ...
-    @property
-    def name(self, job_directory): ...
-
-class ProcessesSubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-class CpuSubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-class DiskSubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-class NetworkSubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-class EnvironmentSubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-class MemorySubsystem(CollectlSubsystem):
-    command_line_arg = ...  # type: str
-    name = ...  # type: str
-
-def get_subsystem(name): ...
diff --git a/typeshed/galaxy/jobs/metrics/formatting.pyi b/typeshed/galaxy/jobs/metrics/formatting.pyi
deleted file mode 100644
index ebc91b1..0000000
--- a/typeshed/galaxy/jobs/metrics/formatting.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.jobs.metrics.formatting (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-class JobMetricFormatter:
-    def format(self, key, value): ...
-
-def seconds_to_str(value): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/__init__.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/__init__.pyi
deleted file mode 100644
index ede6717..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/__init__.pyi
+++ /dev/null
@@ -1,16 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from ...metrics import formatting as formatting
-
-INSTRUMENT_FILE_PREFIX = ...  # type: str
-
-class InstrumentPlugin:
-    formatter = ...  # type: Any
-    @property
-    def plugin_type(self): ...
-    def pre_execute_instrument(self, job_directory): ...
-    def post_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/collectl.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/collectl.pyi
deleted file mode 100644
index 080d2e5..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/collectl.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.collectl (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class CollectlFormatter(formatting.JobMetricFormatter):
-    def format(self, key, value): ...
-
-class CollectlPlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    saved_logs_path = ...  # type: Any
-    summarize_process_data = ...  # type: Any
-    log_collectl_program_output = ...  # type: Any
-    process_statistics = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def post_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/core.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/core.pyi
deleted file mode 100644
index 885df5a..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/core.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.core (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class CorePluginFormatter(formatting.JobMetricFormatter):
-    def format(self, key, value): ...
-
-class CorePlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def post_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi
deleted file mode 100644
index 00744ed..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/cpuinfo.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.cpuinfo (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class CpuInfoFormatter(formatting.JobMetricFormatter):
-    def format(self, key, value): ...
-
-class CpuInfoPlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    verbose = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/env.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/env.pyi
deleted file mode 100644
index 4113322..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/env.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.env (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class EnvFormatter(formatting.JobMetricFormatter): ...
-
-class EnvPlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    variables = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def post_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/meminfo.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/meminfo.pyi
deleted file mode 100644
index 344cfa8..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/meminfo.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.meminfo (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class MemInfoFormatter(formatting.JobMetricFormatter):
-    def format(self, key, value): ...
-
-class MemInfoPlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    verbose = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/jobs/metrics/instrumenters/uname.pyi b/typeshed/galaxy/jobs/metrics/instrumenters/uname.pyi
deleted file mode 100644
index b541bd0..0000000
--- a/typeshed/galaxy/jobs/metrics/instrumenters/uname.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.jobs.metrics.instrumenters.uname (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import formatting
-from ..instrumenters import InstrumentPlugin
-
-class UnameFormatter(formatting.JobMetricFormatter):
-    def format(self, key, value): ...
-
-class UnamePlugin(InstrumentPlugin):
-    plugin_type = ...  # type: str
-    formatter = ...  # type: Any
-    uname_args = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-    def pre_execute_instrument(self, job_directory): ...
-    def job_properties(self, job_id, job_directory): ...
diff --git a/typeshed/galaxy/objectstore/__init__.pyi b/typeshed/galaxy/objectstore/__init__.pyi
deleted file mode 100644
index 82259bc..0000000
--- a/typeshed/galaxy/objectstore/__init__.pyi
+++ /dev/null
@@ -1,80 +0,0 @@
-# Stubs for galaxy.objectstore (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-object_session = ...  # type: Any
-NO_SESSION_ERROR_MESSAGE = ...  # type: str
-log = ...  # type: Any
-
-class ObjectStore:
-    running = ...  # type: bool
-    extra_dirs = ...  # type: Any
-    config = ...  # type: Any
-    check_old_style = ...  # type: Any
-    def __init__(self, config, **kwargs) -> None: ...
-    def shutdown(self): ...
-    def exists(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ...): ...
-    def file_ready(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def create(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def empty(self, obj, base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def size(self, obj, extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def delete(self, obj, entire_dir: bool = ..., base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def get_data(self, obj, start: int = ..., count: int = ..., base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def get_filename(self, obj, base_dir: Optional[Any] = ..., dir_only: bool = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ...): ...
-    def update_from_file(self, obj, base_dir: Optional[Any] = ..., extra_dir: Optional[Any] = ..., extra_dir_at_root: bool = ..., alt_name: Optional[Any] = ..., obj_dir: bool = ..., file_name: Optional[Any] = ..., create: bool = ...): ...
-    def get_object_url(https://github.com/self,%20obj,%20extra_dir:%20Optional[Any]%20=%20...,%20extra_dir_at_root:%20bool%20=%20...,%20alt_name:%20Optional[Any]%20=%20...,%20obj_dir:%20bool%20=%20...): ...
-    def get_store_usage_percent(self): ...
-
-class DiskObjectStore(ObjectStore):
-    file_path = ...  # type: Any
-    def __init__(self, config, config_xml: Optional[Any] = ..., file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ...) -> None: ...
-    def exists(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-    def empty(self, obj, **kwargs): ...
-    def size(self, obj, **kwargs): ...
-    def delete(self, obj, entire_dir: bool = ..., **kwargs): ...
-    def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ...
-    def get_filename(self, obj, **kwargs): ...
-    def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ...
-    def get_object_url(https://github.com/self,%20obj,%20**kwargs): ...
-    def get_store_usage_percent(self): ...
-
-class NestedObjectStore(ObjectStore):
-    backends = ...  # type: Any
-    def __init__(self, config, config_xml: Optional[Any] = ...) -> None: ...
-    def shutdown(self): ...
-    def exists(self, obj, **kwargs): ...
-    def file_ready(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-    def empty(self, obj, **kwargs): ...
-    def size(self, obj, **kwargs): ...
-    def delete(self, obj, **kwargs): ...
-    def get_data(self, obj, **kwargs): ...
-    def get_filename(self, obj, **kwargs): ...
-    def update_from_file(self, obj, **kwargs): ...
-    def get_object_url(https://github.com/self,%20obj,%20**kwargs): ...
-
-class DistributedObjectStore(NestedObjectStore):
-    distributed_config = ...  # type: Any
-    backends = ...  # type: Any
-    weighted_backend_ids = ...  # type: Any
-    original_weighted_backend_ids = ...  # type: Any
-    max_percent_full = ...  # type: Any
-    global_max_percent_full = ...  # type: float
-    sleeper = ...  # type: Any
-    filesystem_monitor_thread = ...  # type: Any
-    def __init__(self, config, config_xml: Optional[Any] = ..., fsmon: bool = ...) -> None: ...
-    def shutdown(self): ...
-    def create(self, obj, **kwargs): ...
-
-class HierarchicalObjectStore(NestedObjectStore):
-    backends = ...  # type: Any
-    def __init__(self, config, config_xml: Optional[Any] = ..., fsmon: bool = ...) -> None: ...
-    def exists(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-
-def build_object_store_from_config(config, fsmon: bool = ..., config_xml: Optional[Any] = ...): ...
-def local_extra_dirs(func): ...
-def convert_bytes(bytes): ...
diff --git a/typeshed/galaxy/objectstore/azure_blob.pyi b/typeshed/galaxy/objectstore/azure_blob.pyi
deleted file mode 100644
index 89b58c1..0000000
--- a/typeshed/galaxy/objectstore/azure_blob.pyi
+++ /dev/null
@@ -1,29 +0,0 @@
-# Stubs for galaxy.objectstore.azure_blob (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..objectstore import convert_bytes as convert_bytes, ObjectStore as ObjectStore
-
-BlockBlobService = ...  # type: Any
-NO_BLOBSERVICE_ERROR_MESSAGE = ...  # type: str
-log = ...  # type: Any
-
-class AzureBlobObjectStore(ObjectStore):
-    staging_path = ...  # type: Any
-    transfer_progress = ...  # type: int
-    cache_size = ...  # type: Any
-    sleeper = ...  # type: Any
-    cache_monitor_thread = ...  # type: Any
-    def __init__(self, config, config_xml) -> None: ...
-    def exists(self, obj, **kwargs): ...
-    def file_ready(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-    def empty(self, obj, **kwargs): ...
-    def size(self, obj, **kwargs): ...
-    def delete(self, obj, entire_dir: bool = ..., **kwargs): ...
-    def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ...
-    def get_filename(self, obj, **kwargs): ...
-    def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ...
-    def get_object_url(https://github.com/self,%20obj,%20**kwargs): ...
-    def get_store_usage_percent(self): ...
diff --git a/typeshed/galaxy/objectstore/pulsar.pyi b/typeshed/galaxy/objectstore/pulsar.pyi
deleted file mode 100644
index bad1045..0000000
--- a/typeshed/galaxy/objectstore/pulsar.pyi
+++ /dev/null
@@ -1,24 +0,0 @@
-# Stubs for galaxy.objectstore.pulsar (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..objectstore import ObjectStore as ObjectStore
-
-ObjectStoreClientManager = ...  # type: Any
-
-class PulsarObjectStore(ObjectStore):
-    pulsar_client = ...  # type: Any
-    def __init__(self, config, config_xml) -> None: ...
-    def exists(self, obj, **kwds): ...
-    def file_ready(self, obj, **kwds): ...
-    def create(self, obj, **kwds): ...
-    def empty(self, obj, **kwds): ...
-    def size(self, obj, **kwds): ...
-    def delete(self, obj, **kwds): ...
-    def get_data(self, obj, **kwds): ...
-    def get_filename(self, obj, **kwds): ...
-    def update_from_file(self, obj, **kwds): ...
-    def get_store_usage_percent(self): ...
-    def get_object_url(https://github.com/self,%20obj,%20extra_dir:%20Optional[Any]%20=%20...,%20extra_dir_at_root:%20bool%20=%20...,%20alt_name:%20Optional[Any]%20=%20...): ...
-    def shutdown(self): ...
diff --git a/typeshed/galaxy/objectstore/rods.pyi b/typeshed/galaxy/objectstore/rods.pyi
deleted file mode 100644
index 125444b..0000000
--- a/typeshed/galaxy/objectstore/rods.pyi
+++ /dev/null
@@ -1,32 +0,0 @@
-# Stubs for galaxy.objectstore.rods (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from posixpath import basename as path_basename
-from posixpath import dirname as path_dirname
-from posixpath import join as path_join
-from ..objectstore import DiskObjectStore as DiskObjectStore, local_extra_dirs as local_extra_dirs
-
-irods = ...  # type: Any
-IRODS_IMPORT_MESSAGE = ...  # type: str
-log = ...  # type: Any
-
-class IRODSObjectStore(DiskObjectStore):
-    cache_path = ...  # type: Any
-    default_resource = ...  # type: Any
-    root_collection_path = ...  # type: Any
-    root_collection = ...  # type: Any
-    def __init__(self, config, file_path: Optional[Any] = ..., extra_dirs: Optional[Any] = ...) -> None: ...
-    def exists(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-    def empty(self, obj, **kwargs): ...
-    def size(self, obj, **kwargs): ...
-    def delete(self, obj, entire_dir: bool = ..., **kwargs): ...
-    def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ...
-    def get_filename(self, obj, **kwargs): ...
-    def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ...
-    def get_object_url(https://github.com/self,%20obj,%20**kwargs): ...
-    def get_store_usage_percent(self): ...
-
-def rods_connect(): ...
diff --git a/typeshed/galaxy/objectstore/s3.pyi b/typeshed/galaxy/objectstore/s3.pyi
deleted file mode 100644
index 8ffbd92..0000000
--- a/typeshed/galaxy/objectstore/s3.pyi
+++ /dev/null
@@ -1,34 +0,0 @@
-# Stubs for galaxy.objectstore.s3 (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .s3_multipart_upload import multipart_upload as multipart_upload
-from ..objectstore import convert_bytes as convert_bytes, ObjectStore as ObjectStore
-
-boto = ...  # type: Any
-NO_BOTO_ERROR_MESSAGE = ...  # type: str
-log = ...  # type: Any
-
-class S3ObjectStore(ObjectStore):
-    staging_path = ...  # type: Any
-    transfer_progress = ...  # type: int
-    bucket = ...  # type: Any
-    cache_size = ...  # type: Any
-    sleeper = ...  # type: Any
-    cache_monitor_thread = ...  # type: Any
-    use_axel = ...  # type: bool
-    def __init__(self, config, config_xml) -> None: ...
-    def file_ready(self, obj, **kwargs): ...
-    def exists(self, obj, **kwargs): ...
-    def create(self, obj, **kwargs): ...
-    def empty(self, obj, **kwargs): ...
-    def size(self, obj, **kwargs): ...
-    def delete(self, obj, entire_dir: bool = ..., **kwargs): ...
-    def get_data(self, obj, start: int = ..., count: int = ..., **kwargs): ...
-    def get_filename(self, obj, **kwargs): ...
-    def update_from_file(self, obj, file_name: Optional[Any] = ..., create: bool = ..., **kwargs): ...
-    def get_object_url(https://github.com/self,%20obj,%20**kwargs): ...
-    def get_store_usage_percent(self): ...
-
-class SwiftObjectStore(S3ObjectStore): ...
diff --git a/typeshed/galaxy/objectstore/s3_multipart_upload.pyi b/typeshed/galaxy/objectstore/s3_multipart_upload.pyi
deleted file mode 100644
index 9bf1d87..0000000
--- a/typeshed/galaxy/objectstore/s3_multipart_upload.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy.objectstore.s3_multipart_upload (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-boto = ...  # type: Any
-
-def map_wrap(f): ...
-def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): ...
-def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): ...
-def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): ...
-def multimap(cores: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/__init__.pyi b/typeshed/galaxy/tools/__init__.pyi
deleted file mode 100644
index ef883e9..0000000
--- a/typeshed/galaxy/tools/__init__.pyi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Stubs for galaxy.tools (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/galaxy/tools/cwl/__init__.pyi b/typeshed/galaxy/tools/cwl/__init__.pyi
deleted file mode 100644
index 72bc049..0000000
--- a/typeshed/galaxy/tools/cwl/__init__.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.tools.cwl (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .cwltool_deps import needs_shell_quoting as needs_shell_quoting, shellescape as shellescape
-from .parser import tool_proxy as tool_proxy, workflow_proxy as workflow_proxy
-from .representation import to_cwl_job as to_cwl_job, to_galaxy_parameters as to_galaxy_parameters
-from .runtime_actions import handle_outputs as handle_outputs
diff --git a/typeshed/galaxy/tools/cwl/cwltool_deps.pyi b/typeshed/galaxy/tools/cwl/cwltool_deps.pyi
deleted file mode 100644
index 351a420..0000000
--- a/typeshed/galaxy/tools/cwl/cwltool_deps.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for galaxy.tools.cwl.cwltool_deps (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from cwltool import main as main, workflow as workflow, process as process, pathmapper as pathmapper
-from cwltool import load_tool as load_tool
-import shellescape as shellescape
-import schema_salad as schema_salad
-from schema_salad import ref_resolver as ref_resolver
-
-main = ...  # type: Any
-workflow = ...  # type: Any
-process = ...  # type: Any
-pathmapper = ...  # type: Any
-load_tool = ...  # type: Any
-shellescape = ...  # type: Any
-schema_salad = ...  # type: Any
-ref_resolver = ...  # type: Any
-needs_shell_quoting = ...  # type: Any
-
-def ensure_cwltool_available(): ...
diff --git a/typeshed/galaxy/tools/cwl/parser.pyi b/typeshed/galaxy/tools/cwl/parser.pyi
deleted file mode 100644
index 369b146..0000000
--- a/typeshed/galaxy/tools/cwl/parser.pyi
+++ /dev/null
@@ -1,94 +0,0 @@
-# Stubs for galaxy.tools.cwl.parser (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def tool_proxy(tool_path, strict_cwl_validation: bool = ...): ...
-def load_job_proxy(job_directory, strict_cwl_validation: bool = ...): ...
-
-class ToolProxy:
-    def __init__(self, tool, tool_path) -> None: ...
-    def job_proxy(self, input_dict, output_dict, job_directory: str = ...): ...
-    def input_instances(self): ...
-    def output_instances(self): ...
-    def docker_identifier(self): ...
-    def description(self): ...
-    def label(self): ...
-
-class CommandLineToolProxy(ToolProxy):
-    def description(self): ...
-    def label(self): ...
-    def input_instances(self): ...
-    def output_instances(self): ...
-    def docker_identifier(self): ...
-
-class ExpressionToolProxy(CommandLineToolProxy): ...
-
-class JobProxy:
-    def __init__(self, tool_proxy, input_dict, output_dict, job_directory) -> None: ...
-    def cwl_job(self): ...
-    @property
-    def is_command_line_job(self): ...
-    @property
-    def command_line(self): ...
-    @property
-    def stdin(self): ...
-    @property
-    def stdout(self): ...
-    @property
-    def environment(self): ...
-    @property
-    def generate_files(self): ...
-    def collect_outputs(self, tool_working_directory): ...
-    def save_job(self): ...
-    def output_id(self, output_name): ...
-    def output_path(self, output_name): ...
-    def output_secondary_files_dir(self, output_name, create: bool = ...): ...
-    def stage_files(self): ...
-
-class WorkflowProxy:
-    def __init__(self, workflow, workflow_path) -> None: ...
-    def step_proxies(self): ...
-    @property
-    def runnables(self): ...
-    def to_dict(self): ...
-
-class StepProxy:
-    def __init__(self, workflow_proxy, step) -> None: ...
-    def to_dict(self): ...
-
-class ConditionalInstance:
-    input_type = ...  # type: Any
-    name = ...  # type: Any
-    case = ...  # type: Any
-    whens = ...  # type: Any
-    def __init__(self, name, case, whens) -> None: ...
-    def to_dict(self): ...
-
-class SelectInputInstance:
-    input_type = ...  # type: Any
-    name = ...  # type: Any
-    label = ...  # type: Any
-    description = ...  # type: Any
-    options = ...  # type: Any
-    def __init__(self, name, label, description, options) -> None: ...
-    def to_dict(self): ...
-
-class InputInstance:
-    input_type = ...  # type: Any
-    name = ...  # type: Any
-    label = ...  # type: Any
-    description = ...  # type: Any
-    required = ...  # type: bool
-    array = ...  # type: Any
-    area = ...  # type: Any
-    def __init__(self, name, label, description, input_type, array: bool = ..., area: bool = ...) -> None: ...
-    def to_dict(self, itemwise: bool = ...): ...
-
-class OutputInstance:
-    name = ...  # type: Any
-    output_data_type = ...  # type: Any
-    output_type = ...  # type: Any
-    path = ...  # type: Any
-    def __init__(self, name, output_data_type, output_type, path: Optional[Any] = ...) -> None: ...
diff --git a/typeshed/galaxy/tools/cwl/representation.pyi b/typeshed/galaxy/tools/cwl/representation.pyi
deleted file mode 100644
index ef2cc45..0000000
--- a/typeshed/galaxy/tools/cwl/representation.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for galaxy.tools.cwl.representation (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-log = ...  # type: Any
-NOT_PRESENT = ...  # type: Any
-GALAXY_TO_CWL_TYPES = ...  # type: Any
-
-def to_cwl_job(tool, param_dict, local_working_directory): ...
-def to_galaxy_parameters(tool, as_dict): ...
diff --git a/typeshed/galaxy/tools/cwl/runtime_actions.pyi b/typeshed/galaxy/tools/cwl/runtime_actions.pyi
deleted file mode 100644
index 4f1558d..0000000
--- a/typeshed/galaxy/tools/cwl/runtime_actions.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.cwl.runtime_actions (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def handle_outputs(job_directory: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/cwl/schema.pyi b/typeshed/galaxy/tools/cwl/schema.pyi
deleted file mode 100644
index 1c51ead..0000000
--- a/typeshed/galaxy/tools/cwl/schema.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for galaxy.tools.cwl.schema (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .cwltool_deps import ensure_cwltool_available as ensure_cwltool_available, load_tool as load_tool, schema_salad as schema_salad, workflow as workflow
-from collections import namedtuple
-
-RawProcessReference = namedtuple('RawProcessReference', ['process_object', 'uri'])
-
-ProcessDefinition = namedtuple('ProcessDefinition', ['process_object', 'metadata', 'document_loader', 'avsc_names', 'raw_process_reference'])
-
-class SchemaLoader:
-    def __init__(self, strict: bool = ...) -> None: ...
-    @property
-    def raw_document_loader(self): ...
-    def raw_process_reference(self, path): ...
-    def process_definition(self, raw_reference): ...
-    def tool(self, **kwds): ...
-
-schema_loader = ...  # type: Any
-non_strict_schema_loader = ...  # type: Any
diff --git a/typeshed/galaxy/tools/deps/__init__.pyi b/typeshed/galaxy/tools/deps/__init__.pyi
deleted file mode 100644
index 1df97ad..0000000
--- a/typeshed/galaxy/tools/deps/__init__.pyi
+++ /dev/null
@@ -1,41 +0,0 @@
-# Stubs for galaxy.tools.deps (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional, List
-from .requirements import ToolRequirement as ToolRequirement, ToolRequirements as ToolRequirements
-from .resolvers import NullDependency as NullDependency
-from .resolvers.conda import CondaDependencyResolver as CondaDependencyResolver
-from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver as GalaxyPackageDependencyResolver
-from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver as ToolShedPackageDependencyResolver
-
-log = ...  # type: Any
-CONFIG_VAL_NOT_FOUND = ...  # type: Any
-
-def build_dependency_manager(config: Any) -> DependencyManager: ...
-
-class NullDependencyManager:
-    dependency_resolvers = ...  # type: Any
-    def uses_tool_shed_dependencies(self): ...
-    def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ...
-    def find_dep(self, name, version: Optional[Any] = ..., type: str = ..., **kwds): ...
-
-class DependencyManager:
-    default_base_path = ...  # type: Any
-    resolver_classes = ...  # type: Any
-    dependency_resolvers = ...  # type: Any
-    def __init__(self, default_base_path, conf_file: Optional[Any] = ..., app_config: Any = ...) -> None: ...
-    def get_resolver_option(self, resolver, key, explicit_resolver_options: Any = ...): ...
-    def get_app_option(self, key, default: Optional[Any] = ...): ...
-    def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ...
-    def requirements_to_dependencies(self, requirements, **kwds): ...
-    def uses_tool_shed_dependencies(self): ...
-    def find_dep(self, name, version: Optional[Any] = ..., type: str = ..., **kwds): ...
-
-class CachedDependencyManager(DependencyManager):
-    tool_dependency_cache_dir = ...  # type: Any
-    def __init__(self, default_base_path, conf_file: Optional[Any] = ..., app_config: Any = ..., tool_dependency_cache_dir: Optional[Any] = ...) -> None: ...
-    def build_cache(self, requirements, **kwds): ...
-    def dependency_shell_commands(self, requirements: ToolRequirements, **kwds) -> List[str]: ...
-    def hash_dependencies(self, resolved_dependencies): ...
-    def get_hashed_dependencies_path(self, resolved_dependencies): ...
diff --git a/typeshed/galaxy/tools/deps/brew_exts.pyi b/typeshed/galaxy/tools/deps/brew_exts.pyi
deleted file mode 100644
index c526375..0000000
--- a/typeshed/galaxy/tools/deps/brew_exts.pyi
+++ /dev/null
@@ -1,74 +0,0 @@
-# Stubs for galaxy.tools.deps.brew_exts (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-WHITESPACE_PATTERN = ...  # type: Any
-DESCRIPTION = ...  # type: str
-DEFAULT_HOMEBREW_ROOT = ...  # type: str
-NO_BREW_ERROR_MESSAGE = ...  # type: str
-CANNOT_DETERMINE_TAP_ERROR_MESSAGE = ...  # type: str
-VERBOSE = ...  # type: bool
-RELAXED = ...  # type: bool
-BREW_ARGS = ...  # type: Any
-
-class BrewContext:
-    homebrew_prefix = ...  # type: Any
-    homebrew_cellar = ...  # type: Any
-    def __init__(self, args: Optional[Any] = ...) -> None: ...
-
-class RecipeContext:
-    @staticmethod
-    def from_args(args, brew_context: Optional[Any] = ...): ...
-    recipe = ...  # type: Any
-    version = ...  # type: Any
-    brew_context = ...  # type: Any
-    def __init__(self, recipe, version, brew_context: Optional[Any] = ...) -> None: ...
-    @property
-    def cellar_path(self): ...
-    @property
-    def tap_path(self): ...
-
-def main(): ...
-
-class CommandLineException(Exception):
-    command = ...  # type: Any
-    stdout = ...  # type: Any
-    stderr = ...  # type: Any
-    message = ...  # type: Any
-    def __init__(self, command, stdout, stderr) -> None: ...
-
-def versioned_install(recipe_context, package: Optional[Any] = ..., version: Optional[Any] = ..., installed_deps: Any = ...): ...
-def commit_for_version(recipe_context, package, version): ...
-def print_versioned_deps(recipe_context, recipe, version): ...
-def load_versioned_deps(cellar_path, relaxed: Optional[Any] = ...): ...
-def unversioned_install(package): ...
-def attempt_unlink_all(package, deps): ...
-def attempt_unlink(package): ...
-def brew_execute(args, env: Optional[Any] = ...): ...
-def build_env_statements_from_recipe_context(recipe_context, **kwds): ...
-def build_env_statements(cellar_root, cellar_path, relaxed: Optional[Any] = ..., custom_only: bool = ...): ...
-def build_env_actions(deps, cellar_root, cellar_path, relaxed: Optional[Any] = ..., custom_only: bool = ...): ...
-
-class EnvAction:
-    variable = ...  # type: Any
-    action = ...  # type: Any
-    value = ...  # type: Any
-    def __init__(self, keg_root, action_description) -> None: ...
-    @staticmethod
-    def build_env(env_actions): ...
-    def modify_environ(self, environ): ...
-    def to_statements(self): ...
-
-def brew_head_at_version(recipe_context, package, version): ...
-def brew_head_at_commit(commit, tap_path): ...
-def git_execute(args): ...
-def execute(cmds, env: Optional[Any] = ...): ...
-def brew_deps(package): ...
-def brew_info(recipe): ...
-def extended_brew_info(recipe): ...
-def brew_versions_info(package, tap_path): ...
-def recipe_cellar_path(cellar_path, recipe, version): ...
-def ensure_brew_on_path(args): ...
-def which(file): ...
diff --git a/typeshed/galaxy/tools/deps/brew_util.pyi b/typeshed/galaxy/tools/deps/brew_util.pyi
deleted file mode 100644
index c791f18..0000000
--- a/typeshed/galaxy/tools/deps/brew_util.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.tools.deps.brew_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from ..deps import brew_exts as brew_exts
-
-DEFAULT_TAP = ...  # type: str
-
-class HomebrewRecipe:
-    recipe = ...  # type: Any
-    version = ...  # type: Any
-    tap = ...  # type: Any
-    def __init__(self, recipe, version, tap) -> None: ...
-
-def requirements_to_recipes(requirements): ...
-def requirement_to_recipe(requirement): ...
-def requirements_to_recipe_contexts(requirements, brew_context): ...
diff --git a/typeshed/galaxy/tools/deps/commands.pyi b/typeshed/galaxy/tools/deps/commands.pyi
deleted file mode 100644
index a11b90d..0000000
--- a/typeshed/galaxy/tools/deps/commands.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for galaxy.tools.deps.commands (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from galaxy.util import which as which
-
-def redirecting_io(sys: Any = ...): ...
-def redirect_aware_commmunicate(p, sys: Any = ...): ...
-def shell(cmds, env: Optional[Any] = ..., **kwds): ...
-def shell_process(cmds, env: Optional[Any] = ..., **kwds): ...
-def execute(cmds): ...
-def argv_to_str(command_argv, quote: bool = ...): ...
-def download_command(url, to: Any = ..., quote_url: bool = ...): ...
-
-class CommandLineException(Exception):
-    command = ...  # type: Any
-    stdout = ...  # type: Any
-    stderr = ...  # type: Any
-    returncode = ...  # type: Any
-    message = ...  # type: Any
-    def __init__(self, command, stdout, stderr, returncode) -> None: ...
diff --git a/typeshed/galaxy/tools/deps/conda_compat.pyi b/typeshed/galaxy/tools/deps/conda_compat.pyi
deleted file mode 100644
index 0cc6382..0000000
--- a/typeshed/galaxy/tools/deps/conda_compat.pyi
+++ /dev/null
@@ -1,21 +0,0 @@
-# Stubs for galaxy.tools.deps.conda_compat (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from conda_build.metadata import MetaData as MetaData
-
-MetaData = ...  # type: Any
-
-class _Memoized:
-    func = ...  # type: Any
-    cache = ...  # type: Any
-    def __init__(self, func) -> None: ...
-    def __call__(self, *args): ...
-
-def raw_metadata(recipe_dir): ...
-
-class _MetaData:
-    meta = ...  # type: Any
-    def __init__(self, input_dir) -> None: ...
-    def get_value(self, field, default: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/deps/conda_util.pyi b/typeshed/galaxy/tools/deps/conda_util.pyi
deleted file mode 100644
index 1e418ba..0000000
--- a/typeshed/galaxy/tools/deps/conda_util.pyi
+++ /dev/null
@@ -1,69 +0,0 @@
-# Stubs for galaxy.tools.deps.conda_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-import installable
-from sys import platform as _platform
-
-class CondaContext(installable.InstallableContext):
-    installable_description = ...  # type: str
-    condarc_override = ...  # type: Any
-    conda_exec = ...  # type: Any
-    debug = ...  # type: Any
-    shell_exec = ...  # type: Any
-    copy_dependencies = ...  # type: Any
-    conda_prefix = ...  # type: Any
-    ensure_channels = ...  # type: Any
-    ensured_channels = ...  # type: bool
-    use_local = ...  # type: Any
-    def __init__(self, conda_prefix: Optional[Any] = ..., conda_exec: Optional[Any] = ..., shell_exec: Optional[Any] = ..., debug: bool = ..., ensure_channels: str = ..., condarc_override: Optional[Any] = ..., use_path_exec: Any = ..., copy_dependencies: bool = ..., use_local: Any = ...) -> None: ...
-    @property
-    def conda_version(self): ...
-    @property
-    def conda_build_available(self): ...
-    def ensure_channels_configured(self): ...
-    def ensure_conda_build_installed_if_needed(self): ...
-    def conda_info(self): ...
-    def is_conda_installed(self): ...
-    def can_install_conda(self): ...
-    def load_condarc(self): ...
-    def save_condarc(self, conf): ...
-    @property
-    def condarc(self): ...
-    def command(self, operation, args): ...
-    def exec_command(self, operation, args): ...
-    def exec_create(self, args, allow_local: bool = ...): ...
-    def exec_remove(self, args): ...
-    def exec_install(self, args, allow_local: bool = ...): ...
-    def exec_clean(self, args: Any = ..., quiet: bool = ...): ...
-    def export_list(self, name, path): ...
-    def env_path(self, env_name): ...
-    @property
-    def envs_path(self): ...
-    def has_env(self, env_name): ...
-    @property
-    def deactivate(self): ...
-    @property
-    def activate(self): ...
-    def is_installed(self): ...
-    def can_install(self): ...
-    @property
-    def parent_path(self): ...
-
-class CondaTarget:
-    package = ...  # type: Any
-    version = ...  # type: Any
-    channel = ...  # type: Any
-    def __init__(self, package, version: Optional[Any] = ..., channel: Optional[Any] = ...) -> None: ...
-    @property
-    def package_specifier(self): ...
-    @property
-    def install_environment(self): ...
-    def __hash__(self): ...
-    def __eq__(self, other): ...
-    def __ne__(self, other): ...
-
-def install_conda(conda_context: Optional[Any] = ..., force_conda_build: bool = ...): ...
-def install_conda_target(conda_target, conda_context: Optional[Any] = ..., skip_environment: bool = ...): ...
-def requirements_to_conda_targets(requirements, conda_context: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/deps/container_resolvers/__init__.pyi b/typeshed/galaxy/tools/deps/container_resolvers/__init__.pyi
deleted file mode 100644
index 4e8c822..0000000
--- a/typeshed/galaxy/tools/deps/container_resolvers/__init__.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for galaxy.tools.deps.container_resolvers (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from galaxy.util.dictifiable import Dictifiable
-
-class ContainerResolver(Dictifiable):
-    dict_collection_visible_keys = ...  # type: Any
-    app_info = ...  # type: Any
-    resolver_kwds = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., **kwds) -> None: ...
-    def resolve(self, tool_info): ...
-    def resolver_type(self): ...
diff --git a/typeshed/galaxy/tools/deps/container_resolvers/explicit.pyi b/typeshed/galaxy/tools/deps/container_resolvers/explicit.pyi
deleted file mode 100644
index 3f45f95..0000000
--- a/typeshed/galaxy/tools/deps/container_resolvers/explicit.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.tools.deps.container_resolvers.explicit (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from ..container_resolvers import ContainerResolver
-
-class ExplicitContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    def resolve(self, enabled_container_types, tool_info): ...
diff --git a/typeshed/galaxy/tools/deps/container_resolvers/mulled.pyi b/typeshed/galaxy/tools/deps/container_resolvers/mulled.pyi
deleted file mode 100644
index 5f7a6b4..0000000
--- a/typeshed/galaxy/tools/deps/container_resolvers/mulled.pyi
+++ /dev/null
@@ -1,55 +0,0 @@
-# Stubs for galaxy.tools.deps.container_resolvers.mulled (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..container_resolvers import ContainerResolver
-from collections import namedtuple
-
-CachedMulledImageSingleTarget = namedtuple('CachedMulledImageSingleTarget', ['package_name', 'version', 'build', 'image_identifier'])
-
-CachedV1MulledImageMultiTarget = namedtuple('CachedV1MulledImageMultiTarget', ['hash', 'build', 'image_identifier'])
-
-CachedV2MulledImageMultiTarget = namedtuple('CachedV2MulledImageMultiTarget', ['package_hash', 'version_hash', 'build', 'image_identifier'])
-
-class CachedMulledDockerContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    container_type = ...  # type: str
-    namespace = ...  # type: Any
-    hash_func = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., namespace: Optional[Any] = ..., hash_func: str = ...) -> None: ...
-    def resolve(self, enabled_container_types, tool_info): ...
-
-class CachedMulledSingularityContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    container_type = ...  # type: str
-    cache_directory = ...  # type: Any
-    hash_func = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., hash_func: str = ...) -> None: ...
-    def resolve(self, enabled_container_types, tool_info): ...
-
-class MulledDockerContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    container_type = ...  # type: str
-    namespace = ...  # type: Any
-    hash_func = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., namespace: str = ..., hash_func: str = ...) -> None: ...
-    def resolve(self, enabled_container_types, tool_info): ...
-
-class BuildMulledDockerContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    container_type = ...  # type: str
-    namespace = ...  # type: Any
-    hash_func = ...  # type: Any
-    auto_init = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., namespace: str = ..., hash_func: str = ..., **kwds) -> None: ...
-    def resolve(self, enabled_container_types, tool_info): ...
-
-class BuildMulledSingularityContainerResolver(ContainerResolver):
-    resolver_type = ...  # type: str
-    container_type = ...  # type: str
-    cache_directory = ...  # type: Any
-    hash_func = ...  # type: Any
-    auto_init = ...  # type: Any
-    def __init__(self, app_info: Optional[Any] = ..., hash_func: str = ..., **kwds) -> None: ...
-    def resolve(self, enabled_container_types, tool_info): ...
diff --git a/typeshed/galaxy/tools/deps/containers.pyi b/typeshed/galaxy/tools/deps/containers.pyi
deleted file mode 100644
index 5a18a63..0000000
--- a/typeshed/galaxy/tools/deps/containers.pyi
+++ /dev/null
@@ -1,99 +0,0 @@
-# Stubs for galaxy.tools.deps.containers (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .container_resolvers.explicit import ExplicitContainerResolver as ExplicitContainerResolver
-from .container_resolvers.mulled import BuildMulledDockerContainerResolver as BuildMulledDockerContainerResolver, BuildMulledSingularityContainerResolver as BuildMulledSingularityContainerResolver, CachedMulledDockerContainerResolver as CachedMulledDockerContainerResolver, CachedMulledSingularityContainerResolver as CachedMulledSingularityContainerResolver, MulledDockerContainerResolver as MulledDockerContainerResolver
-from .requirements import ContainerDescription as ContainerDescription
-from .requirements import DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES as DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES, DEFAULT_CONTAINER_SHELL as DEFAULT_CONTAINER_SHELL
-from ..deps import docker_util as docker_util
-from ..deps import singularity_util as singularity_util
-
-log = ...  # type: Any
-DOCKER_CONTAINER_TYPE = ...  # type: str
-SINGULARITY_CONTAINER_TYPE = ...  # type: str
-DEFAULT_CONTAINER_TYPE = ...  # type: Any
-ALL_CONTAINER_TYPES = ...  # type: Any
-LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = ...  # type: str
-
-class ContainerFinder:
-    app_info = ...  # type: Any
-    container_registry = ...  # type: Any
-    def __init__(self, app_info) -> None: ...
-    def find_best_container_description(self, enabled_container_types, tool_info): ...
-    def find_container(self, tool_info, destination_info, job_info): ...
-
-class NullContainerFinder:
-    def find_container(self, tool_info, destination_info, job_info): ...
-
-class ContainerRegistry:
-    resolver_classes = ...  # type: Any
-    enable_beta_mulled_containers = ...  # type: Any
-    app_info = ...  # type: Any
-    container_resolvers = ...  # type: Any
-    def __init__(self, app_info) -> None: ...
-    def find_best_container_description(self, enabled_container_types, tool_info): ...
-
-class AppInfo:
-    galaxy_root_dir = ...  # type: Any
-    default_file_path = ...  # type: Any
-    outputs_to_working_directory = ...  # type: Any
-    container_image_cache_path = ...  # type: Any
-    library_import_dir = ...  # type: Any
-    enable_beta_mulled_containers = ...  # type: Any
-    containers_resolvers_config_file = ...  # type: Any
-    involucro_path = ...  # type: Any
-    involucro_auto_init = ...  # type: Any
-    def __init__(self, galaxy_root_dir: Optional[Any] = ..., default_file_path: Optional[Any] = ..., outputs_to_working_directory: bool = ..., container_image_cache_path: Optional[Any] = ..., library_import_dir: Optional[Any] = ..., enable_beta_mulled_containers: bool = ..., containers_resolvers_config_file: Optional[Any] = ..., involucro_path: Optional[Any] = ..., involucro_auto_init: bool = ...) -> None: ...
-
-class ToolInfo:
-    container_descriptions = ...  # type: Any
-    requirements = ...  # type: Any
-    requires_galaxy_python_environment = ...  # type: Any
-    env_pass_through = ...  # type: Any
-    def __init__(self, container_descriptions: Any = ..., requirements: Any = ..., requires_galaxy_python_environment: bool = ...) -> None: ...
-
-class JobInfo:
-    working_directory = ...  # type: Any
-    job_directory = ...  # type: Any
-    tool_directory = ...  # type: Any
-    job_directory_type = ...  # type: Any
-    def __init__(self, working_directory, tool_directory, job_directory, job_directory_type) -> None: ...
-
-class Container:
-    container_id = ...  # type: Any
-    app_info = ...  # type: Any
-    tool_info = ...  # type: Any
-    destination_info = ...  # type: Any
-    job_info = ...  # type: Any
-    container_description = ...  # type: Any
-    def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description) -> None: ...
-    @property
-    def resolve_dependencies(self): ...
-    @property
-    def shell(self): ...
-    def containerize_command(self, command): ...
-
-def preprocess_volumes(volumes_raw_str, container_type): ...
-
-class HasDockerLikeVolumes: ...
-
-class DockerContainer(Container, HasDockerLikeVolumes):
-    container_type = ...  # type: Any
-    def containerize_command(self, command): ...
-
-def docker_cache_path(cache_directory, container_id): ...
-
-class SingularityContainer(Container, HasDockerLikeVolumes):
-    container_type = ...  # type: Any
-    def containerize_command(self, command): ...
-
-CONTAINER_CLASSES = ...  # type: Any
-
-class NullContainer:
-    def __init__(self) -> None: ...
-    def __bool__(self): ...
-    __nonzero__ = ...  # type: Any
-
-NULL_CONTAINER = ...  # type: Any
diff --git a/typeshed/galaxy/tools/deps/dependencies.pyi b/typeshed/galaxy/tools/deps/dependencies.pyi
deleted file mode 100644
index 04907fe..0000000
--- a/typeshed/galaxy/tools/deps/dependencies.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy.tools.deps.dependencies (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class DependenciesDescription:
-    requirements = ...  # type: Any
-    installed_tool_dependencies = ...  # type: Any
-    def __init__(self, requirements: Any = ..., installed_tool_dependencies: Any = ...) -> None: ...
-    def to_dict(self): ...
-    @staticmethod
-    def from_dict(as_dict): ...
diff --git a/typeshed/galaxy/tools/deps/docker_util.pyi b/typeshed/galaxy/tools/deps/docker_util.pyi
deleted file mode 100644
index e98b338..0000000
--- a/typeshed/galaxy/tools/deps/docker_util.pyi
+++ /dev/null
@@ -1,41 +0,0 @@
-# Stubs for galaxy.tools.deps.docker_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .commands import argv_to_str as argv_to_str
-
-DEFAULT_DOCKER_COMMAND = ...  # type: str
-DEFAULT_SUDO = ...  # type: bool
-DEFAULT_SUDO_COMMAND = ...  # type: str
-DEFAULT_HOST = ...  # type: Any
-DEFAULT_VOLUME_MOUNT_TYPE = ...  # type: str
-DEFAULT_WORKING_DIRECTORY = ...  # type: Any
-DEFAULT_NET = ...  # type: Any
-DEFAULT_MEMORY = ...  # type: Any
-DEFAULT_VOLUMES_FROM = ...  # type: Any
-DEFAULT_AUTO_REMOVE = ...  # type: bool
-DEFAULT_SET_USER = ...  # type: str
-DEFAULT_RUN_EXTRA_ARGUMENTS = ...  # type: Any
-
-class DockerVolume:
-    from_path = ...  # type: Any
-    to_path = ...  # type: Any
-    how = ...  # type: Any
-    def __init__(self, path, to_path: Optional[Any] = ..., how: Any = ...) -> None: ...
-    @staticmethod
-    def volumes_from_str(volumes_as_str): ...
-    @staticmethod
-    def volume_from_str(as_str): ...
-
-def kill_command(container, signal: Optional[Any] = ..., **kwds): ...
-def logs_command(container, **kwds): ...
-def build_command(image, docker_build_path, **kwds): ...
-def build_save_image_command(image, destination, **kwds): ...
-def build_pull_command(tag, **kwds): ...
-def build_docker_cache_command(image, **kwds): ...
-def build_docker_images_command(truncate: bool = ..., **kwds): ...
-def build_docker_load_command(**kwds): ...
-def build_docker_run_command(container_command, image, interactive: bool = ..., terminal: bool = ..., tag: Optional[Any] = ..., volumes: Any = ..., volumes_from: Any = ..., memory: Any = ..., env_directives: Any = ..., working_directory: Any = ..., name: Optional[Any] = ..., net: Any = ..., run_extra_arguments: Any = ..., docker_cmd: Any = ..., sudo: Any = ..., sudo_cmd: Any = ..., auto_rm: Any = ..., set_user: Any = ..., host: Any = ...): ...
-def command_list(command, command_args: Any = ..., **kwds): ...
-def command_shell(command, command_args: Any = ..., **kwds): ...
diff --git a/typeshed/galaxy/tools/deps/dockerfiles.pyi b/typeshed/galaxy/tools/deps/dockerfiles.pyi
deleted file mode 100644
index 3cf02d5..0000000
--- a/typeshed/galaxy/tools/deps/dockerfiles.pyi
+++ /dev/null
@@ -1,15 +0,0 @@
-# Stubs for galaxy.tools.deps.dockerfiles (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..deps import commands as commands
-from ..deps import docker_util as docker_util
-from ..deps.containers import docker_cache_path as docker_cache_path
-from ..deps.requirements import parse_requirements_from_xml as parse_requirements_from_xml
-from ...tools import loader_directory as loader_directory
-
-log = ...  # type: Any
-
-def docker_host_args(**kwds): ...
-def dockerfile_build(path, dockerfile: Optional[Any] = ..., error: Any = ..., **kwds): ...
diff --git a/typeshed/galaxy/tools/deps/installable.pyi b/typeshed/galaxy/tools/deps/installable.pyi
deleted file mode 100644
index 818eaa2..0000000
--- a/typeshed/galaxy/tools/deps/installable.pyi
+++ /dev/null
@@ -1,15 +0,0 @@
-# Stubs for galaxy.tools.deps.installable (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-log = ...  # type: Any
-
-class InstallableContext:
-    def is_installed(self): ...
-    def can_install(self): ...
-    def installable_description(self): ...
-    def parent_path(self): ...
-
-def ensure_installed(installable_context, install_func, auto_init): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/__init__.pyi b/typeshed/galaxy/tools/deps/mulled/__init__.pyi
deleted file mode 100644
index a3f6bf3..0000000
--- a/typeshed/galaxy/tools/deps/mulled/__init__.pyi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/galaxy/tools/deps/mulled/_cli.pyi b/typeshed/galaxy/tools/deps/mulled/_cli.pyi
deleted file mode 100644
index db35991..0000000
--- a/typeshed/galaxy/tools/deps/mulled/_cli.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled._cli (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def arg_parser(argv, globals): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/mulled_build.pyi b/typeshed/galaxy/tools/deps/mulled/mulled_build.pyi
deleted file mode 100644
index 2565050..0000000
--- a/typeshed/galaxy/tools/deps/mulled/mulled_build.pyi
+++ /dev/null
@@ -1,24 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.mulled_build (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-import installable
-from sys import platform as _platform
-
-class BuildExistsException(Exception): ...
-
-class InvolucroContext(installable.InstallableContext):
-    installable_description = ...  # type: str
-    involucro_bin = ...  # type: str
-    shell_exec = ...  # type: Any
-    verbose = ...  # type: Any
-    def __init__(self, involucro_bin: Optional[Any] = ..., shell_exec: Optional[Any] = ..., verbose: str = ...) -> None: ...
-    def build_command(self, involucro_args): ...
-    def exec_command(self, involucro_args): ...
-    def is_installed(self): ...
-    def can_install(self): ...
-    @property
-    def parent_path(self): ...
-
-def main(argv: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/mulled_build_channel.pyi b/typeshed/galaxy/tools/deps/mulled/mulled_build_channel.pyi
deleted file mode 100644
index c0039bf..0000000
--- a/typeshed/galaxy/tools/deps/mulled/mulled_build_channel.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.mulled_build_channel (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def main(argv: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/mulled_build_files.pyi b/typeshed/galaxy/tools/deps/mulled/mulled_build_files.pyi
deleted file mode 100644
index 0057d4d..0000000
--- a/typeshed/galaxy/tools/deps/mulled/mulled_build_files.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.mulled_build_files (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from collections import namedtuple
-
-def main(argv: Optional[Any] = ...): ...
-
-_Line = namedtuple('_Line', ['targets', 'image_build', 'name_override'])
diff --git a/typeshed/galaxy/tools/deps/mulled/mulled_build_tool.pyi b/typeshed/galaxy/tools/deps/mulled/mulled_build_tool.pyi
deleted file mode 100644
index e4af0da..0000000
--- a/typeshed/galaxy/tools/deps/mulled/mulled_build_tool.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.mulled_build_tool (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def main(argv: Optional[Any] = ...): ...
-def requirements_to_mulled_targets(requirements): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/mulled_search.pyi b/typeshed/galaxy/tools/deps/mulled/mulled_search.pyi
deleted file mode 100644
index 9c8e9c2..0000000
--- a/typeshed/galaxy/tools/deps/mulled/mulled_search.pyi
+++ /dev/null
@@ -1,23 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.mulled_search (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-requests = ...  # type: Any
-Schema = ...  # type: Any
-TEXT = ...  # type: Any
-STORED = ...  # type: Any
-create_in = ...  # type: Any
-QueryParser = ...  # type: Any
-QUAY_API_URL = ...  # type: str
-
-class QuaySearch:
-    index = ...  # type: Any
-    organization = ...  # type: Any
-    def __init__(self, organization) -> None: ...
-    def build_index(self): ...
-    def search_repository(self, search_string, non_strict): ...
-    def get_additional_repository_information(self, repository_string): ...
-
-def main(argv: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/deps/mulled/util.pyi b/typeshed/galaxy/tools/deps/mulled/util.pyi
deleted file mode 100644
index 33063c2..0000000
--- a/typeshed/galaxy/tools/deps/mulled/util.pyi
+++ /dev/null
@@ -1,23 +0,0 @@
-# Stubs for galaxy.tools.deps.mulled.util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from collections import namedtuple
-
-def quay_versions(namespace, pkg_name): ...
-def mulled_tags_for(namespace, image, tag_prefix: Optional[Any] = ...): ...
-def split_tag(tag): ...
-def version_sorted(elements): ...
-
-Target = namedtuple('Target', ['package_name', 'version', 'build'])
-
-def build_target(package_name, version: Optional[Any] = ..., build: Optional[Any] = ..., tag: Optional[Any] = ...): ...
-def conda_build_target_str(target): ...
-def v1_image_name(targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ...): ...
-def v2_image_name(targets, image_build: Optional[Any] = ..., name_override: Optional[Any] = ...): ...
-
-image_name = ...  # type: Any
-
-# Names in __all__ with no definition:
-#   Target
diff --git a/typeshed/galaxy/tools/deps/requirements.pyi b/typeshed/galaxy/tools/deps/requirements.pyi
deleted file mode 100644
index 9cb78c3..0000000
--- a/typeshed/galaxy/tools/deps/requirements.pyi
+++ /dev/null
@@ -1,75 +0,0 @@
-# Stubs for galaxy.tools.deps.requirements (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Dict, List, Optional
-
-DEFAULT_REQUIREMENT_TYPE = ...  # type: str
-DEFAULT_REQUIREMENT_VERSION = ...  # type: Any
-
-class ToolRequirement:
-    name = ...  # type: Any
-    type = ...  # type: Any
-    version = ...  # type: Any
-    specs = ...  # type: Any
-    def __init__(self, name: Optional[Any] = ..., type: Optional[Any] = ..., version: Optional[Any] = ..., specs: Any = ...) -> None: ...
-    def to_dict(self) -> Dict[str, Any]: ...
-    def copy(self): ...
-    @staticmethod
-    def from_dict(dict: Dict[str, Any]) -> ToolRequirement: ...
-    def __eq__(self, other): ...
-    def __ne__(self, other): ...
-    def __hash__(self): ...
-
-class RequirementSpecification:
-    uri = ...  # type: Any
-    version = ...  # type: Any
-    def __init__(self, uri, version: Optional[Any] = ...) -> None: ...
-    @property
-    def specifies_version(self): ...
-    @property
-    def short_name(self): ...
-    def to_dict(self): ...
-    @staticmethod
-    def from_dict(dict: Dict[str, Any]) -> ToolRequirements: ...
-    def __eq__(self, other): ...
-    def __ne__(self, other): ...
-    def __hash__(self): ...
-
-class ToolRequirements:
-    tool_requirements = ...  # type: Any
-    def __init__(self, tool_requirements: Optional[Any] = ...) -> None: ...
-    @staticmethod
-    def from_list(requirements: List[ToolRequirement]) -> ToolRequirements: ...
-    @property
-    def resolvable(self): ...
-    @property
-    def packages(self): ...
-    def to_list(self) -> List[ToolRequirement]: ...
-    def append(self, requirement): ...
-    def __eq__(self, other): ...
-    def __ne__(self, other): ...
-    def __iter__(self): ...
-    def __getitem__(self, ii): ...
-    def __len__(self): ...
-    def __hash__(self): ...
-
-class ToolRequirementsException(Exception): ...
-
-DEFAULT_CONTAINER_TYPE = ...  # type: str
-DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES = ...  # type: bool
-DEFAULT_CONTAINER_SHELL = ...  # type: str
-
-class ContainerDescription:
-    identifier = ...  # type: Any
-    type = ...  # type: Any
-    resolve_dependencies = ...  # type: Any
-    shell = ...  # type: Any
-    def __init__(self, identifier: Optional[Any] = ..., type: Any = ..., resolve_dependencies: Any = ..., shell: Any = ...) -> None: ...
-    def to_dict(self): ...
-    @staticmethod
-    def from_dict(dict): ...
-
-def parse_requirements_from_dict(root_dict): ...
-def parse_requirements_from_xml(xml_root): ...
-def container_from_element(container_elem): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/__init__.pyi b/typeshed/galaxy/tools/deps/resolvers/__init__.pyi
deleted file mode 100644
index a1ffb20..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/__init__.pyi
+++ /dev/null
@@ -1,62 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from galaxy.util.dictifiable import Dictifiable
-from ..requirements import ToolRequirement as ToolRequirement
-
-class DependencyResolver(Dictifiable):
-    dict_collection_visible_keys = ...  # type: Any
-    disabled = ...  # type: bool
-    resolves_simple_dependencies = ...  # type: bool
-    can_uninstall_dependencies = ...  # type: bool
-    config_options = ...  # type: Any
-    def resolve(self, requirement, **kwds): ...
-
-class MultipleDependencyResolver:
-    def resolve_all(self, requirements, **kwds): ...
-
-class ListableDependencyResolver:
-    def list_dependencies(self): ...
-
-class MappableDependencyResolver: ...
-
-FROM_UNVERSIONED = ...  # type: Any
-
-class RequirementMapping:
-    from_name = ...  # type: Any
-    from_version = ...  # type: Any
-    to_name = ...  # type: Any
-    to_version = ...  # type: Any
-    def __init__(self, from_name, from_version, to_name, to_version) -> None: ...
-    def matches_requirement(self, requirement): ...
-    def apply(self, requirement): ...
-    @staticmethod
-    def from_dict(raw_mapping): ...
-
-class SpecificationAwareDependencyResolver: ...
-class SpecificationPatternDependencyResolver: ...
-
-class InstallableDependencyResolver:
-    def install_dependency(self, name, version, type, **kwds): ...
-
-class Dependency(Dictifiable):
-    dict_collection_visible_keys = ...  # type: Any
-    cacheable = ...  # type: bool
-    def shell_commands(self, requirement): ...
-    def exact(self): ...
-    @property
-    def resolver_msg(self): ...
-
-class NullDependency(Dependency):
-    dependency_type = ...  # type: Any
-    exact = ...  # type: bool
-    version = ...  # type: Any
-    name = ...  # type: Any
-    def __init__(self, version: Optional[Any] = ..., name: Optional[Any] = ...) -> None: ...
-    @property
-    def resolver_msg(self): ...
-    def shell_commands(self, requirement): ...
-
-class DependencyException(Exception): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.pyi b/typeshed/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.pyi
deleted file mode 100644
index d581de3..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.pyi
+++ /dev/null
@@ -1,33 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.brewed_tool_shed_packages (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from xml.etree import ElementTree as ET
-from .resolver_mixins import UsesHomebrewMixin, UsesInstalledRepositoriesMixin, UsesToolDependencyDirMixin
-from ..resolvers import DependencyResolver
-
-class HomebrewToolShedDependencyResolver(DependencyResolver, UsesHomebrewMixin, UsesToolDependencyDirMixin, UsesInstalledRepositoriesMixin):
-    resolver_type = ...  # type: str
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def resolve(self, requirement, **kwds): ...
-
-class RawDependencies:
-    root = ...  # type: Any
-    dependencies = ...  # type: Any
-    def __init__(self, dependencies_file) -> None: ...
-    def find(self, package_name, package_version): ...
-
-class RawDependency:
-    dependencies = ...  # type: Any
-    package_el = ...  # type: Any
-    repository_el = ...  # type: Any
-    def __init__(self, dependencies, package_el, repository_el) -> None: ...
-    @property
-    def repository_owner(self): ...
-    @property
-    def repository_name(self): ...
-    @property
-    def package_name(self): ...
-    @property
-    def package_version(self): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/conda.pyi b/typeshed/galaxy/tools/deps/resolvers/conda.pyi
deleted file mode 100644
index 333954d..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/conda.pyi
+++ /dev/null
@@ -1,72 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.conda (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..resolvers import Dependency, DependencyResolver, InstallableDependencyResolver, ListableDependencyResolver, MappableDependencyResolver, MultipleDependencyResolver, SpecificationPatternDependencyResolver
-
-DEFAULT_ENSURE_CHANNELS = ...  # type: str
-
-class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = ...  # type: Any
-    resolver_type = ...  # type: str
-    config_options = ...  # type: Any
-    can_uninstall_dependencies = ...  # type: bool
-    versionless = ...  # type: Any
-    dependency_manager = ...  # type: Any
-    conda_prefix_parent = ...  # type: Any
-    ensure_channels = ...  # type: Any
-    auto_init = ...  # type: Any
-    conda_context = ...  # type: Any
-    disabled = ...  # type: Any
-    auto_install = ...  # type: Any
-    copy_dependencies = ...  # type: Any
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def clean(self, **kwds): ...
-    def uninstall(self, requirements): ...
-    def uninstall_environments(self, environments): ...
-    def install_all(self, conda_targets): ...
-    def resolve_all(self, requirements, **kwds): ...
-    def merged_environment_name(self, conda_targets): ...
-    def resolve(self, requirement, **kwds): ...
-    def unused_dependency_paths(self, toolbox_requirements_status): ...
-    def list_dependencies(self): ...
-    def install_dependency(self, name, version, type, **kwds): ...
-    @property
-    def prefix(self): ...
-
-class MergedCondaDependency(Dependency):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: str
-    activate = ...  # type: Any
-    conda_context = ...  # type: Any
-    environment_path = ...  # type: Any
-    cache_path = ...  # type: Any
-    def __init__(self, conda_context, environment_path, exact, name: Optional[Any] = ..., version: Optional[Any] = ..., preserve_python_environment: bool = ...) -> None: ...
-    @property
-    def exact(self): ...
-    @property
-    def name(self): ...
-    @property
-    def version(self): ...
-    def shell_commands(self, requirement): ...
-
-class CondaDependency(Dependency):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: str
-    cacheable = ...  # type: bool
-    activate = ...  # type: Any
-    conda_context = ...  # type: Any
-    environment_path = ...  # type: Any
-    cache_path = ...  # type: Any
-    def __init__(self, conda_context, environment_path, exact, name: Optional[Any] = ..., version: Optional[Any] = ..., preserve_python_environment: bool = ...) -> None: ...
-    @property
-    def exact(self): ...
-    @property
-    def name(self): ...
-    @property
-    def version(self): ...
-    def build_cache(self, cache_path): ...
-    def set_cache_path(self, cache_path): ...
-    def build_environment(self): ...
-    def shell_commands(self, requirement): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/galaxy_packages.pyi b/typeshed/galaxy/tools/deps/resolvers/galaxy_packages.pyi
deleted file mode 100644
index cb4551f..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/galaxy_packages.pyi
+++ /dev/null
@@ -1,35 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.galaxy_packages (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .resolver_mixins import UsesToolDependencyDirMixin
-from ..resolvers import Dependency, DependencyResolver, ListableDependencyResolver, MappableDependencyResolver
-
-class GalaxyPackageDependency(Dependency):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: str
-    script = ...  # type: Any
-    path = ...  # type: Any
-    version = ...  # type: Any
-    name = ...  # type: Any
-    def __init__(self, script, path, version, name, exact: bool = ...) -> None: ...
-    @property
-    def exact(self): ...
-    def shell_commands(self, requirement): ...
-
-class ToolShedDependency(GalaxyPackageDependency):
-    dependency_type = ...  # type: str
-
-class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependencyDirMixin):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: Any
-    versionless = ...  # type: Any
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def resolve(self, requirement, **kwds): ...
-
-class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver):
-    resolver_type = ...  # type: str
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def resolve(self, requirement, **kwds): ...
-    def list_dependencies(self): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/homebrew.pyi b/typeshed/galaxy/tools/deps/resolvers/homebrew.pyi
deleted file mode 100644
index 7896173..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/homebrew.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.homebrew (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .resolver_mixins import UsesHomebrewMixin
-from ..resolvers import DependencyResolver
-
-class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin):
-    resolver_type = ...  # type: str
-    versionless = ...  # type: Any
-    prefer_version = ...  # type: Any
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def resolve(self, requirement, **kwds): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/modules.pyi b/typeshed/galaxy/tools/deps/resolvers/modules.pyi
deleted file mode 100644
index 5762d95..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/modules.pyi
+++ /dev/null
@@ -1,42 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.modules (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from ..resolvers import Dependency, DependencyResolver, MappableDependencyResolver
-
-class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver):
-    dict_collection_visible_keys = ...  # type: Any
-    resolver_type = ...  # type: str
-    versionless = ...  # type: Any
-    modulecmd = ...  # type: Any
-    modulepath = ...  # type: Any
-    default_indicator = ...  # type: Any
-    module_checker = ...  # type: Any
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-    def resolve(self, requirement, **kwds): ...
-
-class DirectoryModuleChecker:
-    module_dependency_resolver = ...  # type: Any
-    directories = ...  # type: Any
-    def __init__(self, module_dependency_resolver, modulepath, prefetch) -> None: ...
-    def has_module(self, module, version): ...
-
-class AvailModuleChecker:
-    module_dependency_resolver = ...  # type: Any
-    modulepath = ...  # type: Any
-    default_indicator = ...  # type: Any
-    prefetched_modules = ...  # type: Any
-    def __init__(self, module_dependency_resolver, modulepath, prefetch, default_indicator: Any = ...) -> None: ...
-    def has_module(self, module, version): ...
-
-class ModuleDependency(Dependency):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: str
-    module_dependency_resolver = ...  # type: Any
-    module_name = ...  # type: Any
-    module_version = ...  # type: Any
-    def __init__(self, module_dependency_resolver, module_name, module_version: Optional[Any] = ..., exact: bool = ...) -> None: ...
-    @property
-    def exact(self): ...
-    def shell_commands(self, requirement): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/resolver_mixins.pyi b/typeshed/galaxy/tools/deps/resolvers/resolver_mixins.pyi
deleted file mode 100644
index 2b90a98..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/resolver_mixins.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.resolver_mixins (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from ..brew_exts import build_env_statements as build_env_statements, DEFAULT_HOMEBREW_ROOT as DEFAULT_HOMEBREW_ROOT, recipe_cellar_path as recipe_cellar_path
-from ..resolvers import Dependency as Dependency, NullDependency as NullDependency
-
-class UsesHomebrewMixin: ...
-class UsesToolDependencyDirMixin: ...
-class UsesInstalledRepositoriesMixin: ...
-
-class HomebrewDependency(Dependency):
-    commands = ...  # type: Any
-    def __init__(self, commands, exact: bool = ...) -> None: ...
-    @property
-    def exact(self): ...
-    def shell_commands(self, requirement): ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/tool_shed_packages.pyi b/typeshed/galaxy/tools/deps/resolvers/tool_shed_packages.pyi
deleted file mode 100644
index 224d377..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/tool_shed_packages.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.tool_shed_packages (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .galaxy_packages import BaseGalaxyPackageDependencyResolver
-from .resolver_mixins import UsesInstalledRepositoriesMixin
-
-class ToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, UsesInstalledRepositoriesMixin):
-    resolver_type = ...  # type: str
-    dependency_type = ...  # type: Any
-    resolves_simple_dependencies = ...  # type: bool
-    def __init__(self, dependency_manager, **kwds) -> None: ...
diff --git a/typeshed/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.pyi b/typeshed/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.pyi
deleted file mode 100644
index ddf2ee0..0000000
--- a/typeshed/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.pyi
+++ /dev/null
@@ -1,25 +0,0 @@
-# Stubs for galaxy.tools.deps.resolvers.unlinked_tool_shed_packages (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .galaxy_packages import BaseGalaxyPackageDependencyResolver
-from ..resolvers import Dependency
-
-class UnlinkedToolShedPackageDependencyResolver(BaseGalaxyPackageDependencyResolver):
-    dict_collection_visible_keys = ...  # type: Any
-    resolver_type = ...  # type: str
-    preferred_owners = ...  # type: Any
-    select_by_owner = ...  # type: Any
-    def __init__(self, dependency_manager, **kwds) -> None: ...
-
-class CandidateDependency(Dependency):
-    dict_collection_visible_keys = ...  # type: Any
-    dependency_type = ...  # type: str
-    @property
-    def exact(self): ...
-    dependency = ...  # type: Any
-    path = ...  # type: Any
-    owner = ...  # type: Any
-    def __init__(self, dependency, path, owner: Any = ...) -> None: ...
-    def shell_commands(self, requirement): ...
diff --git a/typeshed/galaxy/tools/deps/singularity_util.pyi b/typeshed/galaxy/tools/deps/singularity_util.pyi
deleted file mode 100644
index a701d1f..0000000
--- a/typeshed/galaxy/tools/deps/singularity_util.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.deps.singularity_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-def build_singularity_run_command(container_command, image, volumes: Any = ..., env: Any = ..., working_directory: Any = ..., singularity_cmd: Any = ..., run_extra_arguments: Any = ..., sudo: Any = ..., sudo_cmd: Any = ...): ...
diff --git a/typeshed/galaxy/tools/deps/views.pyi b/typeshed/galaxy/tools/deps/views.pyi
deleted file mode 100644
index 2f57990..0000000
--- a/typeshed/galaxy/tools/deps/views.pyi
+++ /dev/null
@@ -1,32 +0,0 @@
-# Stubs for galaxy.tools.deps.views (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-class DependencyResolversView:
-    def __init__(self, app) -> None: ...
-    def index(self): ...
-    def show(self, index): ...
-    def reload(self): ...
-    def manager_requirements(self): ...
-    def resolver_requirements(self, index): ...
-    def manager_dependency(self, **kwds): ...
-    def resolver_dependency(self, index, **kwds): ...
-    def show_dependencies(self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ...): ...
-    def uninstall_dependencies(self, index: Optional[Any] = ..., **payload): ...
-    @property
-    def unused_dependency_paths(self): ...
-    def remove_unused_dependency_paths(self, envs): ...
-    def install_dependencies(self, requirements): ...
-    def install_dependency(self, index: Optional[Any] = ..., **payload): ...
-    @property
-    def installable_resolvers(self): ...
-    @property
-    def uninstallable_resolvers(self): ...
-    @property
-    def tool_ids_by_requirements(self): ...
-    @property
-    def toolbox_requirements_status(self): ...
-    def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies: Optional[Any] = ...): ...
-    def clean(self, index: Optional[Any] = ..., **kwds): ...
diff --git a/typeshed/galaxy/tools/fetcher.pyi b/typeshed/galaxy/tools/fetcher.pyi
deleted file mode 100644
index 221bc58..0000000
--- a/typeshed/galaxy/tools/fetcher.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for galaxy.tools.fetcher (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class ToolLocationFetcher:
-    resolver_classes = ...  # type: Any
-    def __init__(self) -> None: ...
-    def to_tool_path(self, path_or_uri_like, **kwds): ...
diff --git a/typeshed/galaxy/tools/lint.pyi b/typeshed/galaxy/tools/lint.pyi
deleted file mode 100644
index 9cd7a26..0000000
--- a/typeshed/galaxy/tools/lint.pyi
+++ /dev/null
@@ -1,33 +0,0 @@
-# Stubs for galaxy.tools.lint (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .parser import get_tool_source as get_tool_source
-
-LEVEL_ALL = ...  # type: str
-LEVEL_WARN = ...  # type: str
-LEVEL_ERROR = ...  # type: str
-
-def lint_tool_source(tool_source, level: Any = ..., fail_level: Any = ..., extra_modules: Any = ..., skip_types: Any = ...): ...
-def lint_xml(tool_xml, level: Any = ..., fail_level: Any = ..., extra_modules: Any = ..., skip_types: Any = ...): ...
-def lint_tool_source_with(lint_context, tool_source, extra_modules: Any = ...): ...
-def lint_xml_with(lint_context, tool_xml, extra_modules: Any = ...): ...
-
-class LintContext:
-    skip_types = ...  # type: Any
-    level = ...  # type: Any
-    found_errors = ...  # type: bool
-    found_warns = ...  # type: bool
-    def __init__(self, level, skip_types: Any = ...) -> None: ...
-    printed_linter_info = ...  # type: bool
-    valid_messages = ...  # type: Any
-    info_messages = ...  # type: Any
-    warn_messages = ...  # type: Any
-    error_messages = ...  # type: Any
-    def lint(self, name, lint_func, lint_target): ...
-    def valid(self, message, *args): ...
-    def info(self, message, *args): ...
-    def error(self, message, *args): ...
-    def warn(self, message, *args): ...
-    def failed(self, fail_level): ...
diff --git a/typeshed/galaxy/tools/lint_util.pyi b/typeshed/galaxy/tools/lint_util.pyi
deleted file mode 100644
index e1e1ac0..0000000
--- a/typeshed/galaxy/tools/lint_util.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for galaxy.tools.lint_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def is_datasource(tool_xml): ...
diff --git a/typeshed/galaxy/tools/linters/__init__.pyi b/typeshed/galaxy/tools/linters/__init__.pyi
deleted file mode 100644
index 7f56312..0000000
--- a/typeshed/galaxy/tools/linters/__init__.pyi
+++ /dev/null
@@ -1,4 +0,0 @@
-# Stubs for galaxy.tools.linters (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
diff --git a/typeshed/galaxy/tools/linters/citations.pyi b/typeshed/galaxy/tools/linters/citations.pyi
deleted file mode 100644
index 5378b8d..0000000
--- a/typeshed/galaxy/tools/linters/citations.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for galaxy.tools.linters.citations (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def lint_citations(tool_xml, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/command.pyi b/typeshed/galaxy/tools/linters/command.pyi
deleted file mode 100644
index 2e68635..0000000
--- a/typeshed/galaxy/tools/linters/command.pyi
+++ /dev/null
@@ -1,6 +0,0 @@
-# Stubs for galaxy.tools.linters.command (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def lint_command(tool_xml, lint_ctx): ...
-def get_command(tool_xml): ...
diff --git a/typeshed/galaxy/tools/linters/cwl.pyi b/typeshed/galaxy/tools/linters/cwl.pyi
deleted file mode 100644
index a94292e..0000000
--- a/typeshed/galaxy/tools/linters/cwl.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for galaxy.tools.linters.cwl (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-lint_tool_types = ...  # type: Any
-
-def lint_cwl_validation(tool_source, lint_ctx): ...
-def lint_new_draft(tool_source, lint_ctx): ...
-def lint_docker_image(tool_source, lint_ctx): ...
-def lint_description(tool_source, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/general.pyi b/typeshed/galaxy/tools/linters/general.pyi
deleted file mode 100644
index 812e6e9..0000000
--- a/typeshed/galaxy/tools/linters/general.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for galaxy.tools.linters.general (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-ERROR_VERSION_MSG = ...  # type: str
-VALID_VERSION_MSG = ...  # type: str
-ERROR_NAME_MSG = ...  # type: str
-VALID_NAME_MSG = ...  # type: str
-ERROR_ID_MSG = ...  # type: str
-VALID_ID_MSG = ...  # type: str
-PROFILE_PATTERN = ...  # type: Any
-PROFILE_INFO_DEFAULT_MSG = ...  # type: str
-PROFILE_INFO_SPECIFIED_MSG = ...  # type: str
-PROFILE_INVALID_MSG = ...  # type: str
-lint_tool_types = ...  # type: Any
-
-def lint_general(tool_source, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/help.pyi b/typeshed/galaxy/tools/linters/help.pyi
deleted file mode 100644
index 306fa3b..0000000
--- a/typeshed/galaxy/tools/linters/help.pyi
+++ /dev/null
@@ -1,6 +0,0 @@
-# Stubs for galaxy.tools.linters.help (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def lint_help(tool_xml, lint_ctx): ...
-def rst_invalid(text): ...
diff --git a/typeshed/galaxy/tools/linters/inputs.pyi b/typeshed/galaxy/tools/linters/inputs.pyi
deleted file mode 100644
index c06f46c..0000000
--- a/typeshed/galaxy/tools/linters/inputs.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.tools.linters.inputs (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from ..lint_util import is_datasource as is_datasource
-
-def lint_inputs(tool_xml, lint_ctx): ...
-def lint_repeats(tool_xml, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/outputs.pyi b/typeshed/galaxy/tools/linters/outputs.pyi
deleted file mode 100644
index ecb9220..0000000
--- a/typeshed/galaxy/tools/linters/outputs.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for galaxy.tools.linters.outputs (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def lint_output(tool_xml, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/stdio.pyi b/typeshed/galaxy/tools/linters/stdio.pyi
deleted file mode 100644
index d7c2927..0000000
--- a/typeshed/galaxy/tools/linters/stdio.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.linters.stdio (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .command import get_command as get_command
-
-def lint_stdio(tool_source, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/tests.pyi b/typeshed/galaxy/tools/linters/tests.pyi
deleted file mode 100644
index d9c7cf0..0000000
--- a/typeshed/galaxy/tools/linters/tests.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.linters.tests (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from ..lint_util import is_datasource as is_datasource
-
-def lint_tsts(tool_xml, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/linters/xml_order.pyi b/typeshed/galaxy/tools/linters/xml_order.pyi
deleted file mode 100644
index a3904f6..0000000
--- a/typeshed/galaxy/tools/linters/xml_order.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for galaxy.tools.linters.xml_order (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-TAG_ORDER = ...  # type: Any
-DATASOURCE_TAG_ORDER = ...  # type: Any
-
-def lint_xml_order(tool_xml, lint_ctx): ...
diff --git a/typeshed/galaxy/tools/loader.pyi b/typeshed/galaxy/tools/loader.pyi
deleted file mode 100644
index 4e7cd7f..0000000
--- a/typeshed/galaxy/tools/loader.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.tools.loader (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from galaxy.util.xml_macros import imported_macro_paths as imported_macro_paths, raw_tool_xml_tree as raw_tool_xml_tree, template_macro_params as template_macro_params
-
-load_tool = ...  # type: Any
diff --git a/typeshed/galaxy/tools/loader_directory.pyi b/typeshed/galaxy/tools/loader_directory.pyi
deleted file mode 100644
index 628289f..0000000
--- a/typeshed/galaxy/tools/loader_directory.pyi
+++ /dev/null
@@ -1,15 +0,0 @@
-# Stubs for galaxy.tools.loader_directory (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def find_possible_tools_from_path(path, recursive: bool = ..., enable_beta_formats: bool = ...): ...
-def load_tool_sources_from_path(path, load_exception_handler: Any = ..., recursive: bool = ..., register_load_errors: bool = ...): ...
-def load_tool_elements_from_path(path, load_exception_handler: Any = ..., recursive: bool = ..., register_load_errors: bool = ...): ...
-def is_tool_load_error(obj): ...
-def looks_like_a_tool_xml(path): ...
-def is_a_yaml_with_class(path, classes): ...
-def looks_like_a_tool_yaml(path): ...
-def looks_like_a_cwl_artifact(path, classes: Optional[Any] = ...): ...
-def looks_like_a_tool_cwl(path): ...
diff --git a/typeshed/galaxy/tools/locations/__init__.pyi b/typeshed/galaxy/tools/locations/__init__.pyi
deleted file mode 100644
index af99abd..0000000
--- a/typeshed/galaxy/tools/locations/__init__.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.locations (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-class ToolLocationResolver:
-    def scheme(self): ...
-    def get_tool_source_path(self, uri_like): ...
diff --git a/typeshed/galaxy/tools/locations/dockstore.pyi b/typeshed/galaxy/tools/locations/dockstore.pyi
deleted file mode 100644
index 3420e1e..0000000
--- a/typeshed/galaxy/tools/locations/dockstore.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for galaxy.tools.locations.dockstore (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from ..locations import ToolLocationResolver
-
-class DockStoreResolver(ToolLocationResolver):
-    scheme = ...  # type: str
-    def get_tool_source_path(self, uri_like): ...
-
-class _Ga4ghToolClient:
-    base_url = ...  # type: Any
-    def __init__(self, base_url: str = ...) -> None: ...
-    def get_tools(self): ...
-    def get_tool(self, tool_id): ...
-    def get_tool_version(self, tool_id, version: str = ...): ...
-    def get_tool_descriptor(self, tool_id, version: str = ..., tool_type: str = ...): ...
-    def get_tool_cwl(self, tool_id, version: str = ..., as_string: bool = ...): ...
diff --git a/typeshed/galaxy/tools/locations/file.pyi b/typeshed/galaxy/tools/locations/file.pyi
deleted file mode 100644
index 8268d65..0000000
--- a/typeshed/galaxy/tools/locations/file.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.tools.locations.file (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from ..locations import ToolLocationResolver as ToolLocationResolver
-
-class HttpToolResolver(ToolLocationResolver):
-    scheme = ...  # type: str
-    def get_tool_source_path(self, uri_like): ...
diff --git a/typeshed/galaxy/tools/locations/http.pyi b/typeshed/galaxy/tools/locations/http.pyi
deleted file mode 100644
index 2687afc..0000000
--- a/typeshed/galaxy/tools/locations/http.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy.tools.locations.http (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from ..locations import ToolLocationResolver
-
-class HttpToolResolver(ToolLocationResolver):
-    scheme = ...  # type: str
-    def __init__(self, **kwds) -> None: ...
-    def get_tool_source_path(self, uri_like): ...
-
-class HttpsToolResolver(HttpToolResolver):
-    scheme = ...  # type: str
diff --git a/typeshed/galaxy/tools/parser/__init__.pyi b/typeshed/galaxy/tools/parser/__init__.pyi
deleted file mode 100644
index 0b1bc81..0000000
--- a/typeshed/galaxy/tools/parser/__init__.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.tools.parser (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .factory import get_input_source as get_input_source, get_tool_source as get_tool_source
-from .interface import ToolSource as ToolSource
-from .output_objects import ToolOutputCollectionPart as ToolOutputCollectionPart
diff --git a/typeshed/galaxy/tools/parser/cwl.pyi b/typeshed/galaxy/tools/parser/cwl.pyi
deleted file mode 100644
index 1b754a9..0000000
--- a/typeshed/galaxy/tools/parser/cwl.pyi
+++ /dev/null
@@ -1,41 +0,0 @@
-# Stubs for galaxy.tools.parser.cwl (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from .interface import PageSource as PageSource
-from .interface import PagesSource as PagesSource
-from .interface import ToolSource as ToolSource
-from .interface import ToolStdioExitCode as ToolStdioExitCode
-from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup
-from .output_objects import ToolOutput as ToolOutput
-from .yaml import YamlInputSource as YamlInputSource
-
-log = ...  # type: Any
-
-class CwlToolSource(ToolSource):
-    def __init__(self, tool_file, strict_cwl_validation: bool = ...) -> None: ...
-    @property
-    def tool_proxy(self): ...
-    def parse_tool_type(self): ...
-    def parse_id(self): ...
-    def parse_name(self): ...
-    def parse_command(self): ...
-    def parse_environment_variables(self): ...
-    def parse_edam_operations(self): ...
-    def parse_edam_topics(self): ...
-    def parse_help(self): ...
-    def parse_sanitize(self): ...
-    def parse_strict_shell(self): ...
-    def parse_stdio(self): ...
-    def parse_interpreter(self): ...
-    def parse_version(self): ...
-    def parse_description(self): ...
-    def parse_input_pages(self): ...
-    def parse_outputs(self, tool): ...
-    def parse_requirements_and_containers(self): ...
-    def parse_profile(self): ...
-
-class CwlPageSource(PageSource):
-    def __init__(self, tool_proxy) -> None: ...
-    def parse_input_sources(self): ...
diff --git a/typeshed/galaxy/tools/parser/factory.pyi b/typeshed/galaxy/tools/parser/factory.pyi
deleted file mode 100644
index c6b63d0..0000000
--- a/typeshed/galaxy/tools/parser/factory.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.tools.parser.factory (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from galaxy.tools.loader import load_tool as load_tool_xml
-
-def get_tool_source(config_file: Optional[Any] = ..., xml_tree: Optional[Any] = ..., enable_beta_formats: bool = ..., tool_location_fetcher: Optional[Any] = ...): ...
-def get_input_source(content): ...
diff --git a/typeshed/galaxy/tools/parser/interface.pyi b/typeshed/galaxy/tools/parser/interface.pyi
deleted file mode 100644
index e219c74..0000000
--- a/typeshed/galaxy/tools/parser/interface.pyi
+++ /dev/null
@@ -1,96 +0,0 @@
-# Stubs for galaxy.tools.parser.interface (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-NOT_IMPLEMENTED_MESSAGE = ...  # type: str
-
-class ToolSource:
-    default_is_multi_byte = ...  # type: bool
-    def parse_id(self): ...
-    def parse_version(self): ...
-    def parse_tool_module(self): ...
-    def parse_action_module(self): ...
-    def parse_tool_type(self): ...
-    def parse_name(self): ...
-    def parse_description(self): ...
-    def parse_is_multi_byte(self): ...
-    def parse_display_interface(self, default): ...
-    def parse_require_login(self, default): ...
-    def parse_request_param_translation_elem(self): ...
-    def parse_command(self): ...
-    def parse_environment_variables(self): ...
-    def parse_interpreter(self): ...
-    def parse_redirect_url_params_elem(self): ...
-    def parse_version_command(self): ...
-    def parse_version_command_interpreter(self): ...
-    def parse_parallelism(self): ...
-    def parse_hidden(self): ...
-    def parse_sanitize(self): ...
-    def parse_refresh(self): ...
-    def parse_requirements_and_containers(self): ...
-    def parse_input_pages(self): ...
-    def parse_outputs(self, tool): ...
-    def parse_strict_shell(self): ...
-    def parse_stdio(self): ...
-    def parse_help(self): ...
-    def parse_profile(self): ...
-    def parse_tests_to_dict(self): ...
-
-class PagesSource:
-    page_sources = ...  # type: Any
-    def __init__(self, page_sources) -> None: ...
-    @property
-    def inputs_defined(self): ...
-
-class PageSource:
-    def parse_display(self): ...
-    def parse_input_sources(self): ...
-
-class InputSource:
-    default_optional = ...  # type: bool
-    def elem(self): ...
-    def get(self, key, value: Optional[Any] = ...): ...
-    def get_bool(self, key, default): ...
-    def parse_label(self): ...
-    def parse_help(self): ...
-    def parse_sanitizer_elem(self): ...
-    def parse_validator_elems(self): ...
-    def parse_optional(self, default: Optional[Any] = ...): ...
-    def parse_dynamic_options_elem(self): ...
-    def parse_static_options(self): ...
-    def parse_conversion_tuples(self): ...
-    def parse_nested_inputs_source(self): ...
-    def parse_test_input_source(self): ...
-    def parse_when_input_sources(self): ...
-
-class ToolStdioRegex:
-    match = ...  # type: str
-    stdout_match = ...  # type: bool
-    stderr_match = ...  # type: bool
-    error_level = ...  # type: str
-    desc = ...  # type: str
-    def __init__(self) -> None: ...
-
-class ToolStdioExitCode:
-    range_start = ...  # type: Any
-    range_end = ...  # type: Any
-    error_level = ...  # type: str
-    desc = ...  # type: str
-    def __init__(self) -> None: ...
-
-class TestCollectionDef:
-    elements = ...  # type: Any
-    collection_type = ...  # type: Any
-    name = ...  # type: Any
-    def __init__(self, elem, parse_param_elem) -> None: ...
-    def collect_inputs(self): ...
-
-class TestCollectionOutputDef:
-    name = ...  # type: Any
-    collection_type = ...  # type: Any
-    count = ...  # type: Any
-    attrib = ...  # type: Any
-    element_tests = ...  # type: Any
-    def __init__(self, name, attrib, element_tests) -> None: ...
diff --git a/typeshed/galaxy/tools/parser/output_actions.pyi b/typeshed/galaxy/tools/parser/output_actions.pyi
deleted file mode 100644
index 5945acd..0000000
--- a/typeshed/galaxy/tools/parser/output_actions.pyi
+++ /dev/null
@@ -1,215 +0,0 @@
-# Stubs for galaxy.tools.parser.output_actions (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-log = ...  # type: Any
-COLLECTION_ATTRIBUTES = ...  # type: Any
-
-class ToolOutputActionGroup:
-    tag = ...  # type: str
-    parent = ...  # type: Any
-    actions = ...  # type: Any
-    def __init__(self, parent, config_elem) -> None: ...
-    def apply_action(self, output_dataset, other_values): ...
-    @property
-    def tool(self): ...
-    def __len__(self): ...
-
-class ToolOutputActionConditionalWhen(ToolOutputActionGroup):
-    tag = ...  # type: str
-    @classmethod
-    def from_elem(cls, parent, when_elem): ...
-    value = ...  # type: Any
-    def __init__(self, parent, config_elem, value) -> None: ...
-    def is_case(self, output_dataset, other_values): ...
-    def get_ref(self, output_dataset, other_values): ...
-    def apply_action(self, output_dataset, other_values): ...
-
-class ValueToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
-    tag = ...  # type: str
-    def is_case(self, output_dataset, other_values): ...
-
-class DatatypeIsInstanceToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
-    tag = ...  # type: str
-    value = ...  # type: Any
-    def __init__(self, parent, config_elem, value) -> None: ...
-    def is_case(self, output_dataset, other_values): ...
-
-class ToolOutputActionConditional:
-    tag = ...  # type: str
-    parent = ...  # type: Any
-    name = ...  # type: Any
-    cases = ...  # type: Any
-    def __init__(self, parent, config_elem) -> None: ...
-    def apply_action(self, output_dataset, other_values): ...
-    @property
-    def tool(self): ...
-
-class ToolOutputAction:
-    tag = ...  # type: str
-    @classmethod
-    def from_elem(cls, parent, elem): ...
-    parent = ...  # type: Any
-    default = ...  # type: Any
-    option = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def apply_action(self, output_dataset, other_values): ...
-    @property
-    def tool(self): ...
-
-class ToolOutputActionOption:
-    tag = ...  # type: str
-    @classmethod
-    def from_elem(cls, parent, elem): ...
-    parent = ...  # type: Any
-    filters = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def get_value(self, other_values): ...
-    @property
-    def tool(self): ...
-
-class NullToolOutputActionOption(ToolOutputActionOption):
-    tag = ...  # type: str
-    def get_value(self, other_values): ...
-
-class FromFileToolOutputActionOption(ToolOutputActionOption):
-    tag = ...  # type: str
-    name = ...  # type: Any
-    column = ...  # type: Any
-    offset = ...  # type: Any
-    separator = ...  # type: Any
-    options = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def get_value(self, other_values): ...
-
-class FromParamToolOutputActionOption(ToolOutputActionOption):
-    tag = ...  # type: str
-    name = ...  # type: Any
-    column = ...  # type: Any
-    offset = ...  # type: Any
-    param_attribute = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def get_value(self, other_values): ...
-
-class FromDataTableOutputActionOption(ToolOutputActionOption):
-    tag = ...  # type: str
-    name = ...  # type: Any
-    missing_tool_data_table_name = ...  # type: Any
-    options = ...  # type: Any
-    column = ...  # type: Any
-    offset = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def get_value(self, other_values): ...
-
-class MetadataToolOutputAction(ToolOutputAction):
-    tag = ...  # type: str
-    name = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def apply_action(self, output_dataset, other_values): ...
-
-class FormatToolOutputAction(ToolOutputAction):
-    tag = ...  # type: str
-    default = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def apply_action(self, output_dataset, other_values): ...
-
-class ToolOutputActionOptionFilter:
-    tag = ...  # type: str
-    @classmethod
-    def from_elem(cls, parent, elem): ...
-    parent = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-    @property
-    def tool(self): ...
-
-class ParamValueToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    ref = ...  # type: Any
-    value = ...  # type: Any
-    column = ...  # type: Any
-    keep = ...  # type: Any
-    compare = ...  # type: Any
-    cast = ...  # type: Any
-    param_attribute = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class InsertColumnToolOutputActionOptionFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    ref = ...  # type: Any
-    value = ...  # type: Any
-    column = ...  # type: Any
-    iterate = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class MultipleSplitterFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    column = ...  # type: Any
-    separator = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class ColumnStripFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    column = ...  # type: Any
-    strip = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class ColumnReplaceFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    old_column = ...  # type: Any
-    old_value = ...  # type: Any
-    new_value = ...  # type: Any
-    new_column = ...  # type: Any
-    column = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class MetadataValueFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    ref = ...  # type: Any
-    name = ...  # type: Any
-    column = ...  # type: Any
-    keep = ...  # type: Any
-    compare = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class BooleanFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    column = ...  # type: Any
-    keep = ...  # type: Any
-    cast = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-class StringFunctionFilter(ToolOutputActionOptionFilter):
-    tag = ...  # type: str
-    column = ...  # type: Any
-    function = ...  # type: Any
-    def __init__(self, parent, elem) -> None: ...
-    def filter_options(self, options, other_values): ...
-
-action_types = ...  # type: Any
-option_types = ...  # type: Any
-filter_types = ...  # type: Any
-
-def parse_cast_attribute(cast): ...
-def parse_compare_type(compare): ...
-def compare_eq(value1, value2): ...
-def compare_neq(value1, value2): ...
-def compare_gt(value1, value2): ...
-def compare_gte(value1, value2): ...
-def compare_lt(value1, value2): ...
-def compare_lte(value1, value2): ...
-def compare_in(value1, value2): ...
-def compare_startswith(value1, value2): ...
-def compare_endswith(value1, value2): ...
-def compare_re_search(value1, value2): ...
-
-compare_types = ...  # type: Any
diff --git a/typeshed/galaxy/tools/parser/output_collection_def.pyi b/typeshed/galaxy/tools/parser/output_collection_def.pyi
deleted file mode 100644
index 2cc4b1b..0000000
--- a/typeshed/galaxy/tools/parser/output_collection_def.pyi
+++ /dev/null
@@ -1,29 +0,0 @@
-# Stubs for galaxy.tools.parser.output_collection_def (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-DEFAULT_EXTRA_FILENAME_PATTERN = ...  # type: str
-DEFAULT_SORT_BY = ...  # type: str
-DEFAULT_SORT_COMP = ...  # type: str
-NAMED_PATTERNS = ...  # type: Any
-INPUT_DBKEY_TOKEN = ...  # type: str
-LEGACY_DEFAULT_DBKEY = ...  # type: Any
-
-def dataset_collector_descriptions_from_elem(elem, legacy: bool = ...): ...
-def dataset_collector_descriptions_from_list(discover_datasets_dicts): ...
-
-class DatasetCollectionDescription:
-    pattern = ...  # type: Any
-    default_dbkey = ...  # type: Any
-    default_ext = ...  # type: Any
-    default_visible = ...  # type: Any
-    directory = ...  # type: Any
-    assign_primary_output = ...  # type: Any
-    sort_reverse = ...  # type: bool
-    sort_key = ...  # type: Any
-    sort_comp = ...  # type: Any
-    def __init__(self, **kwargs) -> None: ...
-
-DEFAULT_DATASET_COLLECTOR_DESCRIPTION = ...  # type: Any
diff --git a/typeshed/galaxy/tools/parser/output_objects.pyi b/typeshed/galaxy/tools/parser/output_objects.pyi
deleted file mode 100644
index 68f824e..0000000
--- a/typeshed/galaxy/tools/parser/output_objects.pyi
+++ /dev/null
@@ -1,68 +0,0 @@
-# Stubs for galaxy.tools.parser.output_objects (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from galaxy.util.dictifiable import Dictifiable
-
-class ToolOutputBase(Dictifiable):
-    name = ...  # type: Any
-    label = ...  # type: Any
-    filters = ...  # type: Any
-    hidden = ...  # type: Any
-    collection = ...  # type: bool
-    def __init__(self, name, label: Optional[Any] = ..., filters: Optional[Any] = ..., hidden: bool = ...) -> None: ...
-
-class ToolOutput(ToolOutputBase):
-    dict_collection_visible_keys = ...  # type: Any
-    format = ...  # type: Any
-    format_source = ...  # type: Any
-    metadata_source = ...  # type: Any
-    parent = ...  # type: Any
-    actions = ...  # type: Any
-    change_format = ...  # type: Any
-    implicit = ...  # type: Any
-    from_work_dir = ...  # type: Any
-    def __init__(self, name, format: Optional[Any] = ..., format_source: Optional[Any] = ..., metadata_source: Optional[Any] = ..., parent: Optional[Any] = ..., label: Optional[Any] = ..., filters: Optional[Any] = ..., actions: Optional[Any] = ..., hidden: bool = ..., implicit: bool = ...) -> None: ...
-    def __len__(self): ...
-    def __getitem__(self, index): ...
-    def __iter__(self): ...
-    def to_dict(self, view: str = ..., value_mapper: Optional[Any] = ..., app: Optional[Any] = ...): ...
-
-class ToolOutputCollection(ToolOutputBase):
-    collection = ...  # type: bool
-    default_format = ...  # type: Any
-    structure = ...  # type: Any
-    outputs = ...  # type: Any
-    inherit_format = ...  # type: Any
-    inherit_metadata = ...  # type: Any
-    metadata_source = ...  # type: Any
-    format_source = ...  # type: Any
-    change_format = ...  # type: Any
-    def __init__(self, name, structure, label: Optional[Any] = ..., filters: Optional[Any] = ..., hidden: bool = ..., default_format: str = ..., default_format_source: Optional[Any] = ..., default_metadata_source: Optional[Any] = ..., inherit_format: bool = ..., inherit_metadata: bool = ...) -> None: ...
-    def known_outputs(self, inputs, type_registry): ...
-    @property
-    def dynamic_structure(self): ...
-    @property
-    def dataset_collector_descriptions(self): ...
-
-class ToolOutputCollectionStructure:
-    collection_type = ...  # type: Any
-    collection_type_source = ...  # type: Any
-    structured_like = ...  # type: Any
-    dataset_collector_descriptions = ...  # type: Any
-    dynamic = ...  # type: Any
-    def __init__(self, collection_type, collection_type_source, structured_like, dataset_collector_descriptions) -> None: ...
-
-class ToolOutputCollectionPart:
-    output_collection_def = ...  # type: Any
-    element_identifier = ...  # type: Any
-    output_def = ...  # type: Any
-    parent_ids = ...  # type: Any
-    def __init__(self, output_collection_def, element_identifier, output_def, parent_ids: Any = ...) -> None: ...
-    @property
-    def effective_output_name(self): ...
-    @staticmethod
-    def is_named_collection_part_name(name): ...
-    @staticmethod
-    def split_output_name(name): ...
diff --git a/typeshed/galaxy/tools/parser/util.pyi b/typeshed/galaxy/tools/parser/util.pyi
deleted file mode 100644
index 97b3396..0000000
--- a/typeshed/galaxy/tools/parser/util.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.tools.parser.util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .interface import ToolStdioExitCode as ToolStdioExitCode
-from .interface import ToolStdioRegex as ToolStdioRegex
-
-def error_on_exit_code(): ...
-def aggressive_error_checks(): ...
diff --git a/typeshed/galaxy/tools/parser/xml.pyi b/typeshed/galaxy/tools/parser/xml.pyi
deleted file mode 100644
index ffdd7e9..0000000
--- a/typeshed/galaxy/tools/parser/xml.pyi
+++ /dev/null
@@ -1,89 +0,0 @@
-# Stubs for galaxy.tools.parser.xml (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .interface import InputSource as InputSource, PageSource as PageSource, PagesSource as PagesSource, TestCollectionDef as TestCollectionDef, TestCollectionOutputDef as TestCollectionOutputDef, ToolSource as ToolSource, ToolStdioExitCode as ToolStdioExitCode, ToolStdioRegex as ToolStdioRegex
-from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup
-from .output_collection_def import dataset_collector_descriptions_from_elem as dataset_collector_descriptions_from_elem
-from .output_objects import ToolOutput as ToolOutput, ToolOutputCollection as ToolOutputCollection, ToolOutputCollectionStructure as ToolOutputCollectionStructure
-from .util import aggressive_error_checks as aggressive_error_checks, error_on_exit_code as error_on_exit_code
-
-log = ...  # type: Any
-
-class XmlToolSource(ToolSource):
-    xml_tree = ...  # type: Any
-    root = ...  # type: Any
-    legacy_defaults = ...  # type: Any
-    def __init__(self, xml_tree, source_path: Optional[Any] = ...) -> None: ...
-    def parse_version(self): ...
-    def parse_id(self): ...
-    def parse_tool_module(self): ...
-    def parse_action_module(self): ...
-    def parse_tool_type(self): ...
-    def parse_name(self): ...
-    def parse_edam_operations(self): ...
-    def parse_edam_topics(self): ...
-    def parse_description(self): ...
-    def parse_is_multi_byte(self): ...
-    def parse_display_interface(self, default): ...
-    def parse_require_login(self, default): ...
-    def parse_request_param_translation_elem(self): ...
-    def parse_command(self): ...
-    def parse_environment_variables(self): ...
-    def parse_interpreter(self): ...
-    def parse_version_command(self): ...
-    def parse_version_command_interpreter(self): ...
-    def parse_parallelism(self): ...
-    def parse_hidden(self): ...
-    def parse_redirect_url_params_elem(self): ...
-    def parse_sanitize(self): ...
-    def parse_refresh(self): ...
-    def parse_requirements_and_containers(self): ...
-    def parse_input_pages(self): ...
-    def parse_outputs(self, tool): ...
-    def parse_stdio(self): ...
-    def parse_strict_shell(self): ...
-    def parse_help(self): ...
-    def parse_tests_to_dict(self): ...
-    def parse_profile(self): ...
-
-class StdioParser:
-    stdio_exit_codes = ...  # type: Any
-    stdio_regexes = ...  # type: Any
-    def __init__(self, root) -> None: ...
-    def parse_stdio_exit_codes(self, stdio_elem): ...
-    def parse_stdio_regexes(self, stdio_elem): ...
-    def parse_error_level(self, err_level): ...
-
-class XmlPagesSource(PagesSource):
-    input_elem = ...  # type: Any
-    def __init__(self, root) -> None: ...
-    @property
-    def inputs_defined(self): ...
-
-class XmlPageSource(PageSource):
-    parent_elem = ...  # type: Any
-    def __init__(self, parent_elem) -> None: ...
-    def parse_display(self): ...
-    def parse_input_sources(self): ...
-
-class XmlInputSource(InputSource):
-    input_elem = ...  # type: Any
-    input_type = ...  # type: Any
-    def __init__(self, input_elem) -> None: ...
-    def parse_input_type(self): ...
-    def elem(self): ...
-    def get(self, key, value: Optional[Any] = ...): ...
-    def get_bool(self, key, default): ...
-    def parse_label(self): ...
-    def parse_help(self): ...
-    def parse_sanitizer_elem(self): ...
-    def parse_validator_elems(self): ...
-    def parse_dynamic_options_elem(self): ...
-    def parse_static_options(self): ...
-    def parse_optional(self, default: Optional[Any] = ...): ...
-    def parse_conversion_tuples(self): ...
-    def parse_nested_inputs_source(self): ...
-    def parse_test_input_source(self): ...
-    def parse_when_input_sources(self): ...
diff --git a/typeshed/galaxy/tools/parser/yaml.pyi b/typeshed/galaxy/tools/parser/yaml.pyi
deleted file mode 100644
index ccf2afd..0000000
--- a/typeshed/galaxy/tools/parser/yaml.pyi
+++ /dev/null
@@ -1,56 +0,0 @@
-# Stubs for galaxy.tools.parser.yaml (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .interface import InputSource as InputSource
-from .interface import PageSource as PageSource
-from .interface import PagesSource as PagesSource
-from .interface import ToolSource as ToolSource
-from .output_actions import ToolOutputActionGroup as ToolOutputActionGroup
-from .output_collection_def import dataset_collector_descriptions_from_list as dataset_collector_descriptions_from_list
-from .output_objects import ToolOutput as ToolOutput, ToolOutputCollection as ToolOutputCollection, ToolOutputCollectionStructure as ToolOutputCollectionStructure
-from .util import error_on_exit_code as error_on_exit_code
-
-class YamlToolSource(ToolSource):
-    root_dict = ...  # type: Any
-    def __init__(self, root_dict, source_path: Optional[Any] = ...) -> None: ...
-    def parse_id(self): ...
-    def parse_version(self): ...
-    def parse_name(self): ...
-    def parse_description(self): ...
-    def parse_edam_operations(self): ...
-    def parse_edam_topics(self): ...
-    def parse_is_multi_byte(self): ...
-    def parse_sanitize(self): ...
-    def parse_display_interface(self, default): ...
-    def parse_require_login(self, default): ...
-    def parse_command(self): ...
-    def parse_environment_variables(self): ...
-    def parse_interpreter(self): ...
-    def parse_version_command(self): ...
-    def parse_version_command_interpreter(self): ...
-    def parse_requirements_and_containers(self): ...
-    def parse_input_pages(self): ...
-    def parse_strict_shell(self): ...
-    def parse_stdio(self): ...
-    def parse_help(self): ...
-    def parse_outputs(self, tool): ...
-    def parse_tests_to_dict(self): ...
-    def parse_profile(self): ...
-
-class YamlPageSource(PageSource):
-    inputs_list = ...  # type: Any
-    def __init__(self, inputs_list) -> None: ...
-    def parse_input_sources(self): ...
-
-class YamlInputSource(InputSource):
-    input_dict = ...  # type: Any
-    def __init__(self, input_dict) -> None: ...
-    def get(self, key, default: Optional[Any] = ...): ...
-    def get_bool(self, key, default): ...
-    def parse_input_type(self): ...
-    def parse_nested_inputs_source(self): ...
-    def parse_test_input_source(self): ...
-    def parse_when_input_sources(self): ...
-    def parse_static_options(self): ...
diff --git a/typeshed/galaxy/tools/verify/__init__.pyi b/typeshed/galaxy/tools/verify/__init__.pyi
deleted file mode 100644
index 6242553..0000000
--- a/typeshed/galaxy/tools/verify/__init__.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.tools.verify (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from .asserts import verify_assertions as verify_assertions
-from .test_data import TestDataResolver as TestDataResolver
-
-log = ...  # type: Any
-DEFAULT_TEST_DATA_RESOLVER = ...  # type: Any
-
-def verify(item_label, output_content, attributes, filename: Optional[Any] = ..., get_filename: Optional[Any] = ..., keep_outputs_dir: Optional[Any] = ..., verify_extra_files: Optional[Any] = ...): ...
-def make_temp_fname(fname: Optional[Any] = ...): ...
-def check_command(command, description): ...
-def files_diff(file1, file2, attributes: Optional[Any] = ...): ...
-def files_re_match(file1, file2, attributes: Optional[Any] = ...): ...
-def files_re_match_multiline(file1, file2, attributes: Optional[Any] = ...): ...
-def files_contains(file1, file2, attributes: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/tools/verify/asserts/__init__.pyi b/typeshed/galaxy/tools/verify/asserts/__init__.pyi
deleted file mode 100644
index 3ba17d3..0000000
--- a/typeshed/galaxy/tools/verify/asserts/__init__.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for galaxy.tools.verify.asserts (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-log = ...  # type: Any
-assertion_module_names = ...  # type: Any
-assertion_modules = ...  # type: Any
-full_assertion_module_name = ...  # type: Any
-assertion_module = ...  # type: Any
-
-def verify_assertions(data, assertion_description_list): ...
-def verify_assertion(data, assertion_description): ...
diff --git a/typeshed/galaxy/tools/verify/asserts/tabular.pyi b/typeshed/galaxy/tools/verify/asserts/tabular.pyi
deleted file mode 100644
index 4515eab..0000000
--- a/typeshed/galaxy/tools/verify/asserts/tabular.pyi
+++ /dev/null
@@ -1,6 +0,0 @@
-# Stubs for galaxy.tools.verify.asserts.tabular (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def get_first_line(output): ...
-def assert_has_n_columns(output, n, sep: str = ...): ...
diff --git a/typeshed/galaxy/tools/verify/asserts/text.pyi b/typeshed/galaxy/tools/verify/asserts/text.pyi
deleted file mode 100644
index 549d534..0000000
--- a/typeshed/galaxy/tools/verify/asserts/text.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.tools.verify.asserts.text (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def assert_has_text(output, text): ...
-def assert_not_has_text(output, text): ...
-def assert_has_line(output, line): ...
-def assert_has_text_matching(output, expression): ...
-def assert_has_line_matching(output, expression): ...
diff --git a/typeshed/galaxy/tools/verify/asserts/xml.pyi b/typeshed/galaxy/tools/verify/asserts/xml.pyi
deleted file mode 100644
index 57af9c7..0000000
--- a/typeshed/galaxy/tools/verify/asserts/xml.pyi
+++ /dev/null
@@ -1,15 +0,0 @@
-# Stubs for galaxy.tools.verify.asserts.xml (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def to_xml(output): ...
-def xml_find_text(output, path): ...
-def xml_find(output, path): ...
-def assert_is_valid_xml(output): ...
-def assert_has_element_with_path(output, path): ...
-def assert_has_n_elements_with_path(output, path, n): ...
-def assert_element_text_matches(output, path, expression): ...
-def assert_element_text_is(output, path, text): ...
-def assert_attribute_matches(output, path, attribute, expression): ...
-def assert_attribute_is(output, path, attribute, text): ...
-def assert_element_text(output, path, verify_assertions_function, children): ...
diff --git a/typeshed/galaxy/tools/verify/test_data.pyi b/typeshed/galaxy/tools/verify/test_data.pyi
deleted file mode 100644
index 1fe6f0d..0000000
--- a/typeshed/galaxy/tools/verify/test_data.pyi
+++ /dev/null
@@ -1,31 +0,0 @@
-# Stubs for galaxy.tools.verify.test_data (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-UPDATE_TEMPLATE = ...  # type: Any
-UPDATE_FAILED_TEMPLATE = ...  # type: Any
-LIST_SEP = ...  # type: Any
-
-class TestDataResolver:
-    resolvers = ...  # type: Any
-    def __init__(self, env_var: str = ..., environ: Any = ...) -> None: ...
-    def get_filename(self, name): ...
-
-def build_resolver(uri, environ): ...
-
-class FileDataResolver:
-    file_dir = ...  # type: Any
-    def __init__(self, file_dir) -> None: ...
-    def exists(self, filename): ...
-    def path(self, filename): ...
-
-class GitDataResolver(FileDataResolver):
-    repository = ...  # type: Any
-    updated = ...  # type: bool
-    fetch_data = ...  # type: Any
-    def __init__(self, repository, environ) -> None: ...
-    def exists(self, filename): ...
-    def update_repository(self): ...
-    def execute(self, cmd): ...
diff --git a/typeshed/galaxy/util/__init__.pyi b/typeshed/galaxy/util/__init__.pyi
deleted file mode 100644
index d2c9a1e..0000000
--- a/typeshed/galaxy/util/__init__.pyi
+++ /dev/null
@@ -1,131 +0,0 @@
-# Stubs for galaxy.util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-import collections
-from six.moves.urllib import parse as urlparse, request as urlrequest
-from .inflection import English as English, Inflector as Inflector
-
-grp = ...  # type: Any
-docutils_core = ...  # type: Any
-docutils_html4css1 = ...  # type: Any
-inflector = ...  # type: Any
-log = ...  # type: Any
-CHUNK_SIZE = ...  # type: int
-DATABASE_MAX_STRING_SIZE = ...  # type: int
-DATABASE_MAX_STRING_SIZE_PRETTY = ...  # type: str
-gzip_magic = ...  # type: str
-bz2_magic = ...  # type: str
-DEFAULT_ENCODING = ...  # type: Any
-NULL_CHAR = ...  # type: str
-BINARY_CHARS = ...  # type: Any
-FILENAME_VALID_CHARS = ...  # type: str
-
-def remove_protocol_from_https://github.com/url(url): ...
-def is_binary(value, binary_chars: Optional[Any] = ...): ...
-def is_uuid(value): ...
-def directory_hash_id(id): ...
-def get_charset_from_http_headers(headers, default: Optional[Any] = ...): ...
-def synchronized(func): ...
-def file_iter(fname, sep: Optional[Any] = ...): ...
-def file_reader(fp, chunk_size: Any = ...): ...
-def unique_id(KEY_SIZE: int = ...): ...
-def parse_xml(fname): ...
-def parse_xml_string(xml_string): ...
-def xml_to_string(elem, pretty: bool = ...): ...
-def xml_element_compare(elem1, elem2): ...
-def xml_element_list_compare(elem_list1, elem_list2): ...
-def xml_element_to_dict(elem): ...
-def pretty_print_xml(elem, level: int = ...): ...
-def get_file_size(value, default: Optional[Any] = ...): ...
-def shrink_stream_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ...
-def shrink_string_by_size(value, size, join_by: str = ..., left_larger: bool = ..., beginning_on_size_error: bool = ..., end_on_size_error: bool = ...): ...
-def pretty_print_time_interval(time: bool = ..., precise: bool = ...): ...
-def pretty_print_json(json_data, is_json_string: bool = ...): ...
-
-valid_chars = ...  # type: Any
-mapped_chars = ...  # type: Any
-
-def restore_text(text, character_map: Any = ...): ...
-def sanitize_text(text, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ...
-def sanitize_lists_to_string(values, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ...
-def sanitize_param(value, valid_characters: Any = ..., character_map: Any = ..., invalid_character: str = ...): ...
-
-valid_filename_chars = ...  # type: Any
-invalid_filenames = ...  # type: Any
-
-def sanitize_for_filename(text, default: Optional[Any] = ...): ...
-def mask_password_from_https://github.com/url(url): ...
-def ready_name_for_url(https://github.com/raw_name): ...
-def which(file): ...
-def safe_makedirs(path): ...
-def in_directory(file, directory, local_path_module: Any = ...): ...
-def merge_sorted_iterables(operator, *iterables): ...
-
-class Params:
-    NEVER_SANITIZE = ...  # type: Any
-    def __init__(self, params, sanitize: bool = ...) -> None: ...
-    def flatten(self): ...
-    def __getattr__(self, name): ...
-    def get(self, key, default): ...
-    def __len__(self): ...
-    def __iter__(self): ...
-    def update(self, values): ...
-
-def rst_to_html(s): ...
-def xml_text(root, name: Optional[Any] = ...): ...
-
-truthy = ...  # type: Any
-falsy = ...  # type: Any
-
-def asbool(obj): ...
-def string_as_bool(string): ...
-def string_as_bool_or_none(string): ...
-def listify(item, do_strip: bool = ...): ...
-def commaify(amount): ...
-def roundify(amount, sfs: int = ...): ...
-def unicodify(value, encoding: Any = ..., error: str = ..., default: Optional[Any] = ...): ...
-def smart_str(s, encoding: Any = ..., strings_only: bool = ..., errors: str = ...): ...
-def object_to_string(obj): ...
-def string_to_object(s): ...
-
-class ParamsWithSpecs(collections.defaultdict):
-    specs = ...  # type: Any
-    params = ...  # type: Any
-    def __init__(self, specs: Optional[Any] = ..., params: Optional[Any] = ...) -> None: ...
-    def __missing__(self, name): ...
-    def __getattr__(self, name): ...
-
-def compare_urls(url1, url2, compare_scheme: bool = ..., compare_hostname: bool = ..., compare_path: bool = ...): ...
-def read_dbnames(filename): ...
-def read_build_sites(filename, check_builds: bool = ...): ...
-def relativize_symlinks(path, start: Optional[Any] = ..., followlinks: bool = ...): ...
-def stringify_dictionary_keys(in_dict): ...
-def recursively_stringify_dictionary_keys(d): ...
-def mkstemp_ln(src, prefix: str = ...): ...
-def umask_fix_perms(path, umask, unmasked_perms, gid: Optional[Any] = ...): ...
-def docstring_trim(docstring): ...
-def nice_size(size): ...
-def size_to_bytes(size): ...
-def send_mail(frm, to, subject, body, config, html: Optional[Any] = ...): ...
-def force_symlink(source, link_name): ...
-def move_merge(source, target): ...
-def safe_str_cmp(a, b): ...
-
-galaxy_root_path = ...  # type: Any
-
-def galaxy_directory(): ...
-def config_directories_from_setting(directories_setting, galaxy_root: Any = ...): ...
-def parse_int(value, min_val: Optional[Any] = ..., max_val: Optional[Any] = ..., default: Optional[Any] = ..., allow_none: bool = ...): ...
-def parse_non_hex_float(s): ...
-def build_url(https://github.com/base_url,%20port:%20int%20=%20...,%20scheme:%20str%20=%20...,%20pathspec:%20Optional[Any]%20=%20...,%20params:%20Optional[Any]%20=%20...,%20doseq:%20bool%20=%20...): ...
-def url_get(base_url, password_mgr: Optional[Any] = ..., pathspec: Optional[Any] = ..., params: Optional[Any] = ...): ...
-def download_to_file(url, dest_file_path, timeout: int = ..., chunk_size: Any = ...): ...
-def safe_relpath(path): ...
-
-class ExecutionTimer:
-    begin = ...  # type: Any
-    def __init__(self) -> None: ...
-    @property
-    def elapsed(self): ...
diff --git a/typeshed/galaxy/util/aliaspickler.pyi b/typeshed/galaxy/util/aliaspickler.pyi
deleted file mode 100644
index 95c60a9..0000000
--- a/typeshed/galaxy/util/aliaspickler.pyi
+++ /dev/null
@@ -1,20 +0,0 @@
-# Stubs for galaxy.util.aliaspickler (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import pickle
-from six.moves import cStringIO as StringIO
-
-class AliasUnpickler(pickle.Unpickler):
-    aliases = ...  # type: Any
-    def __init__(self, aliases, *args, **kw) -> None: ...
-    def find_class(self, module, name): ...
-
-class AliasPickleModule:
-    aliases = ...  # type: Any
-    def __init__(self, aliases) -> None: ...
-    def dump(self, obj, fileobj, protocol: int = ...): ...
-    def dumps(self, obj, protocol: int = ...): ...
-    def load(self, fileobj): ...
-    def loads(self, string): ...
diff --git a/typeshed/galaxy/util/bunch.pyi b/typeshed/galaxy/util/bunch.pyi
deleted file mode 100644
index 87dc09b..0000000
--- a/typeshed/galaxy/util/bunch.pyi
+++ /dev/null
@@ -1,17 +0,0 @@
-# Stubs for galaxy.util.bunch (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-class Bunch:
-    def __init__(self, **kwds) -> None: ...
-    def dict(self): ...
-    def get(self, key, default: Optional[Any] = ...): ...
-    def __iter__(self): ...
-    def items(self): ...
-    def keys(self): ...
-    def values(self): ...
-    def __nonzero__(self): ...
-    def __setitem__(self, k, v): ...
-    def __contains__(self, item): ...
diff --git a/typeshed/galaxy/util/checkers.pyi b/typeshed/galaxy/util/checkers.pyi
deleted file mode 100644
index cdcb3ef..0000000
--- a/typeshed/galaxy/util/checkers.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for galaxy.util.checkers (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def check_html(file_path, chunk: Optional[Any] = ...): ...
-def check_binary(name, file_path: bool = ...): ...
-def check_gzip(file_path): ...
-def check_bz2(file_path): ...
-def check_zip(file_path): ...
-def is_bz2(file_path): ...
-def is_gzip(file_path): ...
-def check_image(file_path): ...
diff --git a/typeshed/galaxy/util/compression_utils.pyi b/typeshed/galaxy/util/compression_utils.pyi
deleted file mode 100644
index 0c6ca3a..0000000
--- a/typeshed/galaxy/util/compression_utils.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.util.compression_utils (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .checkers import is_bz2 as is_bz2, is_gzip as is_gzip
-
-def get_fileobj(filename, mode: str = ..., gzip_only: bool = ..., bz2_only: bool = ..., zip_only: bool = ...): ...
diff --git a/typeshed/galaxy/util/dictifiable.pyi b/typeshed/galaxy/util/dictifiable.pyi
deleted file mode 100644
index babdeb4..0000000
--- a/typeshed/galaxy/util/dictifiable.pyi
+++ /dev/null
@@ -1,8 +0,0 @@
-# Stubs for galaxy.util.dictifiable (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-class Dictifiable:
-    def to_dict(self, view: str = ..., value_mapper: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/util/expressions.pyi b/typeshed/galaxy/util/expressions.pyi
deleted file mode 100644
index f1eca5e..0000000
--- a/typeshed/galaxy/util/expressions.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.util.expressions (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from collections import MutableMapping
-
-class ExpressionContext(MutableMapping):
-    dict = ...  # type: Any
-    parent = ...  # type: Any
-    def __init__(self, dict, parent: Optional[Any] = ...) -> None: ...
-    def __delitem__(self, key): ...
-    def __iter__(self): ...
-    def __len__(self): ...
-    def __getitem__(self, key): ...
-    def __setitem__(self, key, value): ...
-    def __contains__(self, key): ...
-    def __nonzero__(self): ...
diff --git a/typeshed/galaxy/util/filelock.pyi b/typeshed/galaxy/util/filelock.pyi
deleted file mode 100644
index f74dd9a..0000000
--- a/typeshed/galaxy/util/filelock.pyi
+++ /dev/null
@@ -1,21 +0,0 @@
-# Stubs for galaxy.util.filelock (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class FileLockException(Exception): ...
-
-class FileLock:
-    is_locked = ...  # type: bool
-    lockfile = ...  # type: Any
-    file_name = ...  # type: Any
-    timeout = ...  # type: Any
-    delay = ...  # type: Any
-    def __init__(self, file_name, timeout: int = ..., delay: float = ...) -> None: ...
-    fd = ...  # type: Any
-    def acquire(self): ...
-    def release(self): ...
-    def __enter__(self): ...
-    def __exit__(self, type, value, traceback): ...
-    def __del__(self): ...
diff --git a/typeshed/galaxy/util/hash_util.pyi b/typeshed/galaxy/util/hash_util.pyi
deleted file mode 100644
index 1a81a16..0000000
--- a/typeshed/galaxy/util/hash_util.pyi
+++ /dev/null
@@ -1,14 +0,0 @@
-# Stubs for galaxy.util.hash_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-import hashlib as hashlib
-
-sha1 = ...  # type: Any
-sha = ...  # type: Any
-md5 = ...  # type: Any
-
-def new_secure_hash(text_type: Optional[Any] = ...): ...
-def hmac_new(key, value): ...
-def is_hashable(value): ...
diff --git a/typeshed/galaxy/util/heartbeat.pyi b/typeshed/galaxy/util/heartbeat.pyi
deleted file mode 100644
index e7152ae..0000000
--- a/typeshed/galaxy/util/heartbeat.pyi
+++ /dev/null
@@ -1,30 +0,0 @@
-# Stubs for galaxy.util.heartbeat (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-import threading
-
-def get_current_thread_object_dict(): ...
-
-class Heartbeat(threading.Thread):
-    config = ...  # type: Any
-    should_stop = ...  # type: bool
-    period = ...  # type: Any
-    fname = ...  # type: Any
-    file = ...  # type: Any
-    fname_nonsleeping = ...  # type: Any
-    file_nonsleeping = ...  # type: Any
-    pid = ...  # type: Any
-    nonsleeping_heartbeats = ...  # type: Any
-    wait_event = ...  # type: Any
-    def __init__(self, config, name: str = ..., period: int = ..., fname: str = ...) -> None: ...
-    def run(self): ...
-    def open_logs(self): ...
-    def close_logs(self): ...
-    def dump(self): ...
-    def shutdown(self): ...
-    def thread_is_sleeping(self, last_stack_frame): ...
-    def get_interesting_stack_frame(self, stack_frames): ...
-    def print_nonsleeping(self, threads_object_dict): ...
-    def dump_signal_handler(self, signum, frame): ...
diff --git a/typeshed/galaxy/util/image_util.pyi b/typeshed/galaxy/util/image_util.pyi
deleted file mode 100644
index ce04019..0000000
--- a/typeshed/galaxy/util/image_util.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for galaxy.util.image_util (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from PIL import Image as PIL
-
-PIL = ...  # type: Any
-log = ...  # type: Any
-
-def image_type(filename): ...
-def check_image_type(filename, types): ...
-def get_image_ext(file_path): ...
diff --git a/typeshed/galaxy/util/inflection.pyi b/typeshed/galaxy/util/inflection.pyi
deleted file mode 100644
index 92f01cb..0000000
--- a/typeshed/galaxy/util/inflection.pyi
+++ /dev/null
@@ -1,46 +0,0 @@
-# Stubs for galaxy.util.inflection (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class Base:
-    def cond_plural(self, number_of_records, word): ...
-    def titleize(self, word, uppercase: str = ...): ...
-    def camelize(self, word): ...
-    def underscore(self, word): ...
-    def humanize(self, word, uppercase: str = ...): ...
-    def variablize(self, word): ...
-    def tableize(self, class_name): ...
-    def classify(self, table_name): ...
-    def ordinalize(self, number): ...
-    def unaccent(self, text): ...
-    def string_replace(self, word, find, replace): ...
-    def urlize(self, text): ...
-    def demodulize(self, module_name): ...
-    def modulize(self, module_description): ...
-    def foreignKey(self, class_name, separate_class_name_and_id_with_underscore: int = ...): ...
-
-class English(Base):
-    def pluralize(self, word): ...
-    def singularize(self, word): ...
-
-class Inflector:
-    Inflector = ...  # type: Any
-    def __init__(self, Inflector: Any = ...) -> None: ...
-    def pluralize(self, word): ...
-    def singularize(self, word): ...
-    def cond_plural(self, number_of_records, word): ...
-    def titleize(self, word, uppercase: str = ...): ...
-    def camelize(self, word): ...
-    def underscore(self, word): ...
-    def humanize(self, word, uppercase: str = ...): ...
-    def variablize(self, word): ...
-    def tableize(self, class_name): ...
-    def classify(self, table_name): ...
-    def ordinalize(self, number): ...
-    def unaccent(self, text): ...
-    def urlize(self, text): ...
-    def demodulize(self, module_name): ...
-    def modulize(self, module_description): ...
-    def foreignKey(self, class_name, separate_class_name_and_id_with_underscore: int = ...): ...
diff --git a/typeshed/galaxy/util/json.pyi b/typeshed/galaxy/util/json.pyi
deleted file mode 100644
index d124bd6..0000000
--- a/typeshed/galaxy/util/json.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for galaxy.util.json (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def json_fix(val): ...
-def safe_dumps(*args, **kwargs): ...
-def validate_jsonrpc_request(request, regular_methods, notification_methods): ...
-def validate_jsonrpc_response(response, id: Optional[Any] = ...): ...
-def jsonrpc_request(method, params: Optional[Any] = ..., id: Optional[Any] = ..., jsonrpc: str = ...): ...
-def jsonrpc_response(request: Optional[Any] = ..., id: Optional[Any] = ..., result: Optional[Any] = ..., error: Optional[Any] = ..., jsonrpc: str = ...): ...
diff --git a/typeshed/galaxy/util/lazy_process.pyi b/typeshed/galaxy/util/lazy_process.pyi
deleted file mode 100644
index 045e42f..0000000
--- a/typeshed/galaxy/util/lazy_process.pyi
+++ /dev/null
@@ -1,22 +0,0 @@
-# Stubs for galaxy.util.lazy_process (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class LazyProcess:
-    command_and_args = ...  # type: Any
-    thread_lock = ...  # type: Any
-    allow_process_request = ...  # type: bool
-    process = ...  # type: Any
-    def __init__(self, command_and_args) -> None: ...
-    def start_process(self): ...
-    def shutdown(self): ...
-    @property
-    def running(self): ...
-
-class NoOpLazyProcess:
-    def start_process(self): ...
-    def shutdown(self): ...
-    @property
-    def running(self): ...
diff --git a/typeshed/galaxy/util/object_wrapper.pyi b/typeshed/galaxy/util/object_wrapper.pyi
deleted file mode 100644
index 8a5cda6..0000000
--- a/typeshed/galaxy/util/object_wrapper.pyi
+++ /dev/null
@@ -1,95 +0,0 @@
-# Stubs for galaxy.util.object_wrapper (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from six.moves import copyreg as copy_reg
-from galaxy.util import sanitize_lists_to_string as _sanitize_lists_to_string
-
-NoneType = ...  # type: Any
-NotImplementedType = ...  # type: Any
-EllipsisType = ...  # type: Any
-XRangeType = ...  # type: Any
-SliceType = ...  # type: Any
-BufferType = ...  # type: Any
-DictProxyType = ...  # type: Any
-log = ...  # type: Any
-__CALLABLE_TYPES__ = ...  # type: Any
-__WRAP_NO_SUBCLASS__ = ...  # type: Any
-__DONT_SANITIZE_TYPES__ = ...  # type: Any
-__DONT_WRAP_TYPES__ = ...  # type: Any
-__WRAP_SEQUENCES__ = ...  # type: Any
-__WRAP_SETS__ = ...  # type: Any
-__WRAP_MAPPINGS__ = ...  # type: Any
-VALID_CHARACTERS = ...  # type: Any
-CHARACTER_MAP = ...  # type: Any
-INVALID_CHARACTER = ...  # type: str
-
-def coerce(x, y): ...
-def cmp(x, y): ...
-def sanitize_lists_to_string(values, valid_characters: Any = ..., character_map: Any = ..., invalid_character: Any = ...): ...
-def wrap_with_safe_string(value, no_wrap_classes: Optional[Any] = ...): ...
-
-class SafeStringWrapper:
-    __UNSANITIZED_ATTRIBUTE_NAME__ = ...  # type: str
-    __NO_WRAP_NAMES__ = ...  # type: Any
-    def __new__(cls, *arg, **kwd): ...
-    unsanitized = ...  # type: Any
-    __safe_string_wrapper_function__ = ...  # type: Any
-    def __init__(self, value, safe_string_wrapper_function: Any = ...) -> None: ...
-    def __lt__(self, other): ...
-    def __le__(self, other): ...
-    def __eq__(self, other): ...
-    def __ne__(self, other): ...
-    def __gt__(self, other): ...
-    def __ge__(self, other): ...
-    def __cmp__(self, other): ...
-    def __hash__(self): ...
-    def __bool__(self): ...
-    __nonzero__ = ...  # type: Any
-    def __getattr__(self, name): ...
-    def __setattr__(self, name, value): ...
-    def __delattr__(self, name): ...
-    def __getattribute__(self, name): ...
-    def __len__(self): ...
-    def __getitem__(self, key): ...
-    def __setitem__(self, key, value): ...
-    def __delitem__(self, key): ...
-    def __iter__(self): ...
-    def __contains__(self, item): ...
-    def __getslice__(self, i, j): ...
-    def __setslice__(self, i, j, value): ...
-    def __delslice__(self, i, j): ...
-    def __add__(self, other): ...
-    def __sub__(self, other): ...
-    def __mul__(self, other): ...
-    def __floordiv__(self, other): ...
-    def __mod__(self, other): ...
-    def __divmod__(self, other): ...
-    def __pow__(self, *other): ...
-    def __lshift__(self, other): ...
-    def __rshift__(self, other): ...
-    def __and__(self, other): ...
-    def __xor__(self, other): ...
-    def __or__(self, other): ...
-    def __div__(self, other): ...
-    def __truediv__(self, other): ...
-    def __rpow__(self, other): ...
-    def __neg__(self): ...
-    def __pos__(self): ...
-    def __abs__(self): ...
-    def __invert__(self): ...
-    def __complex__(self): ...
-    def __int__(self): ...
-    def __float__(self): ...
-    def __oct__(self): ...
-    def __hex__(self): ...
-    def __index__(self): ...
-    def __coerce__(self, other): ...
-    def __enter__(self): ...
-    def __exit__(self, *args): ...
-
-class CallableSafeStringWrapper(SafeStringWrapper):
-    def __call__(self, *args, **kwds): ...
-
-def pickle_SafeStringWrapper(safe_object): ...
diff --git a/typeshed/galaxy/util/odict.pyi b/typeshed/galaxy/util/odict.pyi
deleted file mode 100644
index 459e306..0000000
--- a/typeshed/galaxy/util/odict.pyi
+++ /dev/null
@@ -1,27 +0,0 @@
-# Stubs for galaxy.util.odict (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from six.moves import UserDict
-
-dict_alias = ...  # type: Any
-
-class odict(UserDict):
-    def __init__(self, dict: Optional[Any] = ...) -> None: ...
-    def __delitem__(self, key): ...
-    def __setitem__(self, key, item): ...
-    def clear(self): ...
-    def copy(self): ...
-    def items(self): ...
-    def keys(self): ...
-    def popitem(self): ...
-    def setdefault(self, key, failobj: Optional[Any] = ...): ...
-    def update(self, dict): ...
-    def values(self): ...
-    def iterkeys(self): ...
-    def itervalues(self): ...
-    def iteritems(self): ...
-    def __iter__(self): ...
-    def reverse(self): ...
-    def insert(self, index, key, item): ...
diff --git a/typeshed/galaxy/util/oset.pyi b/typeshed/galaxy/util/oset.pyi
deleted file mode 100644
index 1d1f7bd..0000000
--- a/typeshed/galaxy/util/oset.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for galaxy.util.oset (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-import collections
-
-class OrderedSet(collections.MutableSet):
-    end = ...  # type: Any
-    map = ...  # type: Any
-    def __init__(self, iterable: Optional[Any] = ...) -> None: ...
-    def __len__(self): ...
-    def __contains__(self, key): ...
-    def add(self, key): ...
-    def discard(self, key): ...
-    def __iter__(self): ...
-    def __reversed__(self): ...
-    def pop(self, last: bool = ...): ...
-    def __eq__(self, other): ...
diff --git a/typeshed/galaxy/util/plugin_config.pyi b/typeshed/galaxy/util/plugin_config.pyi
deleted file mode 100644
index 887a82b..0000000
--- a/typeshed/galaxy/util/plugin_config.pyi
+++ /dev/null
@@ -1,11 +0,0 @@
-# Stubs for galaxy.util.plugin_config (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-yaml = ...  # type: Any
-
-def plugins_dict(module, plugin_type_identifier): ...
-def load_plugins(plugins_dict, plugin_source, extra_kwds: Any = ...): ...
-def plugin_source_from_path(path): ...
diff --git a/typeshed/galaxy/util/properties.pyi b/typeshed/galaxy/util/properties.pyi
deleted file mode 100644
index b59fdd0..0000000
--- a/typeshed/galaxy/util/properties.pyi
+++ /dev/null
@@ -1,19 +0,0 @@
-# Stubs for galaxy.util.properties (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-from six.moves.configparser import ConfigParser
-
-def find_config_file(default, old_default, explicit, cwd: Optional[Any] = ...): ...
-def load_app_properties(kwds: Any = ..., ini_file: Optional[Any] = ..., ini_section: str = ..., config_prefix: str = ...): ...
-
-class NicerConfigParser(ConfigParser):
-    filename = ...  # type: Any
-    def __init__(self, filename, *args, **kw) -> None: ...
-    read_file = ...  # type: Any
-    def defaults(self): ...
-    class InterpolateWrapper:
-        def __init__(self, original) -> None: ...
-        def __getattr__(self, name): ...
-        def before_get(self, parser, section, option, value, defaults): ...
diff --git a/typeshed/galaxy/util/simplegraph.pyi b/typeshed/galaxy/util/simplegraph.pyi
deleted file mode 100644
index b1aba1a..0000000
--- a/typeshed/galaxy/util/simplegraph.pyi
+++ /dev/null
@@ -1,26 +0,0 @@
-# Stubs for galaxy.util.simplegraph (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-class SimpleGraphNode:
-    index = ...  # type: Any
-    data = ...  # type: Any
-    def __init__(self, index, **data) -> None: ...
-
-class SimpleGraphEdge:
-    source_index = ...  # type: Any
-    target_index = ...  # type: Any
-    data = ...  # type: Any
-    def __init__(self, source_index, target_index, **data) -> None: ...
-
-class SimpleGraph:
-    nodes = ...  # type: Any
-    edges = ...  # type: Any
-    def __init__(self, nodes: Optional[Any] = ..., edges: Optional[Any] = ...) -> None: ...
-    def add_node(self, node_id, **data): ...
-    def add_edge(self, source_id, target_id, **data): ...
-    def gen_node_dicts(self): ...
-    def gen_edge_dicts(self): ...
-    def as_dict(self): ...
diff --git a/typeshed/galaxy/util/sleeper.pyi b/typeshed/galaxy/util/sleeper.pyi
deleted file mode 100644
index 600adf9..0000000
--- a/typeshed/galaxy/util/sleeper.pyi
+++ /dev/null
@@ -1,11 +0,0 @@
-# Stubs for galaxy.util.sleeper (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class Sleeper:
-    condition = ...  # type: Any
-    def __init__(self) -> None: ...
-    def sleep(self, seconds): ...
-    def wake(self): ...
diff --git a/typeshed/galaxy/util/sockets.pyi b/typeshed/galaxy/util/sockets.pyi
deleted file mode 100644
index 100aba9..0000000
--- a/typeshed/galaxy/util/sockets.pyi
+++ /dev/null
@@ -1,7 +0,0 @@
-# Stubs for galaxy.util.sockets (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-def unused_port(range: Optional[Any] = ...): ...
diff --git a/typeshed/galaxy/util/specs.pyi b/typeshed/galaxy/util/specs.pyi
deleted file mode 100644
index e3a95b9..0000000
--- a/typeshed/galaxy/util/specs.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.util.specs (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def to_str_or_none(value): ...
-def to_bool_or_none(value): ...
-def to_bool(value): ...
-def to_float_or_none(value): ...
-def is_in(*args): ...
diff --git a/typeshed/galaxy/util/sqlite.pyi b/typeshed/galaxy/util/sqlite.pyi
deleted file mode 100644
index 53c7eae..0000000
--- a/typeshed/galaxy/util/sqlite.pyi
+++ /dev/null
@@ -1,6 +0,0 @@
-# Stubs for galaxy.util.sqlite (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def is_read_only_query(query): ...
-def connect(path): ...
diff --git a/typeshed/galaxy/util/submodules.pyi b/typeshed/galaxy/util/submodules.pyi
deleted file mode 100644
index dbae050..0000000
--- a/typeshed/galaxy/util/submodules.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for galaxy.util.submodules (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-log = ...  # type: Any
-
-def submodules(module): ...
diff --git a/typeshed/galaxy/util/topsort.pyi b/typeshed/galaxy/util/topsort.pyi
deleted file mode 100644
index 79396d9..0000000
--- a/typeshed/galaxy/util/topsort.pyi
+++ /dev/null
@@ -1,20 +0,0 @@
-# Stubs for galaxy.util.topsort (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from galaxy.util.odict import odict as OrderedDict
-
-class CycleError(Exception):
-    preds = ...  # type: Any
-    def __init__(self, sofar, numpreds, succs) -> None: ...
-    def get_partial(self): ...
-    def get_pred_counts(self): ...
-    def get_succs(self): ...
-    def get_elements(self): ...
-    def get_pairlist(self): ...
-    def get_preds(self): ...
-    def pick_a_cycle(self): ...
-
-def topsort(pairlist): ...
-def topsort_levels(pairlist): ...
diff --git a/typeshed/galaxy/util/xml_macros.pyi b/typeshed/galaxy/util/xml_macros.pyi
deleted file mode 100644
index 27607df..0000000
--- a/typeshed/galaxy/util/xml_macros.pyi
+++ /dev/null
@@ -1,18 +0,0 @@
-# Stubs for galaxy.util.xml_macros (Python 3.4)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-REQUIRED_PARAMETER = ...  # type: Any
-
-def load(path): ...
-def template_macro_params(root): ...
-def raw_tool_xml_tree(path): ...
-def imported_macro_paths(root): ...
-
-class XmlMacroDef:
-    elements = ...  # type: Any
-    parameters = ...  # type: Any
-    def __init__(self, el) -> None: ...
-    def macro_tokens(self, expand_el): ...
diff --git a/typeshed/junit_xml.pyi b/typeshed/junit_xml.pyi
deleted file mode 100644
index 1f50f8a..0000000
--- a/typeshed/junit_xml.pyi
+++ /dev/null
@@ -1,60 +0,0 @@
-# Stubs for junit_xml (Python 3.5)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-unichr = chr
-
-def decode(var, encoding): ...
-
-class TestSuite:
-    name: Any = ...
-    test_cases: Any = ...
-    timestamp: Any = ...
-    hostname: Any = ...
-    id: Any = ...
-    package: Any = ...
-    file: Any = ...
-    log: Any = ...
-    url: Any = ...
-    stdout: Any = ...
-    stderr: Any = ...
-    properties: Any = ...
-    def __init__(self, name, test_cases: Optional[Any] = ..., hostname: Optional[Any] = ..., id: Optional[Any] = ..., package: Optional[Any] = ..., timestamp: Optional[Any] = ..., properties: Optional[Any] = ..., file: Optional[Any] = ..., log: Optional[Any] = ..., url: Optional[Any] = ..., stdout: Optional[Any] = ..., stderr: Optional[Any] = ...) -> None: ...
-    def build_xml_doc(self, encoding: Optional[Any] = ...): ...
-    @staticmethod
-    def to_xml_string(test_suites, prettyprint: bool = ..., encoding: Optional[Any] = ...): ...
-    @staticmethod
-    def to_file(file_descriptor, test_suites, prettyprint: bool = ..., encoding: Optional[Any] = ...): ...
-
-class TestCase:
-    name: Any = ...
-    assertions: Any = ...
-    elapsed_sec: Any = ...
-    timestamp: Any = ...
-    classname: Any = ...
-    status: Any = ...
-    category: Any = ...
-    file: Any = ...
-    line: Any = ...
-    log: Any = ...
-    url: Any = ...
-    stdout: Any = ...
-    stderr: Any = ...
-    is_enabled: bool = ...
-    error_message: Any = ...
-    error_output: Any = ...
-    error_type: Any = ...
-    failure_message: Any = ...
-    failure_output: Any = ...
-    failure_type: Any = ...
-    skipped_message: Any = ...
-    skipped_output: Any = ...
-    def __init__(self, name, classname: Optional[Any] = ..., elapsed_sec: Optional[Any] = ..., stdout: Optional[Any] = ..., stderr: Optional[Any] = ..., assertions: Optional[Any] = ..., timestamp: Optional[Any] = ..., status: Optional[Any] = ..., category: Optional[Any] = ..., file: Optional[Any] = ..., line: Optional[Any] = ..., log: Optional[Any] = ..., group: Optional[Any] = ..., url: Optional[Any] = ...) -> None: ...
-    def add_error_info(self, message: Optional[Any] = ..., output: Optional[Any] = ..., error_type: Optional[Any] = ...): ...
-    def add_failure_info(self, message: Optional[Any] = ..., output: Optional[Any] = ..., failure_type: Optional[Any] = ...): ...
-    def add_skipped_info(self, message: Optional[Any] = ..., output: Optional[Any] = ...): ...
-    def is_failure(self): ...
-    def is_error(self): ...
-    def is_skipped(self): ...
diff --git a/typeshed/mistune.pyi b/typeshed/mistune.pyi
deleted file mode 100644
index d267d92..0000000
--- a/typeshed/mistune.pyi
+++ /dev/null
@@ -1,271 +0,0 @@
-__author__ = "Aleksandr Slepchenkov"
-__email__ = "Sl.aleksandr28@gmail.com"
-
-from typing import Any, Optional, Pattern, List, Text, Tuple, Dict, Match, Type, Sequence, Iterable
-
-Tokens = List[Dict[Text, Any]]
-# There are too much levels of optional unions of lists of text in cell and align 385 and 396 lines in mistune
-
-
-def escape(text: Text, quote: bool = ..., smart_amp: bool = ...) -> Text: ...
-
-
-class BlockGrammar:
-    def_links = ...  # type: Pattern
-    def_footnotes = ...  # type: Pattern
-    newline = ...  # type: Pattern
-    block_code = ...  # type: Pattern
-    fences = ...  # type: Pattern
-    hrule = ...  # type: Pattern
-    heading = ...  # type: Pattern
-    lheading = ...  # type: Pattern
-    block_quote = ...  # type: Pattern
-    list_block = ...  # type: Pattern
-    list_item = ...  # type: Pattern
-    list_bullet = ...  # type: Pattern
-    paragraph = ...  # type: Pattern
-    block_html = ...  # type: Pattern
-    table = ...  # type: Pattern
-    nptable = ...  # type: Pattern
-    text = ...  # type: Pattern
-
-
-class BlockLexer:
-    grammar_class = ...  # type: Type[BlockGrammar]
-    default_rules = ...  # type: List[Text]
-    list_rules = ...  # type: Tuple[Text]
-    footnote_rules = ...  # type: Tuple[Text]
-    tokens = ...  # type: Tokens
-    def_links = ...  # type: Dict[Text, Dict[Text, Text]]
-    def_footnotes = ...  # type: Dict[Text, int]
-    rules = ...  # type: BlockGrammar
-
-    def __init__(self, rules: Optional[BlockGrammar] = ..., **kwargs) -> None: ...
-
-    def __call__(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Tokens: ...
-
-    def parse(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Tokens: ...
-
-    def parse_newline(self, m: Match) -> None: ...
-
-    def parse_block_code(self, m: Match) -> None: ...
-
-    def parse_fences(self, m: Match) -> None: ...
-
-    def parse_heading(self, m: Match) -> None: ...
-
-    def parse_lheading(self, m: Match) -> None: ...
-
-    def parse_hrule(self, m: Match) -> None: ...
-
-    def parse_list_block(self, m: Match) -> None: ...
-
-    def parse_block_quote(self, m: Match) -> None: ...
-
-    def parse_def_links(self, m: Match) -> None: ...
-
-    def parse_def_footnotes(self, m: Match) -> None: ...
-
-    def parse_table(self, m: Match) -> None: ...
-
-    def parse_nptable(self, m: Match) -> None: ...
-
-    def parse_block_html(self, m: Match) -> None: ...
-
-    def parse_paragraph(self, m: Match) -> None: ...
-
-    def parse_text(self, m: Match) -> None: ...
-
-
-class InlineGrammar:
-    escape = ...  # type: Pattern
-    inline_html = ...  # type: Pattern
-    autolink = ...  # type: Pattern
-    link = ...  # type: Pattern
-    reflink = ...  # type: Pattern
-    nolink = ...  # type: Pattern
-    url = ...  # type: Pattern
-    double_emphasis = ...  # type: Pattern
-    emphasis = ...  # type: Pattern
-    code = ...  # type: Pattern
-    linebreak = ...  # type: Pattern
-    strikethrough = ...  # type: Pattern
-    footnote = ...  # type: Pattern
-    text = ...  # type: Pattern
-
-    def hard_wrap(self) -> None: ...
-
-
-class InlineLexer:
-    grammar_class = ...  # type: Type[InlineGrammar]
-    default_rules = ...  # type: List[Text]
-    inline_html_rules = ...  # type: List[Text]
-    renderer = ...  # type: Renderer
-    links = ...  # type: Dict[Any, Dict]
-    footnotes = ...  # type: Dict[Text, int]
-    footnote_index = ...  # type: int
-    _in_link = ...  # type: bool
-    _in_footnote = ...  # type: bool
-    _parse_inline_html = ...  # type: bool
-    rules = ...  # type: InlineGrammar
-
-    def __init__(self, renderer: Renderer, rules: Optional[InlineGrammar] = ..., **kwargs) -> None: ...
-
-    def __call__(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Text: ...
-
-    def setup(self, links: Optional[Dict[Any, Dict]], footnotes: Optional[Dict[Text, int]]) -> None: ...
-
-    line_match = ...  # type: Match
-    line_started = ...  # type: bool
-
-    def output(self, text: Text, rules: Optional[Sequence[Text]] = ...) -> Text: ...
-
-    def output_escape(self, m: Match) -> Text: ...
-
-    def output_autolink(self, m: Match) -> Text: ...
-
-    def output_url(https://github.com/self,%20m:%20Match) -> Text: ...
-
-    def output_inline_html(self, m: Match) -> Text: ...
-
-    def output_footnote(self, m: Match) -> Optional[Text]: ...
-
-    def output_link(self, m: Match) -> Text: ...
-
-    def output_reflink(self, m: Match) -> Optional[Text]: ...
-
-    def output_nolink(self, m: Match) -> Optional[Text]: ...
-
-    def output_double_emphasis(self, m: Match) -> Text: ...
-
-    def output_emphasis(self, m: Match) -> Text: ...
-
-    def output_code(self, m: Match) -> Text: ...
-
-    def output_linebreak(self, m: Match) -> Text: ...
-
-    def output_strikethrough(self, m: Match) -> Text: ...
-
-    def output_text(self, m: Match) -> Text: ...
-
-
-class Renderer:
-    options = ...  # type: Dict
-
-    def __init__(self, **kwargs) -> None: ...
-
-    def placeholder(self) -> Text: ...
-
-    def block_code(self, code: Text,
-                   lang: Any = ...) -> Text: ...  # It seems that lang should be string, however other types are valid as well
-
-    def block_quote(self, text: Text) -> Text: ...
-
-    def block_html(self, html: Text) -> Text: ...
-
-    def header(self, text: Text, level: int, raw: Optional[Text] = ...) -> Text: ...
-
-    def hrule(self) -> Text: ...
-
-    def list(self, body: Any,
-             ordered: bool = ...) -> Text: ...  # body - same reason as for lang above, and for other Any in this class
-
-    def list_item(self, text: Any) -> Text: ...
-
-    def paragraph(self, text: Text) -> Text: ...
-
-    def table(self, header: Any, body: Any) -> Text: ...
-
-    def table_row(self, content: Any) -> Text: ...
-
-    def table_cell(self, content: Any, **flags) -> Text: ...
-
-    def double_emphasis(self, text: Any) -> Text: ...
-
-    def emphasis(self, text: Any) -> Text: ...
-
-    def codespan(self, text: Text) -> Text: ...
-
-    def linebreak(self) -> Text: ...
-
-    def strikethrough(self, text: Any) -> Text: ...
-
-    def text(self, text: Any) -> Text: ...
-
-    def escape(self, text: Any) -> Text: ...
-
-    def autolink(self, link: Any, is_email: bool = ...) -> Text: ...
-
-    def link(self, link: Any, title: Any, text: Any) -> Text: ...
-
-    def image(self, src: Any, title: Any, text: Any) -> Text: ...
-
-    def inline_html(self, html: Any) -> Text: ...
-
-    def newline(self) -> Text: ...
-
-    def footnote_ref(self, key: Any, index: int) -> Text: ...
-
-    def footnote_item(self, key: Any, text: Text) -> Text: ...
-
-    def footnotes(self, text: Any) -> Text: ...
-
-
-class Markdown:
-    renderer = ...  # type: Renderer
-    inline = ...  # type: InlineLexer
-    block = ...  # type: BlockLexer
-    footnotes = ...  # type: List[Dict[Text, Any]]
-    tokens = ...  # type: Tokens
-
-    def __init__(self, renderer: Optional[Renderer] = ..., inline: Optional[InlineLexer] = ...,
-                 block: Optional[BlockLexer] = ..., **kwargs) -> None: ...
-
-    def __call__(self, text: Text) -> Text: ...
-
-    def render(self, text: Text) -> Text: ...
-
-    def parse(self, text: Text) -> Text: ...
-
-    token = ...  # type: Dict[Text, Any]
-
-    def pop(self) -> Optional[Dict[Text, Any]]: ...
-
-    def peek(self) -> Optional[Dict[Text, Any]]: ...
-
-    def output(self, text: Text, rules: Optional[Sequence[Text]] = ...): ...
-
-    def tok(self) -> Text: ...
-
-    def tok_text(self) -> Text: ...
-
-    def output_newline(self) -> Text: ...
-
-    def output_hrule(self) -> Text: ...
-
-    def output_heading(self) -> Text: ...
-
-    def output_code(self) -> Text: ...
-
-    def output_table(self) -> Text: ...
-
-    def output_block_quote(self) -> Text: ...
-
-    def output_list(self) -> Text: ...
-
-    def output_list_item(self) -> Text: ...
-
-    def output_loose_item(self) -> Text: ...
-
-    def output_footnote(self) -> Text: ...
-
-    def output_close_html(self) -> Text: ...
-
-    def output_open_html(self) -> Text: ...
-
-    def output_paragraph(self) -> Text: ...
-
-    def output_text(self) -> Text: ...
-
-
-def markdown(text: Text, escape: bool = ..., **kwargs) -> Text: ...
\ No newline at end of file
diff --git a/typeshed/rdflib/__init__.pyi b/typeshed/rdflib/__init__.pyi
deleted file mode 100644
index d9587d3..0000000
--- a/typeshed/rdflib/__init__.pyi
+++ /dev/null
@@ -1,9 +0,0 @@
-# Stubs for rdflib (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from rdflib.term import URIRef as URIRef, BNode as BNode, Literal as Literal, Variable as Variable
-from rdflib.namespace import Namespace as Namespace
-from rdflib.graph import Dataset as Dataset, Graph as Graph, ConjunctiveGraph as ConjunctiveGraph
-from rdflib.namespace import RDF as RDF, RDFS as RDFS, OWL as OWL, XSD as XSD
-from rdflib import util as util
diff --git a/typeshed/rdflib/events.pyi b/typeshed/rdflib/events.pyi
deleted file mode 100644
index 7da9fbe..0000000
--- a/typeshed/rdflib/events.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for rdflib.events (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-class Event:
-    def __init__(self, **kw): ...
-
-class Dispatcher:
-    def set_map(self, amap): ...
-    def get_map(self): ...
-    def subscribe(self, event_type, handler): ...
-    def dispatch(self, event): ...
diff --git a/typeshed/rdflib/exceptions.pyi b/typeshed/rdflib/exceptions.pyi
deleted file mode 100644
index 252af85..0000000
--- a/typeshed/rdflib/exceptions.pyi
+++ /dev/null
@@ -1,37 +0,0 @@
-# Stubs for rdflib.exceptions (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class Error(Exception):
-    msg = ... # type: Any
-    def __init__(self, msg=None): ...
-
-class TypeCheckError(Error):
-    type = ... # type: Any
-    node = ... # type: Any
-    def __init__(self, node): ...
-
-class SubjectTypeError(TypeCheckError):
-    msg = ... # type: Any
-    def __init__(self, node): ...
-
-class PredicateTypeError(TypeCheckError):
-    msg = ... # type: Any
-    def __init__(self, node): ...
-
-class ObjectTypeError(TypeCheckError):
-    msg = ... # type: Any
-    def __init__(self, node): ...
-
-class ContextTypeError(TypeCheckError):
-    msg = ... # type: Any
-    def __init__(self, node): ...
-
-class ParserError(Error):
-    msg = ... # type: Any
-    def __init__(self, msg): ...
-
-class UniquenessError(Error):
-    def __init__(self, values): ...
diff --git a/typeshed/rdflib/graph.pyi b/typeshed/rdflib/graph.pyi
deleted file mode 100644
index bf3c076..0000000
--- a/typeshed/rdflib/graph.pyi
+++ /dev/null
@@ -1,159 +0,0 @@
-# Stubs for rdflib.graph (Python 3)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from rdflib.term import Identifier, Node, BNode
-from typing import Any, Iterator, IO, Optional, Text, Tuple, Union
-
-class Graph(Node):
-    context_aware: bool = ...
-    formula_aware: bool = ...
-    default_union: bool = ...
-    def __init__(self, store: str = ..., identifier: Optional[Any] = ..., namespace_manager: Optional[Any] = ...) -> None: ...
-    store: Any = ...
-    identifier: Any = ...
-    namespace_manager: Any = ...
-    def toPython(self): ...
-    def destroy(self, configuration: Any) -> None: ...
-    def commit(self) -> None: ...
-    def rollback(self) -> None: ...
-    def open(self, configuration: Any, create: bool = ...): ...
-    def close(self, commit_pending_transaction: bool = ...) -> None: ...
-    def add(self, xxx_todo_changeme: Any) -> None: ...
-    def addN(self, quads: Any) -> None: ...
-    def remove(self, xxx_todo_changeme1: Any) -> None: ...
-    def triples(self, xxx_todo_changeme2: Tuple[Optional[Union[Text, Identifier]], Optional[Union[Text, Identifier]], Optional[Identifier]]) -> Iterator[Tuple[BNode, BNode, BNode]]: ...
-    def __getitem__(self, item: Any): ...
-    def __len__(self): ...
-    def __iter__(self): ...
-    def __contains__(self, triple: Any): ...
-    def __hash__(self): ...
-    def md5_term_hash(self): ...
-    def __cmp__(self, other: Any): ...
-    def __eq__(self, other: Any): ...
-    def __lt__(self, other: Any): ...
-    def __le__(self, other: Any): ...
-    def __gt__(self, other: Any): ...
-    def __ge__(self, other: Any): ...
-    def __iadd__(self, other: Any): ...
-    def __isub__(self, other: Any): ...
-    def __add__(self, other: Any): ...
-    def __mul__(self, other: Any): ...
-    def __sub__(self, other: Any): ...
-    def __xor__(self, other: Any): ...
-    __or__: Any = ...
-    __and__: Any = ...
-    def set(self, triple: Any) -> None: ...
-    def subjects(self, predicate: Optional[Any] = ..., object: Optional[Any] = ...) -> None: ...
-    def predicates(self, subject: Optional[Any] = ..., object: Optional[Any] = ...) -> None: ...
-    def objects(self, subject: Optional[Any] = ..., predicate: Optional[Any] = ...) -> None: ...
-    def subject_predicates(self, object: Optional[Any] = ...) -> None: ...
-    def subject_objects(self, predicate: Optional[Any] = ...) -> None: ...
-    def predicate_objects(self, subject: Optional[Any] = ...) -> None: ...
-    def triples_choices(self, xxx_todo_changeme3: Any, context: Optional[Any] = ...) -> None: ...
-    def value(self, subject: Optional[Any] = ..., predicate: Any = ..., object: Optional[Any] = ..., default: Optional[Any] = ..., any: bool = ...): ...
-    def label(self, subject: Any, default: str = ...): ...
-    def preferredLabel(self, subject: Any, lang: Optional[Any] = ..., default: Optional[Any] = ..., labelProperties: Any = ...): ...
-    def comment(self, subject: Any, default: str = ...): ...
-    def items(self, list: Any) -> None: ...
-    def transitiveClosure(self, func: Any, arg: Any, seen: Optional[Any] = ...) -> None: ...
-    def transitive_objects(self, subject: Any, property: Any, remember: Optional[Any] = ...) -> None: ...
-    def transitive_subjects(self, predicate: Any, object: Any, remember: Optional[Any] = ...) -> None: ...
-    def seq(self, subject: Any): ...
-    def qname(self, uri: Any): ...
-    def compute_qname(self, uri: Any, generate: bool = ...): ...
-    def bind(self, prefix: Any, namespace: Any, override: bool = ...): ...
-    def namespaces(self) -> None: ...
-    def absolutize(self, uri: Any, defrag: int = ...): ...
-    def serialize(self, destination: Optional[Any] = ..., format: str = ..., base: Optional[Any] = ..., encoding: Optional[Any] = ..., **args: Any): ...
-    def parse(self, source: Optional[Any] = ..., publicID: Optional[Any] = ..., format: Optional[Any] = ..., location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any): ...
-    def load(self, source: Any, publicID: Optional[Any] = ..., format: str = ...) -> None: ...
-    def query(self, query_object: Any, processor: str = ..., result: str = ..., initNs: Optional[Any] = ..., initBindings: Optional[Any] = ..., use_store_provided: bool = ..., **kwargs: Any): ...
-    def update(self, update_object: Any, processor: str = ..., initNs: Optional[Any] = ..., initBindings: Optional[Any] = ..., use_store_provided: bool = ..., **kwargs: Any): ...
-    def n3(self): ...
-    def __reduce__(self): ...
-    def isomorphic(self, other: Any): ...
-    def connected(self): ...
-    def all_nodes(self): ...
-    def collection(self, identifier: Any): ...
-    def resource(self, identifier: Any): ...
-    def skolemize(self, new_graph: Optional[Any] = ..., bnode: Optional[Any] = ...): ...
-    def de_skolemize(self, new_graph: Optional[Any] = ..., uriref: Optional[Any] = ...): ...
-
-class ConjunctiveGraph(Graph):
-    context_aware: bool = ...
-    default_union: bool = ...
-    default_context: Any = ...
-    def __init__(self, store: str = ..., identifier: Optional[Any] = ...) -> None: ...
-    def __contains__(self, triple_or_quad: Any): ...
-    def add(self, triple_or_quad: Any) -> None: ...
-    def addN(self, quads: Any) -> None: ...
-    def remove(self, triple_or_quad: Any) -> None: ...
-    def quads(self, triple_or_quad: Optional[Any] = ...) -> None: ...
-    def triples_choices(self, xxx_todo_changeme4: Any, context: Optional[Any] = ...) -> None: ...
-    def __len__(self): ...
-    def contexts(self, triple: Optional[Any] = ...) -> None: ...
-    def get_context(self, identifier: Any, quoted: bool = ...): ...
-    def remove_context(self, context: Any) -> None: ...
-    def context_id(self, uri: Any, context_id: Optional[Any] = ...): ...
-    def parse(self, source: Optional[Any] = ..., publicID: Optional[Any] = ..., format: Optional[Any] = ..., location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any): ...
-    def __reduce__(self): ...
-
-class Dataset(ConjunctiveGraph):
-    __doc__: Any = ...
-    default_context: Any = ...
-    default_union: Any = ...
-    def __init__(self, store: str = ..., default_union: bool = ...) -> None: ...
-    def graph(self, identifier: Optional[Any] = ...): ...
-    def parse(self, source: Optional[Any] = ..., publicID: Optional[Any] = ..., format: Optional[Any] = ..., location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any): ...
-    def add_graph(self, g: Any): ...
-    def remove_graph(self, g: Any) -> None: ...
-    def contexts(self, triple: Optional[Any] = ...) -> None: ...
-    graphs: Any = ...
-    def quads(self, triple_or_quad: Optional[Any] = ...) -> None: ...
-
-class QuotedGraph(Graph):
-    def __init__(self, store: Any, identifier: Any) -> None: ...
-    def add(self, xxx_todo_changeme5: Any) -> None: ...
-    def addN(self, quads: Any) -> None: ...
-    def n3(self): ...
-    def __reduce__(self): ...
-
-class Seq:
-    def __init__(self, graph: Any, subject: Any) -> None: ...
-    def toPython(self): ...
-    def __iter__(self) -> None: ...
-    def __len__(self): ...
-    def __getitem__(self, index: Any): ...
-
-class ModificationException(Exception):
-    def __init__(self) -> None: ...
-
-class UnSupportedAggregateOperation(Exception):
-    def __init__(self) -> None: ...
-
-class ReadOnlyGraphAggregate(ConjunctiveGraph):
-    graphs: Any = ...
-    def __init__(self, graphs: Any, store: str = ...) -> None: ...
-    def destroy(self, configuration: Any) -> None: ...
-    def commit(self) -> None: ...
-    def rollback(self) -> None: ...
-    def open(self, configuration: Any, create: bool = ...) -> None: ...
-    def close(self, commit_pending_transaction: bool = ...) -> None: ...
-    def add(self, xxx_todo_changeme6: Any) -> None: ...
-    def addN(self, quads: Any) -> None: ...
-    def remove(self, xxx_todo_changeme7: Any) -> None: ...
-    def __contains__(self, triple_or_quad: Any): ...
-    def quads(self, triple_or_quad: Optional[Any] = ...) -> None: ...
-    def __len__(self): ...
-    def __cmp__(self, other: Any): ...
-    def __iadd__(self, other: Any) -> None: ...
-    def __isub__(self, other: Any) -> None: ...
-    def triples_choices(self, xxx_todo_changeme10: Any, context: Optional[Any] = ...) -> None: ...
-    def qname(self, uri: Any): ...
-    def compute_qname(self, uri: Any, generate: bool = ...): ...
-    def bind(self, prefix: Any, namespace: Any, override: bool = ...) -> None: ...
-    def namespaces(self) -> None: ...
-    def absolutize(self, uri: Any, defrag: int = ...) -> None: ...
-    def parse(self, source: Optional[Any] = ..., publicID: Optional[Any] = ..., format: Optional[Any] = ..., location: Optional[Any] = ..., file: Optional[Any] = ..., data: Optional[Any] = ..., **args: Any): ...
-    def n3(self) -> None: ...
diff --git a/typeshed/rdflib/namespace.pyi b/typeshed/rdflib/namespace.pyi
deleted file mode 100644
index c0d305f..0000000
--- a/typeshed/rdflib/namespace.pyi
+++ /dev/null
@@ -1,62 +0,0 @@
-# Stubs for rdflib.namespace (Python 3)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional, Text
-
-from rdflib.term import URIRef
-
-class Namespace(str):
-    __doc__: Any = ...
-    def __new__(cls, value: Any): ...
-    @property
-    def title(self) -> URIRef: ...
-    def term(self, name: Any) -> URIRef: ...
-    def __getitem__(self, key: Any, default: Optional[Any] = ...) -> URIRef: ...
-    def __getattr__(self, name: Any) -> URIRef: ...
-
-class URIPattern(str):
-    __doc__: Any = ...
-    def __new__(cls, value: Any): ...
-    def __mod__(self, *args: Any, **kwargs: Any): ...
-    def format(self, *args: Any, **kwargs: Any): ...
-
-class ClosedNamespace:
-    uri: Any = ...
-    def __init__(self, uri: Any, terms: Any) -> None: ...
-    def term(self, name: Any) -> URIRef: ...
-    def __getitem__(self, key: Any, default: Optional[Any] = ...) -> URIRef: ...
-    def __getattr__(self, name: Any) -> URIRef: ...
-
-class _RDFNamespace(ClosedNamespace):
-    def __init__(self) -> None: ...
-    def term(self, name: Any) -> URIRef: ...
-
-RDF = ClosedNamespace("", [])
-RDFS = ClosedNamespace("", [])
-OWL = Namespace("")
-XSD: Namespace
-SKOS: Namespace
-DOAP: Namespace
-FOAF: Namespace
-DC: Namespace
-DCTERMS: Namespace
-VOID: Namespace
-
-class NamespaceManager:
-    graph: Any = ...
-    def __init__(self, graph: Any) -> None: ...
-    def reset(self) -> None: ...
-    store: Any = ...
-    def qname(self, uri: Any): ...
-    def normalizeUri(self, rdfTerm: Any): ...
-    def compute_qname(self, uri: Any, generate: bool = ...): ...
-    def bind(self, prefix: Any, namespace: Any, override: bool = ..., replace: bool = ...) -> None: ...
-    def namespaces(self) -> None: ...
-    def absolutize(self, uri: Any, defrag: int = ...): ...
-
-def is_ncname(name: Any): ...
-
-XMLNS: str
-
-def split_uri(uri: Any): ...
diff --git a/typeshed/rdflib/parser.pyi b/typeshed/rdflib/parser.pyi
deleted file mode 100644
index fa1ec9a..0000000
--- a/typeshed/rdflib/parser.pyi
+++ /dev/null
@@ -1,10 +0,0 @@
-# Stubs for rdflib.parser (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from io import StringIO as BytesIO
-
-class Parser:
-    def __init__(self): ...
-    def parse(self, source, sink): ...
diff --git a/typeshed/rdflib/plugin.pyi b/typeshed/rdflib/plugin.pyi
deleted file mode 100644
index 30026e2..0000000
--- a/typeshed/rdflib/plugin.pyi
+++ /dev/null
@@ -1,28 +0,0 @@
-# Stubs for rdflib.plugin (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from rdflib.exceptions import Error
-from rdflib.parser import Parser
-
-class PluginException(Error): ...
-
-class Plugin:
-    name = ... # type: Any
-    kind = ... # type: Any
-    module_path = ... # type: Any
-    class_name = ... # type: Any
-    def __init__(self, name, kind, module_path, class_name): ...
-    def getClass(self): ...
-
-class PKGPlugin(Plugin):
-    name = ... # type: Any
-    kind = ... # type: Any
-    ep = ... # type: Any
-    def __init__(self, name, kind, ep): ...
-    def getClass(self): ...
-
-def register(name: str, kind: type, module_path: str, class_name: str) -> None: ...
-def get(name, kind): ...
-def plugins(name=None, kind=None): ...
diff --git a/typeshed/rdflib/plugins/parsers/notation3.pyi b/typeshed/rdflib/plugins/parsers/notation3.pyi
deleted file mode 100644
index 3177634..0000000
--- a/typeshed/rdflib/plugins/parsers/notation3.pyi
+++ /dev/null
@@ -1,12 +0,0 @@
-# Stubs for rdflib.plugins.parsers.notation3 (Python 3.5)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from rdflib.parser import Parser
-
-class BadSyntax(SyntaxError):
-    lines = ...  # type: Any
-    def __init__(self, uri, lines, argstr, i, why): ...
-    @property
-    def message(self): ...
diff --git a/typeshed/rdflib/query.pyi b/typeshed/rdflib/query.pyi
deleted file mode 100644
index fad3c37..0000000
--- a/typeshed/rdflib/query.pyi
+++ /dev/null
@@ -1,54 +0,0 @@
-# Stubs for rdflib.query (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from io import StringIO as BytesIO
-import collections
-
-class Processor:
-    def __init__(self, graph): ...
-    def query(self, strOrQuery, initBindings=..., initNs=..., DEBUG=False): ...
-
-class UpdateProcessor:
-    def __init__(self, graph): ...
-    def update(self, strOrQuery, initBindings=..., initNs=...): ...
-
-class ResultException(Exception): ...
-
-class EncodeOnlyUnicode:
-    def __init__(self, stream): ...
-    def write(self, arg): ...
-    def __getattr__(self, name): ...
-
-class ResultRow(tuple):
-    __doc__ = ... # type: Any
-    def __new__(cls, values, labels): ...
-    def __getattr__(self, name): ...
-    def __getitem__(self, name): ...
-    def asdict(self): ...
-
-class Result(collections.Iterable):
-    type = ... # type: Any
-    vars = ... # type: Any
-    askAnswer = ... # type: Any
-    graph = ... # type: Any
-    def __init__(self, type_): ...
-    bindings = ... # type: Any
-    @staticmethod
-    def parse(source, format='', **kwargs): ...
-    def serialize(self, destination=None, encoding='', format='', **args): ...
-    def __len__(self): ...
-    def __nonzero__(self): ...
-    def __iter__(self): ...
-    def __getattr__(self, name): ...
-    def __eq__(self, other): ...
-
-class ResultParser:
-    def __init__(self): ...
-    def parse(self, source, **kwargs): ...
-
-class ResultSerializer:
-    result = ... # type: Any
-    def __init__(self, result): ...
-    def serialize(self, stream, encoding='', **kwargs): ...
diff --git a/typeshed/rdflib/serializer.pyi b/typeshed/rdflib/serializer.pyi
deleted file mode 100644
index a92dac0..0000000
--- a/typeshed/rdflib/serializer.pyi
+++ /dev/null
@@ -1,13 +0,0 @@
-# Stubs for rdflib.serializer (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-
-class Serializer:
-    store = ... # type: Any
-    encoding = ... # type: Any
-    base = ... # type: Any
-    def __init__(self, store): ...
-    def serialize(self, stream, base=None, encoding=None, **args): ...
-    def relativize(self, uri): ...
diff --git a/typeshed/rdflib/store.pyi b/typeshed/rdflib/store.pyi
deleted file mode 100644
index 6886321..0000000
--- a/typeshed/rdflib/store.pyi
+++ /dev/null
@@ -1,48 +0,0 @@
-# Stubs for rdflib.store (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any
-from rdflib.events import Event
-from io import StringIO as BytesIO
-
-class StoreCreatedEvent(Event): ...
-class TripleAddedEvent(Event): ...
-class TripleRemovedEvent(Event): ...
-
-class NodePickler:
-    def __init__(self): ...
-    def register(self, object, id): ...
-    def loads(self, s): ...
-    def dumps(self, obj, protocol=None, bin=None): ...
-
-class Store:
-    context_aware = ... # type: Any
-    formula_aware = ... # type: Any
-    transaction_aware = ... # type: Any
-    graph_aware = ... # type: Any
-    dispatcher = ... # type: Any
-    def __init__(self, configuration=None, identifier=None): ...
-    node_pickler = ... # type: Any
-    def create(self, configuration): ...
-    def open(self, configuration, create=False): ...
-    def close(self, commit_pending_transaction=False): ...
-    def destroy(self, configuration): ...
-    def gc(self): ...
-    def add(self, __tuple_arg_2, context, quoted=False): ...
-    def addN(self, quads): ...
-    def remove(self, __tuple_arg_2, context=None): ...
-    def triples_choices(self, __tuple_arg_2, context=None): ...
-    def triples(self, triple_pattern, context=None): ...
-    def __len__(self, context=None): ...
-    def contexts(self, triple=None): ...
-    def query(self, query, initNs, initBindings, queryGraph, **kwargs): ...
-    def update(self, update, initNs, initBindings, queryGraph, **kwargs): ...
-    def bind(self, prefix, namespace): ...
-    def prefix(self, namespace): ...
-    def namespace(self, prefix): ...
-    def namespaces(self): ...
-    def commit(self): ...
-    def rollback(self): ...
-    def add_graph(self, graph): ...
-    def remove_graph(self, graph): ...
diff --git a/typeshed/rdflib/term.pyi b/typeshed/rdflib/term.pyi
deleted file mode 100644
index 32b09c7..0000000
--- a/typeshed/rdflib/term.pyi
+++ /dev/null
@@ -1,87 +0,0 @@
-# Stubs for rdflib.term (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from typing import Any, Optional
-
-class Node: ...
-
-class Identifier(Node, str):
-    def __new__(cls, value: Any): ...
-    def eq(self, other: Any): ...
-    def neq(self, other: Any): ...
-    def __ne__(self, other: Any): ...
-    def __eq__(self, other: Any): ...
-    def __gt__(self, other: Any): ...
-    def __lt__(self, other: Any): ...
-    def __le__(self, other: Any): ...
-    def __ge__(self, other: Any): ...
-    def __hash__(self): ...
-
-class URIRef(Identifier):
-    def __new__(cls, value: Any, base: Optional[Any] = ...): ...
-    def toPython(self): ...
-    def n3(self, namespace_manager: Optional[Any] = ...): ...
-    def defrag(self): ...
-    def __reduce__(self): ...
-    def __getnewargs__(self): ...
-    def __add__(self, other: Any): ...
-    def __radd__(self, other: Any): ...
-    def __mod__(self, other: Any): ...
-    def md5_term_hash(self): ...
-    def de_skolemize(self): ...
-
-class Genid(URIRef): ...
-class RDFLibGenid(Genid): ...
-
-class BNode(Identifier):
-    def __new__(cls, value=None, _sn_gen=..., _prefix=...): ...
-    def toPython(self): ...
-    def n3(self, namespace_manager=None): ...
-    def __getnewargs__(self): ...
-    def __reduce__(self): ...
-    def md5_term_hash(self): ...
-    def skolemize(self, authority=''): ...
-
-class Literal(Identifier):
-    __doc__ = ... # type: Any
-    def __new__(cls, lexical_or_value, lang=None, datatype=None, normalize=None): ...
-    def normalize(self): ...
-    @property
-    def value(self): ...
-    @property
-    def language(self): ...
-    @property
-    def datatype(self): ...
-    def __reduce__(self): ...
-    def __add__(self, val): ...
-    def __nonzero__(self): ...
-    def __neg__(self): ...
-    def __pos__(self): ...
-    def __abs__(self): ...
-    def __invert__(self): ...
-    def __gt__(self, other): ...
-    def __lt__(self, other): ...
-    def __le__(self, other): ...
-    def __ge__(self, other): ...
-    def __hash__(self): ...
-    def __eq__(self, other): ...
-    def eq(self, other): ...
-    def neq(self, other): ...
-    def n3(self, namespace_manager=None): ...
-    def toPython(self): ...
-    def md5_term_hash(self): ...
-
-def bind(datatype, pythontype, constructor=None, lexicalizer=None): ...
-
-class Variable(Identifier):
-    def __new__(cls, value): ...
-    def toPython(self): ...
-    def n3(self, namespace_manager=None): ...
-    def __reduce__(self): ...
-    def md5_term_hash(self): ...
-
-class Statement(Node, tuple):
-    def __new__(cls, __tuple_arg_2, context): ...
-    def __reduce__(self): ...
-    def toPython(self): ...
diff --git a/typeshed/rdflib/util.pyi b/typeshed/rdflib/util.pyi
deleted file mode 100644
index 0921d30..0000000
--- a/typeshed/rdflib/util.pyi
+++ /dev/null
@@ -1,21 +0,0 @@
-# Stubs for rdflib.util (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-def list2set(seq): ...
-def first(seq): ...
-def uniq(sequence, strip=0): ...
-def more_than(sequence, number): ...
-def to_term(s, default=None): ...
-def from_n3(s, default=None, backend=None): ...
-def check_context(c): ...
-def check_subject(s): ...
-def check_predicate(p): ...
-def check_object(o): ...
-def check_statement(triple): ...
-def check_pattern(triple): ...
-def date_time(t=None, local_time_zone=False): ...
-def parse_date_time(val): ...
-def guess_format(fpath, fmap=None): ...
-def find_roots(graph, prop, roots=None): ...
-def get_tree(graph, root, prop, mapper=..., sortkey=None, done=None, dir=''): ...
diff --git a/typeshed/select.pyi b/typeshed/select.pyi
deleted file mode 100644
index 094bb91..0000000
--- a/typeshed/select.pyi
+++ /dev/null
@@ -1,137 +0,0 @@
-import sys
-from typing import Any, Optional, Sequence, Tuple, Iterable, List, Union
-
-# When we have protocols, this should change to a protocol with a fileno method
-# See https://docs.python.org/3/c-api/file.html#c.PyObject_AsFileDescriptor
-_FileDescriptor = Union[int, Any]
-
-EPOLLERR: int
-EPOLLET: int
-EPOLLHUP: int
-EPOLLIN: int
-EPOLLMSG: int
-EPOLLONESHOT: int
-EPOLLOUT: int
-EPOLLPRI: int
-EPOLLRDBAND: int
-EPOLLRDNORM: int
-EPOLLWRBAND: int
-EPOLLWRNORM: int
-EPOLL_RDHUP: int
-KQ_EV_ADD: int
-KQ_EV_CLEAR: int
-KQ_EV_DELETE: int
-KQ_EV_DISABLE: int
-KQ_EV_ENABLE: int
-KQ_EV_EOF: int
-KQ_EV_ERROR: int
-KQ_EV_FLAG1: int
-KQ_EV_ONESHOT: int
-KQ_EV_SYSFLAGS: int
-KQ_FILTER_AIO: int
-KQ_FILTER_NETDEV: int
-KQ_FILTER_PROC: int
-KQ_FILTER_READ: int
-KQ_FILTER_SIGNAL: int
-KQ_FILTER_TIMER: int
-KQ_FILTER_VNODE: int
-KQ_FILTER_WRITE: int
-KQ_NOTE_ATTRIB: int
-KQ_NOTE_CHILD: int
-KQ_NOTE_DELETE: int
-KQ_NOTE_EXEC: int
-KQ_NOTE_EXIT: int
-KQ_NOTE_EXTEND: int
-KQ_NOTE_FORK: int
-KQ_NOTE_LINK: int
-KQ_NOTE_LINKDOWN: int
-KQ_NOTE_LINKINV: int
-KQ_NOTE_LINKUP: int
-KQ_NOTE_LOWAT: int
-KQ_NOTE_PCTRLMASK: int
-KQ_NOTE_PDATAMASK: int
-KQ_NOTE_RENAME: int
-KQ_NOTE_REVOKE: int
-KQ_NOTE_TRACK: int
-KQ_NOTE_TRACKERR: int
-KQ_NOTE_WRITE: int
-PIPE_BUF: int
-POLLERR: int
-POLLHUP: int
-POLLIN: int
-POLLMSG: int
-POLLNVAL: int
-POLLOUT: int
-POLLPRI: int
-POLLRDBAND: int
-POLLRDNORM: int
-POLLWRBAND: int
-POLLWRNORM: int
-
-class poll:
-    def __init__(self) -> None: ...
-    def register(self, fd: _FileDescriptor, eventmask: int = ...) -> None: ...
-    def modify(self, fd: _FileDescriptor, eventmask: int) -> None: ...
-    def unregister(self, fd: _FileDescriptor) -> None: ...
-    def poll(self, timeout: Optional[float] = ...) -> List[Tuple[int, int]]: ...
-
-def select(rlist: Sequence[Any], wlist: Sequence[Any], xlist: Sequence[Any],
-           timeout: Optional[float] = ...) -> Tuple[List[Any],
-                                                    List[Any],
-                                                    List[Any]]: ...
-
-if sys.version_info >= (3, 3):
-    error = OSError
-else:
-    class error(Exception): ...
-
-# BSD only
-class kevent(object):
-    data: Any
-    fflags: int
-    filter: int
-    flags: int
-    ident: int
-    udata: Any
-    def __init__(self, ident: _FileDescriptor, filter: int = ..., flags: int = ..., fflags: int = ..., data: Any = ..., udata: Any = ...) -> None: ...
-
-# BSD only
-class kqueue(object):
-    closed: bool
-    def __init__(self) -> None: ...
-    def close(self) -> None: ...
-    def control(self, changelist: Optional[Iterable[kevent]], max_events: int, timeout: float = ...) -> List[kevent]: ...
-    def fileno(self) -> int: ...
-    @classmethod
-    def fromfd(cls, fd: _FileDescriptor) -> kqueue: ...
-
-# Linux only
-class epoll(object):
-    if sys.version_info >= (3, 3):
-        def __init__(self, sizehint: int = ..., flags: int = ...) -> None: ...
-    else:
-        def __init__(self, sizehint: int = ...) -> None: ...
-    if sys.version_info >= (3, 4):
-        def __enter__(self) -> epoll: ...
-        def __exit__(self, *args: Any) -> None: ...
-    def close(self) -> None: ...
-    closed: bool
-    def fileno(self) -> int: ...
-    def register(self, fd: _FileDescriptor, eventmask: int = ...) -> None: ...
-    def modify(self, fd: _FileDescriptor, eventmask: int) -> None: ...
-    def unregister(self, fd: _FileDescriptor) -> None: ...
-    def poll(self, timeout: float = ..., maxevents: int = ...) -> List[Tuple[int, int]]: ...
-    @classmethod
-    def fromfd(cls, fd: _FileDescriptor) -> epoll: ...
-
-if sys.version_info >= (3, 3):
-    # Solaris only
-    class devpoll:
-        if sys.version_info >= (3, 4):
-            def close(self) -> None: ...
-            closed: bool
-            def fileno(self) -> int: ...
-        def register(self, fd: _FileDescriptor, eventmask: int = ...) -> None: ...
-        def modify(self, fd: _FileDescriptor, eventmask: int = ...) -> None: ...
-        def unregister(self, fd: _FileDescriptor) -> None: ...
-        def poll(self, timeout: Optional[float] = ...) -> List[Tuple[int, int]]: ...
\ No newline at end of file
diff --git a/typeshed/shellescape/__init__.pyi b/typeshed/shellescape/__init__.pyi
deleted file mode 100644
index 621241e..0000000
--- a/typeshed/shellescape/__init__.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for shellescape (Python 2)
-#
-# NOTE: This dynamically typed stub was automatically generated by stubgen.
-
-from .main import quote as quote
diff --git a/typeshed/shellescape/main.pyi b/typeshed/shellescape/main.pyi
deleted file mode 100644
index 69eade6..0000000
--- a/typeshed/shellescape/main.pyi
+++ /dev/null
@@ -1,5 +0,0 @@
-# Stubs for shellescape.main (Python 2)
-
-from typing import AnyStr
-
-def quote(s: AnyStr) -> AnyStr: ...
diff --git a/typeshed/urllib/__init__.py b/typeshed/urllib/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/typeshed/urllib/parse.pyi b/typeshed/urllib/parse.pyi
deleted file mode 100644
index cb7837e..0000000
--- a/typeshed/urllib/parse.pyi
+++ /dev/null
@@ -1,152 +0,0 @@
-# Stubs for urllib.parse
-from typing import Any, List, Dict, Tuple, AnyStr, Generic, Iterator, overload, Sequence, Mapping, Union, NamedTuple, Callable, Optional
-import sys
-
-_Str = Union[bytes, str]
-
-
-uses_relative: List[str]
-uses_netloc: List[str]
-uses_params: List[str]
-non_hierarchical: List[str]
-uses_query: List[str]
-uses_fragment: List[str]
-scheme_chars: str
-MAX_CACHE_SIZE = 0
-
-class _ResultMixinBase(Generic[AnyStr]):
-    def geturl(https://github.com/self) -> AnyStr: ...
-
-class _ResultMixinStr(_ResultMixinBase[str]):
-    def encode(self, encoding: str = ..., errors: str = ...) -> _ResultMixinBytes: ...
-
-
-class _ResultMixinBytes(_ResultMixinBase[str]):
-    def decode(self, encoding: str = ..., errors: str = ...) -> _ResultMixinStr: ...
-
-
-class _NetlocResultMixinBase(Generic[AnyStr]):
-    username: AnyStr
-    password: AnyStr
-    hostname: AnyStr
-    port: int
-
-class _NetlocResultMixinStr(_NetlocResultMixinBase[str], _ResultMixinStr): ...
-
-class _NetlocResultMixinBytes(_NetlocResultMixinBase[bytes], _ResultMixinBytes): ...
-
-class _DefragResultBase(Generic[AnyStr]):
-    url: AnyStr
-    fragment: AnyStr
-    @overload
-    def __getitem__(self, x: slice) -> AnyStr: ...
-    @overload
-    def __getitem__(self, x: int) -> AnyStr: ...
-    def __iter__(self) -> Iterator[AnyStr]: ...
-
-
-
-_SplitResultBase = NamedTuple(
-    '_SplitResultBase',
-    [
-        ('scheme', str), ('netloc', str), ('path', str), ('query', str), ('fragment', str)
-    ]
-)
-_SplitResultBytesBase = NamedTuple(
-    '_SplitResultBytesBase',
-    [
-        ('scheme', bytes), ('netloc', bytes), ('path', bytes), ('query', bytes), ('fragment', bytes)
-    ]
-)
-
-_ParseResultBase = NamedTuple(
-    '_ParseResultBase',
-    [
-        ('scheme', str), ('netloc', str), ('path', str), ('params', str), ('query', str), ('fragment', str)
-    ]
-)
-_ParseResultBytesBase = NamedTuple(
-    '_ParseResultBytesBase',
-    [
-        ('scheme', bytes), ('netloc', bytes), ('path', bytes), ('params', bytes), ('query', bytes), ('fragment', bytes)
-    ]
-)
-
-# Structured result objects for string data
-class DefragResult(_DefragResultBase[str], _ResultMixinStr): ...
-
-class SplitResult(_SplitResultBase, _NetlocResultMixinStr): ...
-
-class ParseResult(_ParseResultBase, _NetlocResultMixinStr): ...
-
-# Structured result objects for bytes data
-class DefragResultBytes(_DefragResultBase[bytes], _ResultMixinBytes): ...
-
-class SplitResultBytes(_SplitResultBytesBase, _NetlocResultMixinBytes): ...
-
-class ParseResultBytes(_ParseResultBytesBase, _NetlocResultMixinBytes): ...
-
-
-def parse_qs(qs: AnyStr, keep_blank_values: bool = ..., strict_parsing: bool = ..., encoding: str = ..., errors: str = ...) -> Dict[AnyStr, List[AnyStr]]: ...
-
-def parse_qsl(qs: AnyStr, keep_blank_values: bool = ..., strict_parsing: bool = ..., encoding: str = ..., errors: str = ...) -> List[Tuple[AnyStr, AnyStr]]: ...
-
-
-@overload
-def quote(string: str, safe: _Str = ..., encoding: str = ..., errors: str = ...) -> str: ...
-@overload
-def quote(string: bytes, safe: _Str = ...) -> str: ...
-
-def quote_from_bytes(bs: bytes, safe: _Str = ...) -> str: ...
-
-@overload
-def quote_plus(string: str, safe: _Str = ..., encoding: str = ..., errors: str = ...) -> str: ...
-@overload
-def quote_plus(string: bytes, safe: _Str = ...) -> str: ...
-
-def unquote(string: str, encoding: str = ..., errors: str = ...) -> str: ...
-
-def unquote_to_bytes(string: _Str) -> bytes: ...
-
-def unquote_plus(string: str, encoding: str = ..., errors: str = ...) -> str: ...
-
-@overload
-def urldefrag(url: str) -> DefragResult: ...
-@overload
-def urldefrag(url: bytes) -> DefragResultBytes: ...
-
-if sys.version_info >= (3, 5):
-    def urlencode(query: Union[Mapping[Any, Any],
-                               Mapping[Any, Sequence[Any]],
-                               Sequence[Tuple[Any, Any]],
-                               Sequence[Tuple[Any, Sequence[Any]]]],
-                  doseq: bool = ..., safe: AnyStr = ..., encoding: str = ..., errors: str = ...,
-                  quote_via: Callable[[str, AnyStr, str, str], str] = ...) -> str: ...
-else:
-    def urlencode(query: Union[Mapping[Any, Any],
-                               Mapping[Any, Sequence[Any]],
-                               Sequence[Tuple[Any, Any]],
-                               Sequence[Tuple[Any, Sequence[Any]]]],
-                  doseq: bool = ..., safe: AnyStr = ..., encoding: str = ..., errors: str = ...) -> str: ...
-
-def urljoin(base: Optional[AnyStr], url: Optional[AnyStr], allow_fragments: bool = ...) -> AnyStr: ...
-
-@overload
-def urlparse(url: str, scheme: str = ..., allow_fragments: bool = ...) -> ParseResult: ...
-@overload
-def urlparse(url: bytes, scheme: bytes = ..., allow_fragments: bool = ...) -> ParseResultBytes: ...
-
-@overload
-def urlsplit(url: Optional[str], scheme: str = ..., allow_fragments: bool = ...) -> SplitResult: ...
-@overload
-def urlsplit(url: bytes, scheme: bytes = ..., allow_fragments: bool = ...) -> SplitResultBytes: ...
-
-@overload
-def urlunparse(components: Tuple[AnyStr, AnyStr, AnyStr, AnyStr, AnyStr, AnyStr]) -> AnyStr: ...
-@overload
-def urlunparse(components: Sequence[AnyStr]) -> AnyStr: ...
-
-@overload
-def urlunsplit(components: Tuple[AnyStr, AnyStr, AnyStr, AnyStr, AnyStr]) -> AnyStr: ...
-@overload
-def urlunsplit(components: Sequence[AnyStr]) -> AnyStr: ...
diff --git a/typeshed/urllib/subprocess.pyi b/typeshed/urllib/subprocess.pyi
deleted file mode 100644
index 2fd8b5b..0000000
--- a/typeshed/urllib/subprocess.pyi
+++ /dev/null
@@ -1,1208 +0,0 @@
-# Stubs for subprocess
-
-# Based on http://docs.python.org/3.6/library/subprocess.html
-import sys
-from typing import Sequence, Any, Mapping, Callable, Tuple, IO, Optional, Union, Type, Text, Generic, TypeVar, AnyStr, overload
-from types import TracebackType
-
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
-
-# We prefer to annotate inputs to methods (eg subprocess.check_call) with these
-# union types.
-# For outputs we use laborious literal based overloads to try to determine
-# which specific return types to use, and prefer to fall back to Any when
-# this does not work, so the caller does not have to use an assertion to confirm
-# which type.
-#
-# For example:
-#
-# try:
-#    x = subprocess.check_output(["ls", "-l"])
-#    reveal_type(x)  # bytes, based on the overloads
-# except TimeoutError as e:
-#    reveal_type(e.cmd)  # Any, but morally is _CMD
-_FILE = Union[None, int, IO[Any]]
-_TXT = Union[bytes, Text]
-if sys.version_info >= (3, 6):
-    from builtins import _PathLike
-    _PATH = Union[bytes, Text, _PathLike]
-else:
-    _PATH = Union[bytes, Text]
-# Python 3.6 does't support _CMD being a single PathLike.
-# See: https://bugs.python.org/issue31961
-_CMD = Union[_TXT, Sequence[_PATH]]
-_ENV = Union[Mapping[bytes, _TXT], Mapping[Text, _TXT]]
-
-_S = TypeVar('_S')
-_T = TypeVar('_T')
-
-class CompletedProcess(Generic[_T]):
-    # morally: _CMD
-    args: Any
-    returncode: int
-    # These are really both Optional, but requiring checks would be tedious
-    # and writing all the overloads would be horrific.
-    stdout: _T
-    stderr: _T
-    def __init__(self, args: _CMD, returncode: int, stdout: Optional[_T] = ..., stderr: Optional[_T] = ...) -> None: ...
-    def check_returncode(self) -> None: ...
-
-if sys.version_info >= (3, 7):
-    # Nearly the same args as for 3.6, except for capture_output and text
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: Optional[str] = ...,
-        input: Optional[str] = ...,
-        text: Literal[True],
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: str,
-        errors: Optional[str] = ...,
-        input: Optional[str] = ...,
-        text: Optional[bool] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: str,
-        input: Optional[str] = ...,
-        text: Optional[bool] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        *,
-        universal_newlines: Literal[True],
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        # where the *real* keyword only args start
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: Optional[str] = ...,
-        input: Optional[str] = ...,
-        text: Optional[bool] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: Literal[False] = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: None = ...,
-        errors: None = ...,
-        input: Optional[bytes] = ...,
-        text: Literal[None, False] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[bytes]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        capture_output: bool = ...,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: Optional[str] = ...,
-        input: Optional[_TXT] = ...,
-        text: Optional[bool] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[Any]: ...
-elif sys.version_info >= (3, 6):
-    # Nearly same args as Popen.__init__ except for timeout, input, and check
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        encoding: str,
-        errors: Optional[str] = ...,
-        input: Optional[str] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: str,
-        input: Optional[str] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        *,
-        universal_newlines: Literal[True],
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        # where the *real* keyword only args start
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: Optional[str] = ...,
-        input: Optional[str] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: Literal[False] = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        encoding: None = ...,
-        errors: None = ...,
-        input: Optional[bytes] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[bytes]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        encoding: Optional[str] = ...,
-        errors: Optional[str] = ...,
-        input: Optional[_TXT] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[Any]: ...
-else:
-    # Nearly same args as Popen.__init__ except for timeout, input, and check
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        *,
-        universal_newlines: Literal[True],
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        # where the *real* keyword only args start
-        check: bool = ...,
-        input: Optional[str] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[str]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: Literal[False] = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        input: Optional[bytes] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[bytes]: ...
-    @overload
-    def run(
-        args: _CMD,
-        bufsize: int = ...,
-        executable: _PATH = ...,
-        stdin: _FILE = ...,
-        stdout: _FILE = ...,
-        stderr: _FILE = ...,
-        preexec_fn: Callable[[], Any] = ...,
-        close_fds: bool = ...,
-        shell: bool = ...,
-        cwd: Optional[_PATH] = ...,
-        env: Optional[_ENV] = ...,
-        universal_newlines: bool = ...,
-        startupinfo: Any = ...,
-        creationflags: int = ...,
-        restore_signals: bool = ...,
-        start_new_session: bool = ...,
-        pass_fds: Any = ...,
-        *,
-        check: bool = ...,
-        input: Optional[_TXT] = ...,
-        timeout: Optional[float] = ...,
-    ) -> CompletedProcess[Any]: ...
-
-# Same args as Popen.__init__
-def call(args: _CMD,
-         bufsize: int = ...,
-         executable: _PATH = ...,
-         stdin: _FILE = ...,
-         stdout: _FILE = ...,
-         stderr: _FILE = ...,
-         preexec_fn: Callable[[], Any] = ...,
-         close_fds: bool = ...,
-         shell: bool = ...,
-         cwd: Optional[_PATH] = ...,
-         env: Optional[_ENV] = ...,
-         universal_newlines: bool = ...,
-         startupinfo: Any = ...,
-         creationflags: int = ...,
-         restore_signals: bool = ...,
-         start_new_session: bool = ...,
-         pass_fds: Any = ...,
-         timeout: Optional[float] = ...) -> int: ...
-
-# Same args as Popen.__init__
-def check_call(args: _CMD,
-               bufsize: int = ...,
-               executable: _PATH = ...,
-               stdin: _FILE = ...,
-               stdout: _FILE = ...,
-               stderr: _FILE = ...,
-               preexec_fn: Callable[[], Any] = ...,
-               close_fds: bool = ...,
-               shell: bool = ...,
-               cwd: Optional[_PATH] = ...,
-               env: Optional[_ENV] = ...,
-               universal_newlines: bool = ...,
-               startupinfo: Any = ...,
-               creationflags: int = ...,
-               restore_signals: bool = ...,
-               start_new_session: bool = ...,
-               pass_fds: Any = ...,
-               timeout: Optional[float] = ...) -> int: ...
-
-if sys.version_info >= (3, 7):
-    # 3.7 added text
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: Optional[str] = ...,
-                     text: Literal[True],
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: str,
-                     errors: Optional[str] = ...,
-                     text: Optional[bool] = ...,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: str,
-                     text: Optional[bool] = ...,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     *,
-                     universal_newlines: Literal[True],
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     # where the real keyword only ones start
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: Optional[str] = ...,
-                     text: Optional[bool] = ...,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: Literal[False] = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: None = ...,
-                     errors: None = ...,
-                     text: Literal[None, False] = ...,
-                     ) -> bytes: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: Optional[str] = ...,
-                     text: Optional[bool] = ...,
-                     ) -> Any: ...  # morally: -> _TXT
-elif sys.version_info >= (3, 6):
-    # 3.6 added encoding and errors
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: str,
-                     errors: Optional[str] = ...,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: str,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     universal_newlines: Literal[True],
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: Optional[str] = ...,
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: Literal[False] = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: None = ...,
-                     errors: None = ...,
-                     ) -> bytes: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     *,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     encoding: Optional[str] = ...,
-                     errors: Optional[str] = ...,
-                     ) -> Any: ...  # morally: -> _TXT
-else:
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     *,
-                     universal_newlines: Literal[True],
-                     ) -> str: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: Literal[False] = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     ) -> bytes: ...
-    @overload
-    def check_output(args: _CMD,
-                     bufsize: int = ...,
-                     executable: _PATH = ...,
-                     stdin: _FILE = ...,
-                     stderr: _FILE = ...,
-                     preexec_fn: Callable[[], Any] = ...,
-                     close_fds: bool = ...,
-                     shell: bool = ...,
-                     cwd: Optional[_PATH] = ...,
-                     env: Optional[_ENV] = ...,
-                     universal_newlines: bool = ...,
-                     startupinfo: Any = ...,
-                     creationflags: int = ...,
-                     restore_signals: bool = ...,
-                     start_new_session: bool = ...,
-                     pass_fds: Any = ...,
-                     timeout: Optional[float] = ...,
-                     input: _TXT = ...,
-                     ) -> Any: ...  # morally: -> _TXT
-
-
-PIPE: int
-STDOUT: int
-DEVNULL: int
-class SubprocessError(Exception): ...
-class TimeoutExpired(SubprocessError):
-    def __init__(self, cmd: _CMD, timeout: float, output: Optional[_TXT] = ..., stderr: Optional[_TXT] = ...) -> None: ...
-    # morally: _CMD
-    cmd: Any
-    timeout: float
-    # morally: Optional[_TXT]
-    output: Any
-    stdout: Any
-    stderr: Any
-
-
-class CalledProcessError(Exception):
-    returncode: int
-    # morally: _CMD
-    cmd: Any
-    # morally: Optional[_TXT]
-    output: Any
-
-    # morally: Optional[_TXT]
-    stdout: Any
-    stderr: Any
-
-    def __init__(self,
-                 returncode: int,
-                 cmd: _CMD,
-                 output: Optional[_TXT] = ...,
-                 stderr: Optional[_TXT] = ...) -> None: ...
-
-class Popen(Generic[AnyStr]):
-    args: _CMD
-    stdin: IO[AnyStr]
-    stdout: IO[AnyStr]
-    stderr: IO[AnyStr]
-    pid: int
-    returncode: int
-
-    # Technically it is wrong that Popen provides __new__ instead of __init__
-    # but this shouldn't come up hopefully?
-
-    if sys.version_info >= (3, 7):
-        # text is added in 3.7
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    text: Optional[bool] = ...,
-                    encoding: str,
-                    errors: Optional[str] = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    text: Optional[bool] = ...,
-                    encoding: Optional[str] = ...,
-                    errors: str) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    *,
-                    universal_newlines: Literal[True],
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    # where the *real* keyword only args start
-                    text: Optional[bool] = ...,
-                    encoding: Optional[str] = ...,
-                    errors: Optional[str] = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    text: Literal[True],
-                    encoding: Optional[str] = ...,
-                    errors: Optional[str] = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: Literal[False] = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    text: Literal[None, False] = ...,
-                    encoding: None = ...,
-                    errors: None = ...) -> Popen[bytes]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    text: Optional[bool] = ...,
-                    encoding: Optional[str] = ...,
-                    errors: Optional[str] = ...) -> Popen[Any]: ...
-    elif sys.version_info >= (3, 6):
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    encoding: str,
-                    errors: Optional[str] = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    encoding: Optional[str] = ...,
-                    errors: str) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    *,
-                    universal_newlines: Literal[True],
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    # where the *real* keyword only args start
-                    encoding: Optional[str] = ...,
-                    errors: Optional[str] = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: Literal[False] = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    encoding: None = ...,
-                    errors: None = ...) -> Popen[bytes]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...,
-                    *,
-                    encoding: Optional[str] = ...,
-                    errors: Optional[str] = ...) -> Popen[Any]: ...
-    else:
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    *,
-                    universal_newlines: Literal[True],
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...) -> Popen[str]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    *,
-                    universal_newlines: Literal[False] = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...) -> Popen[bytes]: ...
-        @overload
-        def __new__(cls,
-                    args: _CMD,
-                    bufsize: int = ...,
-                    executable: Optional[_PATH] = ...,
-                    stdin: Optional[_FILE] = ...,
-                    stdout: Optional[_FILE] = ...,
-                    stderr: Optional[_FILE] = ...,
-                    preexec_fn: Optional[Callable[[], Any]] = ...,
-                    close_fds: bool = ...,
-                    shell: bool = ...,
-                    cwd: Optional[_PATH] = ...,
-                    env: Optional[_ENV] = ...,
-                    universal_newlines: bool = ...,
-                    startupinfo: Optional[Any] = ...,
-                    creationflags: int = ...,
-                    restore_signals: bool = ...,
-                    start_new_session: bool = ...,
-                    pass_fds: Any = ...) -> Popen[Any]: ...
-
-    def poll(self) -> int: ...
-    def wait(self, timeout: Optional[float] = ...) -> int: ...
-    # Return str/bytes
-    def communicate(self,
-                    input: Optional[AnyStr] = ...,
-                    timeout: Optional[float] = ...,
-                    # morally this should be optional
-                    ) -> Tuple[AnyStr, AnyStr]: ...
-    def send_signal(self, signal: int) -> None: ...
-    def terminate(self) -> None: ...
-    def kill(self) -> None: ...
-    def __enter__(self: _S) -> _S: ...
-    def __exit__(self, type: Optional[Type[BaseException]], value: Optional[BaseException], traceback: Optional[TracebackType]) -> None: ...
-
-# The result really is always a str.
-def getstatusoutput(cmd: _TXT) -> Tuple[int, str]: ...
-def getoutput(cmd: _TXT) -> str: ...
-
-def list2cmdline(seq: Sequence[str]) -> str: ...  # undocumented
-
-if sys.platform == 'win32':
-    class STARTUPINFO:
-        if sys.version_info >= (3, 7):
-            def __init__(self, *, dwFlags: int = ..., hStdInput: Optional[Any] = ..., hStdOutput: Optional[Any] = ..., hStdError: Optional[Any] = ..., wShowWindow: int = ..., lpAttributeList: Optional[Mapping[str, Any]] = ...) -> None: ...
-        dwFlags: int
-        hStdInput: Optional[Any]
-        hStdOutput: Optional[Any]
-        hStdError: Optional[Any]
-        wShowWindow: int
-        if sys.version_info >= (3, 7):
-            lpAttributeList: Mapping[str, Any]
-
-    STD_INPUT_HANDLE: Any
-    STD_OUTPUT_HANDLE: Any
-    STD_ERROR_HANDLE: Any
-    SW_HIDE: int
-    STARTF_USESTDHANDLES: int
-    STARTF_USESHOWWINDOW: int
-    CREATE_NEW_CONSOLE: int
-    CREATE_NEW_PROCESS_GROUP: int
-    if sys.version_info >= (3, 7):
-        ABOVE_NORMAL_PRIORITY_CLASS: int
-        BELOW_NORMAL_PRIORITY_CLASS: int
-        HIGH_PRIORITY_CLASS: int
-        IDLE_PRIORITY_CLASS: int
-        NORMAL_PRIORITY_CLASS: int
-        REALTIME_PRIORITY_CLASS: int
-        CREATE_NO_WINDOW: int
-        DETACHED_PROCESS: int
-        CREATE_DEFAULT_ERROR_MODE: int
-        CREATE_BREAKAWAY_FROM_JOB: int

From 198f4991180a3c2b3ad0243d22067334ebadbf99 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 27 Sep 2022 11:37:37 +0200
Subject: [PATCH 042/165] update Makefile

---
 Makefile | 50 +++++++++++++++++++++++++++++---------------------
 1 file changed, 29 insertions(+), 21 deletions(-)

diff --git a/Makefile b/Makefile
index b655cd9..ab41f86 100644
--- a/Makefile
+++ b/Makefile
@@ -37,36 +37,39 @@ VERSION=2.2.$(shell TZ=UTC git log --first-parent --max-count=1 \
 ## all         : default task
 all: dev
 
-## help        : print this help message and exit
+## help                   : print this help message and exit
 help: Makefile
 	@sed -n 's/^##//p' $<
 
-## install-dep : install most of the development dependencies via pip
+## cleanup                : shortcut for "make sort_imports format flake8 diff_pydocstyle_report"
+cleanup: sort_imports format flake8 diff_pydocstyle_report
+
+## install-dep            : install most of the development dependencies via pip
 install-dep: install-dependencies
 
 install-dependencies: FORCE
 	pip install --upgrade $(DEVPKGS)
 	pip install -r requirements.txt
 
-## install-deb-dep: install most of the dev dependencies via apt-get
+## install-deb-dep        : install most of the dev dependencies via apt-get
 install-deb-dep:
 	sudo apt-get install $(DEBDEVPKGS)
 
-## install     : install the ${MODULE} module and cwltest
+## install                : install the cwltest package and cwltest script
 install: FORCE
 	pip install .
 
-## dev     : install the ${MODULE} module in dev mode
+## dev                    : install the cwltest package in dev mode
 dev: install-dep
 	pip install -e .
 
-## dist        : create a module package for distribution
+## dist                   : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
 dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
 	python setup.py sdist bdist_wheel
 
-## clean       : clean up all temporary / machine-generated files
+## clean                  : clean up all temporary / machine-generated files
 clean: FORCE
 	rm -f ${MODILE}/*.pyc tests/*.pyc
 	python setup.py clean --all || true
@@ -74,32 +77,37 @@ clean: FORCE
 	rm -f diff-cover.html
 
 # Linting and code style related targets
-## sorting imports using isort: https://github.com/timothycrosley/isort
-sort_imports: $(PYSOURCES)
+## sort_import            : sorting imports using isort: https://github.com/timothycrosley/isort
+sort_imports: $(PYSOURCES) mypy-stubs
 	isort $^
 
 remove_unused_imports: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
 	autoflake --in-place --remove-all-unused-imports $^
 
 pep257: pydocstyle
-## pydocstyle      : check Python code style
+## pydocstyle             : check Python docstring style
 pydocstyle: $(PYSOURCES)
 	pydocstyle --add-ignore=D100,D101,D102,D103 $^ || true
 
 pydocstyle_report.txt: $(PYSOURCES)
 	pydocstyle setup.py $^ > $@ 2>&1 || true
 
+## diff_pydocstyle_report : check Python docstring style for changed files only
 diff_pydocstyle_report: pydocstyle_report.txt
 	diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
 
-## format      : check/fix all code indentation and formatting (runs black)
+## codespell              : check for common misspellings
+codespell:
+	codespell -w $(shell git ls-files | grep -v mypy-stubs | grep -v gitignore)
+
+## format                 : check/fix all code indentation and formatting (runs black)
 format:
-	black setup.py cwltest setup.py
+	black setup.py cwltest setup.py mypy-stubs
 
 format-check:
-	black --diff --check setup.py cwltest
+	black --diff --check setup.py cwltest mypy-stubs
 
-## pylint      : run static code analysis on Python code
+## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
 	pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
                 $^ -j0|| true
@@ -109,9 +117,9 @@ pylint_report.txt: $(PYSOURCES)
 		$^ -j0> $@ || true
 
 diff_pylint_report: pylint_report.txt
-	diff-quality --violations=pylint pylint_report.txt
+	diff-quality --compare-branch=main --violations=pylint pylint_report.txt
 
-.coverage: $(PYSOURCES) all
+.coverage: $(PYSOURCES)
 	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}"
 
 coverage.xml: .coverage
@@ -127,23 +135,23 @@ coverage-report: .coverage
 	coverage report
 
 diff-cover: coverage.xml
-	diff-cover $^
+	diff-cover --compare-branch=main $^
 
 diff-cover.html: coverage.xml
-	diff-cover $^ --html-report $@
+	diff-cover --compare-branch=main $^ --html-report $@
 
-## test        : run the ${MODULE} test suite
+## test                   : run the cwltest test suite
 test: $(PYSOURCES) all
 	python setup.py test ${PYTEST_EXTRA}
 
-## testcov     : run the ${MODULE} test suite and collect coverage
+## testcov                : run the cwltest test suite and collect coverage
 testcov: $(PYSOURCES)
 	python setup.py test --addopts "--cov" ${PYTEST_EXTRA}
 
 sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@
 
-## sloccount   : count lines of code
+## sloccount              : count lines of code
 sloccount: $(PYSOURCES) Makefile
 	sloccount $^
 

From 9a567b2914d6bc37bad7fae9a9a0b6ad81cc7acf Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 27 Sep 2022 11:54:25 +0200
Subject: [PATCH 043/165] spellcheck

---
 .github/workflows/ci-tests.yml |  2 +-
 Makefile                       |  2 +-
 cwltest/__init__.py            | 14 +++++++-------
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 9ea22be..3fef60a 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -1,4 +1,4 @@
-name: Continous integration tests
+name: Continuous integration tests
 
 on:
   push:
diff --git a/Makefile b/Makefile
index ab41f86..1e84799 100644
--- a/Makefile
+++ b/Makefile
@@ -182,7 +182,7 @@ pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
 	pyupgrade --exit-zero-even-if-changed --py36-plus $^
 
 release-test: FORCE
-	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )
+	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
 	./release-test.sh
 
 release: release-test
diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index e16c828..8f5dbef 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -382,18 +382,18 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 
 def expand_number_range(nr: str) -> List[int]:
-    ans: List[int] = []
+    result: List[int] = []
     for s in nr.split(","):
         sp = s.split("-")
         if len(sp) == 2:
-            ans.extend(range(int(sp[0]) - 1, int(sp[1])))
+            result.extend(range(int(sp[0]) - 1, int(sp[1])))
         else:
-            ans.append(int(s) - 1)
-    return ans
+            result.append(int(s) - 1)
+    return result
 
 
-def main():  # type: () -> int
-
+def main() -> int:
+    """Run the main logic loop."""
     args = arg_parser().parse_args(sys.argv[1:])
     if "--" in args.args:
         args.args.remove("--")
@@ -432,7 +432,7 @@ def main():  # type: () -> int
     suite_name, _ = os.path.splitext(os.path.basename(args.test))
     report = junit_xml.TestSuite(suite_name, [])
 
-    # the number of total tests, failured tests, unsupported tests and passed tests for each tag
+    # the number of total tests, failed tests, unsupported tests and passed tests for each tag
     ntotal = defaultdict(int)  # type: Dict[str, int]
     nfailures = defaultdict(int)  # type: Dict[str, int]
     nunsupported = defaultdict(int)  # type: Dict[str, int]

From ea68925cb6726c07363a7e5526d9adfd3ffbe23d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 29 Sep 2022 14:19:58 +0200
Subject: [PATCH 044/165] start testing with Python 3.11

---
 .github/dependabot.yml         | 19 ++++++---
 .github/workflows/ci-tests.yml | 36 ++++++++++-------
 README.rst                     |  2 +-
 setup.py                       |  1 +
 tox.ini                        | 73 +++++++++++++++-------------------
 5 files changed, 71 insertions(+), 60 deletions(-)

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 491deae..bf1d70a 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -1,7 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
 version: 2
 updates:
-- package-ecosystem: pip
-  directory: "/"
-  schedule:
-    interval: daily
-  open-pull-requests-limit: 10
+  - package-ecosystem: "pip"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 3fef60a..03d7c3b 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -15,13 +15,13 @@ jobs:
   tox:
     name: CI tests via Tox
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-20.04  # 22.04 doesn't support Python 3.6
 
     strategy:
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [6, 7, 8, 9, 10]
+        py-ver-minor: [6, 7, 8, 9, 10, 11]
         step: [lint, unit, mypy]
         exclude:
           - py-ver-major: 3
@@ -33,15 +33,23 @@ jobs:
       TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        if: matrix.py-ver-minor != 11
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
 
+      - name: Set up Python 3.11.0-rc.2
+        if: matrix.py-ver-minor == 11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11.0-rc.2
+
+
       - name: Cache for pip
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt', 'tox.ini') }}
@@ -53,7 +61,7 @@ jobs:
 
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: .mypy_cache/${{ env.py-semver }}
           key: mypy-${{ env.py-semver }}
@@ -63,7 +71,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ matrix.step == 'unit' }}
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3
         with:
           fail_ci_if_error: true
 
@@ -81,17 +89,17 @@ jobs:
       TOXENV: ${{ format('py310-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
 
       - name: Cache for pip
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
@@ -111,18 +119,18 @@ jobs:
   release_test:
     name: cwltest release test
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
 
       - name: Cache for pip
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-release-${{ hashFiles('requirements.txt', 'test-requirements.txt') }}
diff --git a/README.rst b/README.rst
index e93d862..15066a6 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.6, 3.7, 3.8, 3.9, and 3.10.
+This is written and tested for Python 3.6, 3.7, 3.8, 3.9, 3.10, and 3.11.
 
 Install
 -------
diff --git a/setup.py b/setup.py
index 445d543..6466981 100644
--- a/setup.py
+++ b/setup.py
@@ -62,6 +62,7 @@
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
         "Typing :: Typed",
     ],
 )
diff --git a/tox.ini b/tox.ini
index 430d084..37b83b3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,12 +1,11 @@
 [tox]
 envlist =
-  py{36,37,38,39,310}-lint,
-  py{36,37,38,39,310}-unit,
-  py{36,37,38,39,310}-bandit,
-  py{37,38,39,310}-mypy,
-  py39-pipconflictchecker,
-  py39-lintreadme,
-  py39-pydocstyle
+  py{36,37,38,39,310,311}-lint,
+  py{36,37,38,39,310,311}-unit,
+  py{36,37,38,39,310,311}-bandit,
+  py{37,38,39,310,311}-mypy,
+  py310-lintreadme,
+  py310-pydocstyle
 
 skip_missing_interpreters = True
 
@@ -21,50 +20,51 @@ python =
   3.8: py38
   3.9: py39
   3.10: py310
+  3.11: py311
 
 [testenv]
 description =
-  py{36,37,38,39,310}-unit: Run the unit tests
-  py{36,37,38,39,310}-lint: Lint the Python code
-  py{36,37,38,39,310}-bandit: Search for common security issues
-  py{37,38,39,310}-mypy: Check for type safety
-  py39-pydocstyle: docstring style checker
-  py39-lintreadme: Lint the README.rst->.md conversion
+  py{36,37,38,39,310,311}-unit: Run the unit tests
+  py{36,37,38,39,310,311}-lint: Lint the Python code
+  py{36,37,38,39,310,311}-bandit: Search for common security issues
+  py{37,38,39,310,311}-mypy: Check for type safety
+  py310-pydocstyle: docstring style checker
+  py310-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 deps =
-  py{36,37,38,39,310}-{unit,mypy}: -rrequirements.txt
-  py{36,37,38,39,310}-{unit,mypy}: -rtest-requirements.txt
-  py{36,37,38,39,310}-lint: flake8-bugbear
-  py{36,37,38,39,310}-lint: black
-  py{36,37,38,39,310}-bandit: bandit
-  py{37,38,39,310}-mypy: -rmypy-requirements.txt
+  py{36,37,38,39,310,311}-{unit,mypy}: -rrequirements.txt
+  py{36,37,38,39,310,311}-{unit,mypy}: -rtest-requirements.txt
+  py{36,37,38,39,310,311}-lint: flake8-bugbear
+  py{36,37,38,39,310,311}-lint: black
+  py{36,37,38,39,310,311}-bandit: bandit
+  py{37,38,39,310,311}-mypy: -rmypy-requirements.txt
 
 setenv =
-  py{36,37,38,39,310}-unit: LC_ALL = C.UTF-8
+  py{36,37,38,39,310,311}-unit: LC_ALL = C.UTF-8
 
 commands =
-  py{36,37,38,39,310}-unit: python -m pip install -U pip setuptools wheel
-  py{36,37,38,39,310}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
-  py{36,37,38,39,310}-bandit: bandit --recursive cwltest --exclude cwltest/tests/*
-  py{36,37,38,39,310}-lint: make flake8
-  py{36,37,38,39,310}-lint: make format-check
-  py{37,38,39,310}-mypy: make mypy
+  py{36,37,38,39,310,311}-unit: python -m pip install -U pip setuptools wheel
+  py{36,37,38,39,310,311}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest --exclude cwltest/tests/*
+  py{36,37,38,39,310,311}-lint: make flake8
+  py{36,37,38,39,310,311}-lint: make format-check
+  py{37,38,39,310,311}-mypy: make mypy
   py37-mypy: make mypy_3.6
 
 whitelist_externals =
-  py{36,37,38,39,310}-lint: flake8
-  py{36,37,38,39,310}-lint: black
-  py{36,37,38,39,310}-{mypy,shellcheck,lint,unit}: make
+  py{36,37,38,39,310,311}-lint: flake8
+  py{36,37,38,39,310,311}-lint: black
+  py{36,37,38,39,310,311}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py{36,37,38,39,310}-lint: true
-  py{36,37,38,39,310}-bandit: true
+  py{36,37,38,39,310,311}-lint: true
+  py{36,37,38,39,310,311}-bandit: true
 
 
-[testenv:py39-pydocstyle]
+[testenv:py310-pydocstyle]
 whitelist_externals = make
 commands = make diff_pydocstyle_report
 deps =
@@ -72,14 +72,7 @@ deps =
     diff-cover
 skip_install = true
 
-[testenv:py39-pipconflictchecker]
-commands = pipconflictchecker
-whitelist_externals = pipconflictchecker
-deps =
-  pip-conflict-checker
-  pip==9.0.3
-
-[testenv:py39-lintreadme]
+[testenv:py310-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
   python setup.py sdist

From c0f8224097ab67c15ba8fd680a2cfef77628da6d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 29 Sep 2022 12:31:51 +0000
Subject: [PATCH 045/165] Bump github/codeql-action from 1 to 2

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 1 to 2.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v1...v2)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/codeql-analysis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 3cd36ce..b88bbd0 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -26,9 +26,9 @@ jobs:
       
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: python
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2

From c73bd305ba00a406df3bddbaf5111cf239e9d2ab Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 29 Sep 2022 12:43:49 +0000
Subject: [PATCH 046/165] Bump actions/checkout from 2 to 3

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/codeql-analysis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index b88bbd0..7993d84 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -13,7 +13,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.

From 36040848655cd6b6597c4a6350f08270ed97f402 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 4 Oct 2022 00:11:23 +0000
Subject: [PATCH 047/165] Bump mypy from 0.981 to 0.982

Bumps [mypy](https://github.com/python/mypy) from 0.981 to 0.982.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.981...v0.982)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 7678736..f04612c 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.981
+mypy==0.982
 types-setuptools
 types-requests

From e3eae1aa1dae2fb8db51d595b13620753fd11b5e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 26 Oct 2022 00:18:26 +0000
Subject: [PATCH 048/165] Update pytest requirement from <7.2,>=6.2 to
 >=6.2,<7.3

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/6.2.0...7.2.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 test-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test-requirements.txt b/test-requirements.txt
index 072f0cc..e5540ed 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,2 +1,2 @@
-pytest >= 6.2, < 7.2
+pytest >= 6.2, < 7.3
 pytest-cov

From cc6caeb6d45fdeba753244feea6623a38cbb7da2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 8 Nov 2022 09:48:33 +0100
Subject: [PATCH 049/165] Bump mypy from 0.982 to 0.990 (#153)

* Bump mypy from 0.982 to 0.990

Bumps [mypy](https://github.com/python/mypy) from 0.982 to 0.990.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.982...v0.990)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* mypy 0.990 needs this override

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>
---
 mypy-requirements.txt                    | 2 +-
 mypy-stubs/rdflib/namespace/__init__.pyi | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f04612c..05121dd 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.982
+mypy==0.990
 types-setuptools
 types-requests
diff --git a/mypy-stubs/rdflib/namespace/__init__.pyi b/mypy-stubs/rdflib/namespace/__init__.pyi
index e5342fd..63af929 100644
--- a/mypy-stubs/rdflib/namespace/__init__.pyi
+++ b/mypy-stubs/rdflib/namespace/__init__.pyi
@@ -33,7 +33,7 @@ __all__ = [
 
 class Namespace(str):
     @property
-    def title(self) -> URIRef: ...
+    def title(self) -> URIRef: ...  # type: ignore[override]
     def term(self, name: Any) -> URIRef: ...
     def __getitem__(self, key: Any) -> URIRef: ...
     def __getattr__(self, name: str) -> URIRef: ...

From 220dfb6de68afee82a5bad0ca563f0b190de4e85 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 16 Nov 2022 09:24:29 +0100
Subject: [PATCH 050/165] Bump mypy from 0.990 to 0.991 (#154)

Bumps [mypy](https://github.com/python/mypy) from 0.990 to 0.991.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.990...v0.991)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 05121dd..f620fb9 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,3 @@
-mypy==0.990
+mypy==0.991
 types-setuptools
 types-requests

From 0ce17ac5a963cb80873aa5e967f401080061a1a9 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Wed, 7 Dec 2022 08:58:13 +0100
Subject: [PATCH 051/165] remove redundant comparison

---
 cwltest/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 8f5dbef..c0e58ad 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -567,7 +567,7 @@ def main() -> int:
                     passed += 1
                     for t in tags:
                         npassed[t] += 1
-                elif return_code != 0 and return_code != UNSUPPORTED_FEATURE:
+                elif return_code != UNSUPPORTED_FEATURE:
                     failures += 1
                     for t in tags:
                         nfailures[t] += 1

From 80ec2a34da15d860f83836dfd5f50d6085804699 Mon Sep 17 00:00:00 2001
From: Iacopo Colonnelli <iacopo.c92@gmail.com>
Date: Wed, 4 Jan 2023 10:11:09 +0100
Subject: [PATCH 052/165] Code reorganization (#155)

This commit improves code organization by extracting functionalities
from the `__init__.py` file and dividing them into more specialized
Python modules. In particular:

 - An `argparser.py` module contains the argument parser for the cwltest
   CLI
 - A `main.py` module contains the code to run the tests
 - A `__main__.py` file serves as the main entrypoint for the package
 - Some logic has been moved from the `__init__.py` file to the
   `utils.py` module

* CI: test with Python 3.11 final, bandit
Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>
---
 .github/workflows/ci-tests.yml        |  10 +-
 cwltest/__init__.py                   | 638 +-------------------------
 cwltest/__main__.py                   |   5 +
 cwltest/argparser.py                  | 114 +++++
 cwltest/main.py                       | 458 ++++++++++++++++++
 cwltest/tests/test_argparse.py        |   2 +-
 cwltest/tests/test_categories.py      |   2 +-
 cwltest/tests/test_compare.py         |   3 +-
 cwltest/tests/test_exclude_tags.py    |   5 +-
 cwltest/tests/test_integer_id.py      |   7 +-
 cwltest/tests/test_multi_lined_doc.py |   5 +-
 cwltest/tests/test_prepare.py         |   5 +-
 cwltest/tests/test_short_names.py     |   4 +-
 cwltest/tests/test_string_id.py       |   5 +-
 cwltest/tests/test_timeout.py         |  10 +-
 cwltest/utils.py                      |  69 ++-
 setup.py                              |   2 +-
 tox.ini                               |   4 +-
 18 files changed, 669 insertions(+), 679 deletions(-)
 create mode 100644 cwltest/__main__.py
 create mode 100644 cwltest/argparser.py
 create mode 100644 cwltest/main.py

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 03d7c3b..3738b7b 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -22,7 +22,7 @@ jobs:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
         py-ver-minor: [6, 7, 8, 9, 10, 11]
-        step: [lint, unit, mypy]
+        step: [lint, unit, mypy, bandit]
         exclude:
           - py-ver-major: 3
             py-ver-minor: 6
@@ -36,18 +36,10 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: Set up Python
-        if: matrix.py-ver-minor != 11
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
 
-      - name: Set up Python 3.11.0-rc.2
-        if: matrix.py-ver-minor == 11
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11.0-rc.2
-
-
       - name: Cache for pip
         uses: actions/cache@v3
         with:
diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index c0e58ad..5b6419f 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -1,640 +1,14 @@
-#!/usr/bin/env python
+"""Common Workflow Language testing framework."""
 
-import argparse
-import json
 import logging
-import os
-import re
-import shutil
-import subprocess  # nosec
-import sys
-import tempfile
 import threading
-import time
-from collections import defaultdict
-from concurrent.futures import ThreadPoolExecutor
-from shlex import quote
-from typing import Any, Dict, List, Optional, Set, Union
-
-import junit_xml
-import pkg_resources  # part of setuptools
-import ruamel.yaml.scanner as yamlscanner
-import schema_salad.avro.schema
-import schema_salad.ref_resolver
-import schema_salad.schema
-from rdflib import Graph
-
-from cwltest.utils import (
-    REQUIRED,
-    CompareFail,
-    TestResult,
-    compare,
-    get_test_number_by_key,
-)
-
-_logger = logging.getLogger("cwltest")
-_logger.addHandler(logging.StreamHandler())
-_logger.setLevel(logging.INFO)
 
 UNSUPPORTED_FEATURE = 33
 DEFAULT_TIMEOUT = 600  # 10 minutes
+REQUIRED = "required"
 
-templock = threading.Lock()
-
-
-def shortname(
-    name,  # type: str
-):  # type: (...) -> str
-    """
-    Return the short name of a given name.
-    It is a workaround of https://github.com/common-workflow-language/schema_salad/issues/511.
-    """
-    return [n for n in re.split("[/#]", name) if len(n)][-1]
-
-
-def prepare_test_command(
-    tool,  # type: str
-    args,  # type: List[str]
-    testargs,  # type: Optional[List[str]]
-    test,  # type: Dict[str, str]
-    cwd,  # type: str
-    verbose=False,  # type: bool
-):  # type: (...) -> List[str]
-    """Turn the test into a command line."""
-    test_command = [tool]
-    test_command.extend(args)
-
-    # Add additional arguments given in test case
-    if testargs is not None:
-        for testarg in testargs:
-            (test_case_name, prefix) = testarg.split("==")
-            if test_case_name in test:
-                test_command.extend([prefix, test[test_case_name]])
-
-    # Add prefixes if running on MacOSX so that boot2docker writes to /Users
-    with templock:
-        if "darwin" in sys.platform and tool.endswith("cwltool"):
-            outdir = tempfile.mkdtemp(prefix=os.path.abspath(os.path.curdir))
-            test_command.extend(
-                [
-                    f"--tmp-outdir-prefix={outdir}",
-                    f"--tmpdir-prefix={outdir}",
-                ]
-            )
-        else:
-            outdir = tempfile.mkdtemp()
-    test_command.extend([f"--outdir={outdir}"])
-    if not verbose:
-        test_command.extend(["--quiet"])
-
-    cwd = schema_salad.ref_resolver.file_uri(cwd)
-    toolpath = test["tool"]
-    if toolpath.startswith(cwd):
-        toolpath = toolpath[len(cwd) + 1 :]
-    test_command.extend([os.path.normcase(toolpath)])
-
-    jobpath = test.get("job")
-    if jobpath:
-        if jobpath.startswith(cwd):
-            jobpath = jobpath[len(cwd) + 1 :]
-        test_command.append(os.path.normcase(jobpath))
-    return test_command
-
-
-def run_test(
-    args,  # type: argparse.Namespace
-    test,  # type: Dict[str, str]
-    test_number,  # type: int
-    total_tests,  # type: int
-    timeout,  # type: int
-    junit_verbose=False,  # type: bool
-    verbose=False,  # type: bool
-):  # type: (...) -> TestResult
-
-    global templock
-
-    out = {}  # type: Dict[str,Any]
-    outdir = outstr = outerr = ""
-    test_command = []  # type: List[str]
-    duration = 0.0
-    prefix = ""
-    suffix = ""
-    if sys.stderr.isatty():
-        prefix = "\r"
-    else:
-        suffix = "\n"
-    try:
-        process = None  # type: Optional[subprocess.Popen[str]]
-        cwd = os.getcwd()
-        test_command = prepare_test_command(
-            args.tool, args.args, args.testargs, test, cwd, junit_verbose
-        )
-
-        if test.get("short_name"):
-            sys.stderr.write(
-                "%sTest [%i/%i] %s: %s%s\n"
-                % (
-                    prefix,
-                    test_number,
-                    total_tests,
-                    test.get("short_name"),
-                    test.get("doc", "").replace("\n", " ").strip(),
-                    suffix,
-                )
-            )
-        else:
-            sys.stderr.write(
-                "%sTest [%i/%i] %s%s\n"
-                % (
-                    prefix,
-                    test_number,
-                    total_tests,
-                    test.get("doc", "").replace("\n", " ").strip(),
-                    suffix,
-                )
-            )
-        if verbose:
-            sys.stderr.write(f"Running: {' '.join(test_command)}\n")
-        sys.stderr.flush()
-
-        start_time = time.time()
-        stderr = subprocess.PIPE if not args.verbose else None
-        process = subprocess.Popen(  # nosec
-            test_command,
-            stdout=subprocess.PIPE,
-            stderr=stderr,
-            universal_newlines=True,
-            cwd=cwd,
-        )
-        outstr, outerr = process.communicate(timeout=timeout)
-        return_code = process.poll()
-        duration = time.time() - start_time
-        if return_code:
-            raise subprocess.CalledProcessError(return_code, " ".join(test_command))
-
-        out = json.loads(outstr)
-    except ValueError as err:
-        _logger.error(str(err))
-        _logger.error(outstr)
-        _logger.error(outerr)
-    except subprocess.CalledProcessError as err:
-        if err.returncode == UNSUPPORTED_FEATURE and REQUIRED not in test.get(
-            "tags", ["required"]
-        ):
-            return TestResult(
-                UNSUPPORTED_FEATURE, outstr, outerr, duration, args.classname
-            )
-        if test.get("should_fail", False):
-            return TestResult(0, outstr, outerr, duration, args.classname)
-        _logger.error(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        _logger.error(test.get("doc", "").replace("\n", " ").strip())
-        if err.returncode == UNSUPPORTED_FEATURE:
-            _logger.error("Does not support required feature")
-        else:
-            _logger.error("Returned non-zero")
-        _logger.error(outerr)
-        return TestResult(1, outstr, outerr, duration, args.classname, str(err))
-    except (yamlscanner.ScannerError, TypeError) as err:
-        _logger.error(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        _logger.error(outstr)
-        _logger.error("Parse error %s", str(err))
-        _logger.error(outerr)
-    except KeyboardInterrupt:
-        _logger.error(
-            """Test %i interrupted: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        raise
-    except subprocess.TimeoutExpired:
-        _logger.error(
-            """Test %i timed out: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        _logger.error(test.get("doc", "").replace("\n", " ").strip())
-        # Kill and re-communicate to get the logs and reap the child, as
-        # instructed in the subprocess docs.
-        if process:
-            process.kill()
-            outstr, outerr = process.communicate()
-        return TestResult(2, outstr, outerr, timeout, args.classname, "Test timed out")
-    finally:
-        if process is not None and process.returncode is None:
-            _logger.error("""Terminating lingering process""")
-            process.terminate()
-            for _ in range(0, 3):
-                time.sleep(1)
-                if process.poll() is not None:
-                    break
-            if process.returncode is None:
-                process.kill()
-
-    fail_message = ""
-
-    if test.get("should_fail", False):
-        _logger.warning(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        _logger.warning(test.get("doc", "").replace("\n", " ").strip())
-        _logger.warning("Returned zero but it should be non-zero")
-        return TestResult(1, outstr, outerr, duration, args.classname)
-
-    try:
-        compare(test.get("output"), out)
-    except CompareFail as ex:
-        _logger.warning(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([quote(tc) for tc in test_command]),
-        )
-        _logger.warning(test.get("doc", "").replace("\n", " ").strip())
-        _logger.warning("Compare failure %s", ex)
-        fail_message = str(ex)
-
-    if outdir:
-        shutil.rmtree(outdir, True)
-
-    return TestResult(
-        (1 if fail_message else 0),
-        outstr,
-        outerr,
-        duration,
-        args.classname,
-        fail_message,
-    )
-
-
-def arg_parser():  # type: () -> argparse.ArgumentParser
-    parser = argparse.ArgumentParser(
-        description="Common Workflow Language testing framework"
-    )
-    parser.add_argument(
-        "--test", type=str, help="YAML file describing test cases", required=True
-    )
-    parser.add_argument(
-        "--basedir", type=str, help="Basedir to use for tests", default="."
-    )
-    parser.add_argument("-l", action="https://github.com/store_true", help="List tests then exit")
-    parser.add_argument(
-        "-n", type=str, default=None, help="Run specific tests, format is 1,3-6,9"
-    )
-    parser.add_argument(
-        "-s",
-        type=str,
-        default=None,
-        help="Run specific tests using their short names separated by comma",
-    )
-    parser.add_argument(
-        "-N",
-        type=str,
-        default=None,
-        help="Exclude specific tests by number, format is 1,3-6,9",
-    )
-    parser.add_argument(
-        "-S",
-        type=str,
-        default=None,
-        help="Exclude specific tests by short names separated by comma",
-    )
-    parser.add_argument(
-        "--tool",
-        type=str,
-        default="cwl-runner",
-        help="CWL runner executable to use (default 'cwl-runner'",
-    )
-    parser.add_argument(
-        "--only-tools", action="https://github.com/store_true", help="Only test CommandLineTools"
-    )
-    parser.add_argument("--tags", type=str, default=None, help="Tags to be tested")
-    parser.add_argument(
-        "--exclude-tags", type=str, default=None, help="Tags not to be tested"
-    )
-    parser.add_argument("--show-tags", action="https://github.com/store_true", help="Show all Tags.")
-    parser.add_argument(
-        "--junit-xml", type=str, default=None, help="Path to JUnit xml file"
-    )
-    parser.add_argument(
-        "--junit-verbose",
-        action="https://github.com/store_true",
-        help="Store more verbose output to JUnit xml file",
-    )
-    parser.add_argument(
-        "--test-arg",
-        type=str,
-        help="Additional argument "
-        "given in test cases and required prefix for tool runner.",
-        default=None,
-        metavar="cache==--cache-dir",
-        action="https://github.com/append",
-        dest="testargs",
-    )
-    parser.add_argument(
-        "args", help="arguments to pass first to tool runner", nargs=argparse.REMAINDER
-    )
-    parser.add_argument(
-        "-j",
-        type=int,
-        default=1,
-        help="Specifies the number of tests to run simultaneously "
-        "(defaults to one).",
-    )
-    parser.add_argument(
-        "--verbose", action="https://github.com/store_true", help="More verbose output during test run."
-    )
-    parser.add_argument(
-        "--classname",
-        type=str,
-        default="",
-        help="Specify classname for the Test Suite.",
-    )
-    parser.add_argument(
-        "--timeout",
-        type=int,
-        default=DEFAULT_TIMEOUT,
-        help="Time of execution in seconds after which the test will be "
-        "skipped. Defaults to {} seconds ({} minutes).".format(
-            DEFAULT_TIMEOUT, DEFAULT_TIMEOUT / 60
-        ),
-    )
-    parser.add_argument(
-        "--badgedir", type=str, help="Directory that stores JSON files for badges."
-    )
-
-    pkg = pkg_resources.require("cwltest")
-    if pkg:
-        ver = f"{sys.argv[0]} {pkg[0].version}"
-    else:
-        ver = "{} {}".format(sys.argv[0], "unknown version")
-    parser.add_argument("--version", action="https://github.com/version", version=ver)
-
-    return parser
-
+logger = logging.getLogger("cwltest")
+logger.addHandler(logging.StreamHandler())
+logger.setLevel(logging.INFO)
 
-def expand_number_range(nr: str) -> List[int]:
-    result: List[int] = []
-    for s in nr.split(","):
-        sp = s.split("-")
-        if len(sp) == 2:
-            result.extend(range(int(sp[0]) - 1, int(sp[1])))
-        else:
-            result.append(int(s) - 1)
-    return result
-
-
-def main() -> int:
-    """Run the main logic loop."""
-    args = arg_parser().parse_args(sys.argv[1:])
-    if "--" in args.args:
-        args.args.remove("--")
-
-    # Remove test arguments with wrong syntax
-    if args.testargs is not None:
-        args.testargs = [
-            testarg for testarg in args.testargs if testarg.count("==") == 1
-        ]
-
-    if not args.test:
-        arg_parser().print_help()
-        return 1
-
-    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
-    cache = {
-        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
-            "utf-8"
-        )
-    }  # type: Optional[Dict[str, Union[str, Graph, bool]]]
-    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
-        "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
-    )
-
-    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
-        print(avsc_names)
-        return 1
-
-    tests, metadata = schema_salad.schema.load_and_validate(
-        document_loader, avsc_names, args.test, True
-    )
-
-    failures = 0
-    unsupported = 0
-    passed = 0
-    suite_name, _ = os.path.splitext(os.path.basename(args.test))
-    report = junit_xml.TestSuite(suite_name, [])
-
-    # the number of total tests, failed tests, unsupported tests and passed tests for each tag
-    ntotal = defaultdict(int)  # type: Dict[str, int]
-    nfailures = defaultdict(int)  # type: Dict[str, int]
-    nunsupported = defaultdict(int)  # type: Dict[str, int]
-    npassed = defaultdict(int)  # type: Dict[str, int]
-
-    if args.only_tools:
-        alltests = tests
-        tests = []
-        for t in alltests:
-            loader = schema_salad.ref_resolver.Loader({"id": "@id"})
-            cwl = loader.resolve_ref(t["tool"])[0]
-            if isinstance(cwl, dict):
-                if cwl["class"] == "CommandLineTool":
-                    tests.append(t)
-            else:
-                raise Exception("Unexpected code path.")
-
-    if args.tags:
-        alltests = tests
-        tests = []
-        tags = args.tags.split(",")
-        for t in alltests:
-            ts = t.get("tags", [])
-            if any(tag in ts for tag in tags):
-                tests.append(t)
-
-    if args.exclude_tags:
-        ex_tests = []
-        tags = args.exclude_tags.split(",")
-        for t in tests:
-            ts = t.get("tags", [])
-            if all(tag not in ts for tag in tags):
-                ex_tests.append(t)
-        tests = ex_tests
-
-    for t in tests:
-        if t.get("label"):
-            _logger.warning("The `label` field is deprecated. Use `id` field instead.")
-            t["short_name"] = t["label"]
-        elif t.get("id"):
-            if isinstance(t.get("id"), str):
-                t["short_name"] = shortname(t["id"])
-            else:
-                _logger.warning(
-                    "The `id` field with integer is deprecated. Use string identifier instead."
-                )
-        else:
-            _logger.warning("The `id` field is missing.")
-
-    if args.show_tags:
-        alltags = set()  # type: Set[str]
-        for t in tests:
-            ts = t.get("tags", [])
-            alltags |= set(ts)
-        for tag in alltags:
-            print(tag)
-        return 0
-
-    if args.l:
-        for i, t in enumerate(tests):
-            if t.get("short_name"):
-                print(
-                    "[%i] %s: %s"
-                    % (
-                        i + 1,
-                        t["short_name"],
-                        t.get("doc", "").replace("\n", " ").strip(),
-                    )
-                )
-            else:
-                print("[%i] %s" % (i + 1, t.get("doc", "").replace("\n", " ").strip()))
-
-        return 0
-
-    if args.n is not None or args.s is not None:
-        ntest = []
-        if args.n is not None:
-            ntest = expand_number_range(args.n)
-        if args.s is not None:
-            for s in args.s.split(","):
-                test_number = get_test_number_by_key(tests, "short_name", s)
-                if test_number:
-                    ntest.append(test_number)
-                else:
-                    _logger.error('Test with short name "%s" not found ', s)
-                    return 1
-    else:
-        ntest = list(range(0, len(tests)))
-
-    exclude_n = []
-    if args.N is not None:
-        exclude_n = expand_number_range(args.N)
-    if args.S is not None:
-        for s in args.S.split(","):
-            test_number = get_test_number_by_key(tests, "short_name", s)
-            if test_number:
-                exclude_n.append(test_number)
-            else:
-                _logger.error('Test with short name "%s" not found ', s)
-                return 1
-
-    ntest = list(filter(lambda x: x not in exclude_n, ntest))
-
-    total = 0
-    with ThreadPoolExecutor(max_workers=args.j) as executor:
-        jobs = [
-            executor.submit(
-                run_test,
-                args,
-                tests[i],
-                i + 1,
-                len(tests),
-                args.timeout,
-                args.junit_verbose,
-                args.verbose,
-            )
-            for i in ntest
-        ]
-        try:
-            for i, job in zip(ntest, jobs):
-                test_result = job.result()
-                test_case = test_result.create_test_case(tests[i])
-                test_case.url = f"cwltest:{suite_name}#{i + 1}"
-                total += 1
-                tags = tests[i].get("tags", [])
-                for t in tags:
-                    ntotal[t] += 1
-
-                return_code = test_result.return_code
-                category = test_case.category
-                if return_code == 0:
-                    passed += 1
-                    for t in tags:
-                        npassed[t] += 1
-                elif return_code != UNSUPPORTED_FEATURE:
-                    failures += 1
-                    for t in tags:
-                        nfailures[t] += 1
-                    test_case.add_failure_info(output=test_result.message)
-                elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
-                    failures += 1
-                    for t in tags:
-                        nfailures[t] += 1
-                    test_case.add_failure_info(output=test_result.message)
-                elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
-                    unsupported += 1
-                    for t in tags:
-                        nunsupported[t] += 1
-                    test_case.add_skipped_info("Unsupported")
-                else:
-                    raise Exception(
-                        "This is impossible, return_code: {}, category: "
-                        "{}".format(return_code, category)
-                    )
-                report.test_cases.append(test_case)
-        except KeyboardInterrupt:
-            for job in jobs:
-                job.cancel()
-            _logger.error("Tests interrupted")
-
-    if args.junit_xml:
-        with open(args.junit_xml, "w") as xml:
-            junit_xml.to_xml_report_file(xml, [report])
-
-    if args.badgedir:
-        os.mkdir(args.badgedir)
-        for t, v in ntotal.items():
-            percent = int((npassed[t] / float(v)) * 100)
-            if npassed[t] == v:
-                color = "green"
-            elif t == "required":
-                color = "red"
-            else:
-                color = "yellow"
-
-            with open(f"{args.badgedir}/{t}.json", "w") as out:
-                out.write(
-                    json.dumps(
-                        {
-                            "subject": f"{t}",
-                            "status": f"{percent}%",
-                            "color": color,
-                        }
-                    )
-                )
-
-    if failures == 0 and unsupported == 0:
-        _logger.info("All tests passed")
-        return 0
-    if failures == 0 and unsupported > 0:
-        _logger.warning(
-            "%i tests passed, %i unsupported features", total - unsupported, unsupported
-        )
-        return 0
-    _logger.warning(
-        "%i tests passed, %i failures, %i unsupported features",
-        total - (failures + unsupported),
-        failures,
-        unsupported,
-    )
-    return 1
-
-
-if __name__ == "__main__":
-    sys.exit(main())
+templock = threading.Lock()
diff --git a/cwltest/__main__.py b/cwltest/__main__.py
new file mode 100644
index 0000000..ee36e8b
--- /dev/null
+++ b/cwltest/__main__.py
@@ -0,0 +1,5 @@
+"""Default entrypoint for the cwltest module."""
+
+from . import main
+
+main.main()
diff --git a/cwltest/argparser.py b/cwltest/argparser.py
new file mode 100644
index 0000000..b567622
--- /dev/null
+++ b/cwltest/argparser.py
@@ -0,0 +1,114 @@
+"""Command line argument parsing for cwltest."""
+import argparse
+import sys
+
+import pkg_resources
+
+from cwltest import DEFAULT_TIMEOUT
+
+
+def arg_parser():  # type: () -> argparse.ArgumentParser
+    """Generate a command Line argument parser for cwltest."""
+    parser = argparse.ArgumentParser(
+        description="Common Workflow Language testing framework"
+    )
+    parser.add_argument(
+        "--test", type=str, help="YAML file describing test cases", required=True
+    )
+    parser.add_argument(
+        "--basedir", type=str, help="Basedir to use for tests", default="."
+    )
+    parser.add_argument("-l", action="https://github.com/store_true", help="List tests then exit")
+    parser.add_argument(
+        "-n", type=str, default=None, help="Run specific tests, format is 1,3-6,9"
+    )
+    parser.add_argument(
+        "-s",
+        type=str,
+        default=None,
+        help="Run specific tests using their short names separated by comma",
+    )
+    parser.add_argument(
+        "-N",
+        type=str,
+        default=None,
+        help="Exclude specific tests by number, format is 1,3-6,9",
+    )
+    parser.add_argument(
+        "-S",
+        type=str,
+        default=None,
+        help="Exclude specific tests by short names separated by comma",
+    )
+    parser.add_argument(
+        "--tool",
+        type=str,
+        default="cwl-runner",
+        help="CWL runner executable to use (default 'cwl-runner'",
+    )
+    parser.add_argument(
+        "--only-tools", action="https://github.com/store_true", help="Only test CommandLineTools"
+    )
+    parser.add_argument("--tags", type=str, default=None, help="Tags to be tested")
+    parser.add_argument(
+        "--exclude-tags", type=str, default=None, help="Tags not to be tested"
+    )
+    parser.add_argument("--show-tags", action="https://github.com/store_true", help="Show all Tags.")
+    parser.add_argument(
+        "--junit-xml", type=str, default=None, help="Path to JUnit xml file"
+    )
+    parser.add_argument(
+        "--junit-verbose",
+        action="https://github.com/store_true",
+        help="Store more verbose output to JUnit xml file",
+    )
+    parser.add_argument(
+        "--test-arg",
+        type=str,
+        help="Additional argument "
+        "given in test cases and required prefix for tool runner.",
+        default=None,
+        metavar="cache==--cache-dir",
+        action="https://github.com/append",
+        dest="testargs",
+    )
+    parser.add_argument(
+        "args", help="arguments to pass first to tool runner", nargs=argparse.REMAINDER
+    )
+    parser.add_argument(
+        "-j",
+        type=int,
+        default=1,
+        help="Specifies the number of tests to run simultaneously "
+        "(defaults to one).",
+    )
+    parser.add_argument(
+        "--verbose", action="https://github.com/store_true", help="More verbose output during test run."
+    )
+    parser.add_argument(
+        "--classname",
+        type=str,
+        default="",
+        help="Specify classname for the Test Suite.",
+    )
+    parser.add_argument(
+        "--timeout",
+        type=int,
+        default=DEFAULT_TIMEOUT,
+        help="Time of execution in seconds after which the test will be "
+        "skipped. Defaults to {} seconds ({} minutes).".format(
+            DEFAULT_TIMEOUT, DEFAULT_TIMEOUT / 60
+        ),
+    )
+    parser.add_argument(
+        "--badgedir", type=str, help="Directory that stores JSON files for badges."
+    )
+
+    pkg = pkg_resources.require("cwltest")
+    if pkg:
+        ver = f"{sys.argv[0]} {pkg[0].version}"
+    else:
+        ver = "{} {}".format(sys.argv[0], "unknown version")
+    parser.add_argument("--version", action="https://github.com/version", version=ver)
+
+    return parser
diff --git a/cwltest/main.py b/cwltest/main.py
new file mode 100644
index 0000000..3652764
--- /dev/null
+++ b/cwltest/main.py
@@ -0,0 +1,458 @@
+#!/usr/bin/env python3
+"""Entry point for cwltest."""
+
+import argparse
+import json
+import os
+import shlex
+import shutil
+import subprocess  # nosec
+import sys
+import time
+from collections import defaultdict
+from concurrent.futures import ThreadPoolExecutor
+from typing import Any, Dict, List, Optional, Set, Union
+
+import junit_xml
+import pkg_resources
+import ruamel.yaml.scanner
+import schema_salad.avro
+import schema_salad.ref_resolver
+import schema_salad.schema
+from rdflib import Graph
+
+from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
+from cwltest.argparser import arg_parser
+from cwltest.utils import TestResult
+
+
+def _run_test(
+    args,  # type: argparse.Namespace
+    test,  # type: Dict[str, str]
+    test_number,  # type: int
+    total_tests,  # type: int
+    timeout,  # type: int
+    junit_verbose=False,  # type: bool
+    verbose=False,  # type: bool
+):  # type: (...) -> TestResult
+    out = {}  # type: Dict[str,Any]
+    outdir = outstr = outerr = ""
+    test_command = []  # type: List[str]
+    duration = 0.0
+    process = None  # type: Optional[subprocess.Popen[str]]
+    prefix = ""
+    suffix = ""
+    if sys.stderr.isatty():
+        prefix = "\r"
+    else:
+        suffix = "\n"
+    try:
+        cwd = os.getcwd()
+        test_command = utils.prepare_test_command(
+            args.tool, args.args, args.testargs, test, cwd, junit_verbose
+        )
+
+        if test.get("short_name"):
+            sys.stderr.write(
+                "%sTest [%i/%i] %s: %s%s\n"
+                % (
+                    prefix,
+                    test_number,
+                    total_tests,
+                    test.get("short_name"),
+                    test.get("doc", "").replace("\n", " ").strip(),
+                    suffix,
+                )
+            )
+        else:
+            sys.stderr.write(
+                "%sTest [%i/%i] %s%s\n"
+                % (
+                    prefix,
+                    test_number,
+                    total_tests,
+                    test.get("doc", "").replace("\n", " ").strip(),
+                    suffix,
+                )
+            )
+        if verbose:
+            sys.stderr.write(f"Running: {' '.join(test_command)}\n")
+        sys.stderr.flush()
+
+        start_time = time.time()
+        stderr = subprocess.PIPE if not args.verbose else None
+        process = subprocess.Popen(  # nosec
+            test_command,
+            stdout=subprocess.PIPE,
+            stderr=stderr,
+            universal_newlines=True,
+            cwd=cwd,
+        )
+        outstr, outerr = process.communicate(timeout=timeout)
+        return_code = process.poll()
+        duration = time.time() - start_time
+        if return_code:
+            raise subprocess.CalledProcessError(return_code, " ".join(test_command))
+
+        out = json.loads(outstr)
+    except ValueError as err:
+        logger.error(str(err))
+        logger.error(outstr)
+        logger.error(outerr)
+    except subprocess.CalledProcessError as err:
+        if err.returncode == UNSUPPORTED_FEATURE and REQUIRED not in test.get(
+            "tags", ["required"]
+        ):
+            return utils.TestResult(
+                UNSUPPORTED_FEATURE, outstr, outerr, duration, args.classname
+            )
+        if test.get("should_fail", False):
+            return utils.TestResult(0, outstr, outerr, duration, args.classname)
+        logger.error(
+            """Test %i failed: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(test.get("doc", "").replace("\n", " ").strip())
+        if err.returncode == UNSUPPORTED_FEATURE:
+            logger.error("Does not support required feature")
+        else:
+            logger.error("Returned non-zero")
+        logger.error(outerr)
+        return utils.TestResult(1, outstr, outerr, duration, args.classname, str(err))
+    except (ruamel.yaml.scanner.ScannerError, TypeError) as err:
+        logger.error(
+            """Test %i failed: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(outstr)
+        logger.error("Parse error %s", str(err))
+        logger.error(outerr)
+    except KeyboardInterrupt:
+        logger.error(
+            """Test %i interrupted: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        raise
+    except subprocess.TimeoutExpired:
+        logger.error(
+            """Test %i timed out: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(test.get("doc", "").replace("\n", " ").strip())
+        # Kill and re-communicate to get the logs and reap the child, as
+        # instructed in the subprocess docs.
+        if process:
+            process.kill()
+            outstr, outerr = process.communicate()
+        return utils.TestResult(
+            2, outstr, outerr, timeout, args.classname, "Test timed out"
+        )
+    finally:
+        if process is not None and process.returncode is None:
+            logger.error("""Terminating lingering process""")
+            process.terminate()
+            for _ in range(0, 3):
+                time.sleep(1)
+                if process.poll() is not None:
+                    break
+            if process.returncode is None:
+                process.kill()
+
+    fail_message = ""
+
+    if test.get("should_fail", False):
+        logger.warning(
+            """Test %i failed: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.warning(test.get("doc", "").replace("\n", " ").strip())
+        logger.warning("Returned zero but it should be non-zero")
+        return utils.TestResult(1, outstr, outerr, duration, args.classname)
+
+    try:
+        utils.compare(test.get("output"), out)
+    except utils.CompareFail as ex:
+        logger.warning(
+            """Test %i failed: %s""",
+            test_number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.warning(test.get("doc", "").replace("\n", " ").strip())
+        logger.warning("Compare failure %s", ex)
+        fail_message = str(ex)
+
+    if outdir:
+        shutil.rmtree(outdir, True)
+
+    return utils.TestResult(
+        (1 if fail_message else 0),
+        outstr,
+        outerr,
+        duration,
+        args.classname,
+        fail_message,
+    )
+
+
+def _expand_number_range(nr: str) -> List[int]:
+    result: List[int] = []
+    for s in nr.split(","):
+        sp = s.split("-")
+        if len(sp) == 2:
+            result.extend(range(int(sp[0]) - 1, int(sp[1])))
+        else:
+            result.append(int(s) - 1)
+    return result
+
+
+def main() -> int:
+    """Run the main logic loop."""
+    args = arg_parser().parse_args(sys.argv[1:])
+    if "--" in args.args:
+        args.args.remove("--")
+
+    # Remove test arguments with wrong syntax
+    if args.testargs is not None:
+        args.testargs = [
+            testarg for testarg in args.testargs if testarg.count("==") == 1
+        ]
+
+    if not args.test:
+        arg_parser().print_help()
+        return 1
+
+    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
+    cache = {
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
+            "utf-8"
+        )
+    }  # type: Optional[Dict[str, Union[str, Graph, bool]]]
+    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
+    )
+
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        return 1
+
+    tests, metadata = schema_salad.schema.load_and_validate(
+        document_loader, avsc_names, args.test, True
+    )
+
+    failures = 0
+    unsupported = 0
+    passed = 0
+    suite_name, _ = os.path.splitext(os.path.basename(args.test))
+    report = junit_xml.TestSuite(suite_name, [])
+
+    # the number of total tests, failed tests, unsupported tests and passed tests for each tag
+    ntotal = defaultdict(int)  # type: Dict[str, int]
+    nfailures = defaultdict(int)  # type: Dict[str, int]
+    nunsupported = defaultdict(int)  # type: Dict[str, int]
+    npassed = defaultdict(int)  # type: Dict[str, int]
+
+    if args.only_tools:
+        alltests = tests
+        tests = []
+        for t in alltests:
+            loader = schema_salad.ref_resolver.Loader({"id": "@id"})
+            cwl = loader.resolve_ref(t["tool"])[0]
+            if isinstance(cwl, dict):
+                if cwl["class"] == "CommandLineTool":
+                    tests.append(t)
+            else:
+                raise Exception("Unexpected code path.")
+
+    if args.tags:
+        alltests = tests
+        tests = []
+        tags = args.tags.split(",")
+        for t in alltests:
+            ts = t.get("tags", [])
+            if any(tag in ts for tag in tags):
+                tests.append(t)
+
+    if args.exclude_tags:
+        ex_tests = []
+        tags = args.exclude_tags.split(",")
+        for t in tests:
+            ts = t.get("tags", [])
+            if all(tag not in ts for tag in tags):
+                ex_tests.append(t)
+        tests = ex_tests
+
+    for t in tests:
+        if t.get("label"):
+            logger.warning("The `label` field is deprecated. Use `id` field instead.")
+            t["short_name"] = t["label"]
+        elif t.get("id"):
+            if isinstance(t.get("id"), str):
+                t["short_name"] = utils.shortname(t["id"])
+            else:
+                logger.warning(
+                    "The `id` field with integer is deprecated. Use string identifier instead."
+                )
+        else:
+            logger.warning("The `id` field is missing.")
+
+    if args.show_tags:
+        alltags = set()  # type: Set[str]
+        for t in tests:
+            ts = t.get("tags", [])
+            alltags |= set(ts)
+        for tag in alltags:
+            print(tag)
+        return 0
+
+    if args.l:
+        for i, t in enumerate(tests):
+            if t.get("short_name"):
+                print(
+                    "[%i] %s: %s"
+                    % (
+                        i + 1,
+                        t["short_name"],
+                        t.get("doc", "").replace("\n", " ").strip(),
+                    )
+                )
+            else:
+                print("[%i] %s" % (i + 1, t.get("doc", "").replace("\n", " ").strip()))
+
+        return 0
+
+    if args.n is not None or args.s is not None:
+        ntest = []
+        if args.n is not None:
+            ntest = _expand_number_range(args.n)
+        if args.s is not None:
+            for s in args.s.split(","):
+                test_number = utils.get_test_number_by_key(tests, "short_name", s)
+                if test_number:
+                    ntest.append(test_number)
+                else:
+                    logger.error('Test with short name "%s" not found ', s)
+                    return 1
+    else:
+        ntest = list(range(0, len(tests)))
+
+    exclude_n = []
+    if args.N is not None:
+        exclude_n = _expand_number_range(args.N)
+    if args.S is not None:
+        for s in args.S.split(","):
+            test_number = utils.get_test_number_by_key(tests, "short_name", s)
+            if test_number:
+                exclude_n.append(test_number)
+            else:
+                logger.error('Test with short name "%s" not found ', s)
+                return 1
+
+    ntest = list(filter(lambda x: x not in exclude_n, ntest))
+
+    total = 0
+    with ThreadPoolExecutor(max_workers=args.j) as executor:
+        jobs = [
+            executor.submit(
+                _run_test,
+                args,
+                tests[i],
+                i + 1,
+                len(tests),
+                args.timeout,
+                args.junit_verbose,
+                args.verbose,
+            )
+            for i in ntest
+        ]
+        try:
+            for i, job in zip(ntest, jobs):
+                test_result = job.result()
+                test_case = test_result.create_test_case(tests[i])
+                test_case.url = f"cwltest:{suite_name}#{i + 1}"
+                total += 1
+                tags = tests[i].get("tags", [])
+                for t in tags:
+                    ntotal[t] += 1
+
+                return_code = test_result.return_code
+                category = test_case.category
+                if return_code == 0:
+                    passed += 1
+                    for t in tags:
+                        npassed[t] += 1
+                elif return_code != UNSUPPORTED_FEATURE:
+                    failures += 1
+                    for t in tags:
+                        nfailures[t] += 1
+                    test_case.add_failure_info(output=test_result.message)
+                elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
+                    failures += 1
+                    for t in tags:
+                        nfailures[t] += 1
+                    test_case.add_failure_info(output=test_result.message)
+                elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
+                    unsupported += 1
+                    for t in tags:
+                        nunsupported[t] += 1
+                    test_case.add_skipped_info("Unsupported")
+                else:
+                    raise Exception(
+                        "This is impossible, return_code: {}, category: "
+                        "{}".format(return_code, category)
+                    )
+                report.test_cases.append(test_case)
+        except KeyboardInterrupt:
+            for job in jobs:
+                job.cancel()
+            logger.error("Tests interrupted")
+
+    if args.junit_xml:
+        with open(args.junit_xml, "w") as xml:
+            junit_xml.to_xml_report_file(xml, [report])
+
+    if args.badgedir:
+        os.mkdir(args.badgedir)
+        for t, v in ntotal.items():
+            percent = int((npassed[t] / float(v)) * 100)
+            if npassed[t] == v:
+                color = "green"
+            elif t == "required":
+                color = "red"
+            else:
+                color = "yellow"
+
+            with open(f"{args.badgedir}/{t}.json", "w") as out:
+                out.write(
+                    json.dumps(
+                        {
+                            "subject": f"{t}",
+                            "status": f"{percent}%",
+                            "color": color,
+                        }
+                    )
+                )
+
+    if failures == 0 and unsupported == 0:
+        logger.info("All tests passed")
+        return 0
+    if failures == 0 and unsupported > 0:
+        logger.warning(
+            "%i tests passed, %i unsupported features", total - unsupported, unsupported
+        )
+        return 0
+    logger.warning(
+        "%i tests passed, %i failures, %i unsupported features",
+        total - (failures + unsupported),
+        failures,
+        unsupported,
+    )
+    return 1
+
+
+if __name__ == "__main__":
+    sys.exit(main())
diff --git a/cwltest/tests/test_argparse.py b/cwltest/tests/test_argparse.py
index 729cd5c..4234ba6 100644
--- a/cwltest/tests/test_argparse.py
+++ b/cwltest/tests/test_argparse.py
@@ -1,4 +1,4 @@
-from cwltest import arg_parser
+from cwltest.argparser import arg_parser
 
 
 def test_arg():
diff --git a/cwltest/tests/test_categories.py b/cwltest/tests/test_categories.py
index 9da4e30..38461fc 100644
--- a/cwltest/tests/test_categories.py
+++ b/cwltest/tests/test_categories.py
@@ -16,8 +16,8 @@ def test_unsupported_with_required_tests():
             get_data("tests/test-data/required-unsupported.yml")
         ),
     ]
+    cwd = os.getcwd()
     try:
-        cwd = os.getcwd()
         os.chdir(get_data("tests/test-data/"))
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     finally:
diff --git a/cwltest/tests/test_compare.py b/cwltest/tests/test_compare.py
index 15003ed..826a253 100644
--- a/cwltest/tests/test_compare.py
+++ b/cwltest/tests/test_compare.py
@@ -1,6 +1,5 @@
 from .util import get_data
-from cwltest import CompareFail
-from cwltest.utils import compare_file, compare
+from cwltest.utils import CompareFail, compare_file, compare
 
 import pytest
 
diff --git a/cwltest/tests/test_exclude_tags.py b/cwltest/tests/test_exclude_tags.py
index db01989..26283bd 100644
--- a/cwltest/tests/test_exclude_tags.py
+++ b/cwltest/tests/test_exclude_tags.py
@@ -1,9 +1,6 @@
-import os
 from os import linesep as n
-from pathlib import Path
 
-from .util import run_with_mock_cwl_runner, get_data
-import defusedxml.ElementTree as ET
+from .util import get_data, run_with_mock_cwl_runner
 
 
 def test_list_only_exclude():
diff --git a/cwltest/tests/test_integer_id.py b/cwltest/tests/test_integer_id.py
index 7993111..7b0363f 100644
--- a/cwltest/tests/test_integer_id.py
+++ b/cwltest/tests/test_integer_id.py
@@ -1,9 +1,4 @@
-import os
-from os import linesep as n
-from pathlib import Path
-
-from .util import run_with_mock_cwl_runner, get_data
-import defusedxml.ElementTree as ET
+from .util import get_data, run_with_mock_cwl_runner
 
 
 def test_warning_with_integer_id():
diff --git a/cwltest/tests/test_multi_lined_doc.py b/cwltest/tests/test_multi_lined_doc.py
index 9b6f4b3..a5d8ea9 100644
--- a/cwltest/tests/test_multi_lined_doc.py
+++ b/cwltest/tests/test_multi_lined_doc.py
@@ -1,9 +1,6 @@
-import os
 from os import linesep as n
-from pathlib import Path
 
-from .util import run_with_mock_cwl_runner, get_data
-import defusedxml.ElementTree as ET
+from .util import get_data, run_with_mock_cwl_runner
 
 
 def test_run():
diff --git a/cwltest/tests/test_prepare.py b/cwltest/tests/test_prepare.py
index 3c2ff6f..f93a19b 100644
--- a/cwltest/tests/test_prepare.py
+++ b/cwltest/tests/test_prepare.py
@@ -1,11 +1,12 @@
 """Test prepare_test_command()"""
 import os
-from cwltest import prepare_test_command
+
+from cwltest import utils
 
 
 def test_unix_relative_path():
     """Confirm unix style to windows style path corrections."""
-    command = prepare_test_command(
+    command = utils.prepare_test_command(
         tool="cwl-runner",
         args=[],
         testargs=None,
diff --git a/cwltest/tests/test_short_names.py b/cwltest/tests/test_short_names.py
index 84a594c..d16c762 100644
--- a/cwltest/tests/test_short_names.py
+++ b/cwltest/tests/test_short_names.py
@@ -1,10 +1,10 @@
-import os
 from os import linesep as n
 from pathlib import Path
 
-from .util import run_with_mock_cwl_runner, get_data
 import defusedxml.ElementTree as ET
 
+from .util import get_data, run_with_mock_cwl_runner
+
 
 def test_stderr_output():
     args = ["--test", get_data("tests/test-data/short-names.yml")]
diff --git a/cwltest/tests/test_string_id.py b/cwltest/tests/test_string_id.py
index 77180ae..09e58c3 100644
--- a/cwltest/tests/test_string_id.py
+++ b/cwltest/tests/test_string_id.py
@@ -1,9 +1,6 @@
-import os
 from os import linesep as n
-from pathlib import Path
 
-from .util import run_with_mock_cwl_runner, get_data
-import defusedxml.ElementTree as ET
+from .util import get_data, run_with_mock_cwl_runner
 
 
 def test_list():
diff --git a/cwltest/tests/test_timeout.py b/cwltest/tests/test_timeout.py
index 431e665..bd27c86 100644
--- a/cwltest/tests/test_timeout.py
+++ b/cwltest/tests/test_timeout.py
@@ -1,14 +1,10 @@
-import re
 import os
-from os import linesep as n
-from os import sep as p
-from pathlib import Path
 
 import defusedxml.ElementTree as ET
-
-from .util import run_with_mock_cwl_runner, get_data
 import schema_salad.ref_resolver
 
+from .util import get_data, run_with_mock_cwl_runner
+
 
 def test_timeout_stderr_stdout(tmp_path):
     junit_xml_report = tmp_path / "junit-report.xml"
@@ -21,8 +17,8 @@ def test_timeout_stderr_stdout(tmp_path):
         "--junit-xml",
         str(junit_xml_report),
     ]
+    cwd = os.getcwd()
     try:
-        cwd = os.getcwd()
         os.chdir(get_data("tests/test-data/"))
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     finally:
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 50e1cb5..632e513 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -1,13 +1,17 @@
 import json
+import os
+import re
+import sys
+import tempfile
 from typing import Any, Dict, List, Optional, Set, Text
 
 import junit_xml
+import schema_salad.ref_resolver
 
-REQUIRED = "required"
+from cwltest import REQUIRED, templock
 
 
 class TestResult:
-
     """Encapsulate relevant test result data."""
 
     def __init__(
@@ -20,6 +24,7 @@ def __init__(
         message="",
     ):
         # type: (int, Text, Text, float, Text, str) -> None
+        """Initialize a TestResult object."""
         self.return_code = return_code
         self.standard_output = standard_output
         self.error_output = error_output
@@ -209,3 +214,63 @@ def get_test_number_by_key(tests, key, value):
         if key in test and test[key] == value:
             return i
     return None
+
+
+def prepare_test_command(
+    tool,  # type: str
+    args,  # type: List[str]
+    testargs,  # type: Optional[List[str]]
+    test,  # type: Dict[str, Any]
+    cwd,  # type: str
+    verbose=False,  # type: bool
+):  # type: (...) -> List[str]
+    """Turn the test into a command line."""
+    test_command = [tool]
+    test_command.extend(args)
+
+    # Add additional arguments given in test case
+    if testargs is not None:
+        for testarg in testargs:
+            (test_case_name, prefix) = testarg.split("==")
+            if test_case_name in test:
+                test_command.extend([prefix, test[test_case_name]])
+
+    # Add prefixes if running on MacOSX so that boot2docker writes to /Users
+    with templock:
+        if "darwin" in sys.platform and tool.endswith("cwltool"):
+            outdir = tempfile.mkdtemp(prefix=os.path.abspath(os.path.curdir))
+            test_command.extend(
+                [
+                    f"--tmp-outdir-prefix={outdir}",
+                    f"--tmpdir-prefix={outdir}",
+                ]
+            )
+        else:
+            outdir = tempfile.mkdtemp()
+    test_command.extend([f"--outdir={outdir}"])
+    if not verbose:
+        test_command.extend(["--quiet"])
+
+    cwd = schema_salad.ref_resolver.file_uri(cwd)
+    toolpath = test["tool"]
+    if toolpath.startswith(cwd):
+        toolpath = toolpath[len(cwd) + 1 :]
+    test_command.extend([os.path.normcase(toolpath)])
+
+    jobpath = test.get("job")
+    if jobpath:
+        if jobpath.startswith(cwd):
+            jobpath = jobpath[len(cwd) + 1 :]
+        test_command.append(os.path.normcase(jobpath))
+    return test_command
+
+
+def shortname(
+    name,  # type: str
+):  # type: (...) -> str
+    """
+    Return the short name of a given name.
+
+    It is a workaround of https://github.com/common-workflow-language/schema_salad/issues/511.
+    """
+    return [n for n in re.split("[/#]", name) if len(n)][-1]
diff --git a/setup.py b/setup.py
index 6466981..cd9349d 100644
--- a/setup.py
+++ b/setup.py
@@ -45,7 +45,7 @@
     tests_require=["pytest<8"],
     entry_points={
         "console_scripts": [
-            "cwltest=cwltest:main",
+            "cwltest=cwltest.main:main",
             "mock-cwl-runner=cwltest.tests.mock_cwl_runner:main",
         ]
     },
diff --git a/tox.ini b/tox.ini
index 37b83b3..bd79838 100644
--- a/tox.ini
+++ b/tox.ini
@@ -54,7 +54,7 @@ commands =
   py{37,38,39,310,311}-mypy: make mypy
   py37-mypy: make mypy_3.6
 
-whitelist_externals =
+allowlist_externals =
   py{36,37,38,39,310,311}-lint: flake8
   py{36,37,38,39,310,311}-lint: black
   py{36,37,38,39,310,311}-{mypy,shellcheck,lint,unit}: make
@@ -65,7 +65,7 @@ skip_install =
 
 
 [testenv:py310-pydocstyle]
-whitelist_externals = make
+allowlist_externals = make
 commands = make diff_pydocstyle_report
 deps =
     pydocstyle

From 88bfd6e981e884e2647953956db67ce674a572fd Mon Sep 17 00:00:00 2001
From: Iacopo Colonnelli <iacopo.c92@gmail.com>
Date: Wed, 4 Jan 2023 14:30:46 +0100
Subject: [PATCH 053/165] Refactoring test suite (#156)

* Refactoring test suite

This commit reorganizes the test suite in three ways:

 - It moves the tests folder to the top of the hierarchy
 - It extends format, mypy, and pydocstyle checks to test folder
 - It better types the test functions to make them compatible with MyPy
   checks

* cwltest/tests -> tests

* Adjusted mypy for defusedxml
---
 .coveragerc                                   |  5 ++--
 MANIFEST.in                                   |  6 ++---
 Makefile                                      |  4 ++--
 mypy-stubs/defusedxml/ElementTree.pyi         |  6 +++++
 .../defusedxml}/__init__.py                   |  0
 setup.py                                      |  6 +++--
 tests/__init__.py                             |  1 +
 {cwltest/tests => tests}/test-data/cores.txt  |  0
 .../test-data/exclude-tags.yml                |  0
 .../tests => tests}/test-data/integer-id.yml  |  0
 .../test-data}/mock_cwl_runner.py             |  3 +++
 .../test-data/multi-lined-doc.yml             |  0
 .../test-data/optional-error.yml              |  0
 .../test-data/optional-unsupported.yml        |  0
 .../test-data/required-unsupported.yml        |  0
 .../tests => tests}/test-data/return-0.cwl    |  0
 .../tests => tests}/test-data/return-1.cwl    |  0
 .../test-data/return-unsupported.cwl          |  0
 .../tests => tests}/test-data/short-names.yml |  0
 .../tests => tests}/test-data/string-id.yml   |  0
 .../tests => tests}/test-data/timeout.cwl     |  0
 .../tests => tests}/test-data/timeout.yml     |  0
 .../test-data/v1.0/cat-job.json               |  0
 .../test-data/v1.0/cat1-job.json              |  0
 .../test-data/v1.0/cat2-job.json              |  0
 .../tests => tests}/test-data/v1.0/empty.json |  0
 .../with-and-without-short-names.yml          |  0
 {cwltest/tests => tests}/test_argparse.py     |  2 +-
 {cwltest/tests => tests}/test_categories.py   | 23 ++++++++++++-------
 {cwltest/tests => tests}/test_compare.py      |  6 ++---
 {cwltest/tests => tests}/test_exclude_tags.py |  4 ++--
 {cwltest/tests => tests}/test_integer_id.py   |  2 +-
 .../tests => tests}/test_multi_lined_doc.py   |  4 ++--
 {cwltest/tests => tests}/test_prepare.py      |  2 +-
 {cwltest/tests => tests}/test_short_names.py  | 14 +++++++----
 {cwltest/tests => tests}/test_string_id.py    |  2 +-
 {cwltest/tests => tests}/test_timeout.py      | 23 +++++++++++++++----
 {cwltest/tests => tests}/util.py              | 13 +++++++----
 tox.ini                                       |  6 ++---
 39 files changed, 85 insertions(+), 47 deletions(-)
 create mode 100644 mypy-stubs/defusedxml/ElementTree.pyi
 rename {cwltest/tests => mypy-stubs/defusedxml}/__init__.py (100%)
 create mode 100644 tests/__init__.py
 rename {cwltest/tests => tests}/test-data/cores.txt (100%)
 rename {cwltest/tests => tests}/test-data/exclude-tags.yml (100%)
 rename {cwltest/tests => tests}/test-data/integer-id.yml (100%)
 rename {cwltest/tests => tests/test-data}/mock_cwl_runner.py (91%)
 mode change 100644 => 100755
 rename {cwltest/tests => tests}/test-data/multi-lined-doc.yml (100%)
 rename {cwltest/tests => tests}/test-data/optional-error.yml (100%)
 rename {cwltest/tests => tests}/test-data/optional-unsupported.yml (100%)
 rename {cwltest/tests => tests}/test-data/required-unsupported.yml (100%)
 rename {cwltest/tests => tests}/test-data/return-0.cwl (100%)
 rename {cwltest/tests => tests}/test-data/return-1.cwl (100%)
 rename {cwltest/tests => tests}/test-data/return-unsupported.cwl (100%)
 rename {cwltest/tests => tests}/test-data/short-names.yml (100%)
 rename {cwltest/tests => tests}/test-data/string-id.yml (100%)
 rename {cwltest/tests => tests}/test-data/timeout.cwl (100%)
 rename {cwltest/tests => tests}/test-data/timeout.yml (100%)
 rename {cwltest/tests => tests}/test-data/v1.0/cat-job.json (100%)
 rename {cwltest/tests => tests}/test-data/v1.0/cat1-job.json (100%)
 rename {cwltest/tests => tests}/test-data/v1.0/cat2-job.json (100%)
 rename {cwltest/tests => tests}/test-data/v1.0/empty.json (100%)
 rename {cwltest/tests => tests}/test-data/with-and-without-short-names.yml (100%)
 rename {cwltest/tests => tests}/test_argparse.py (93%)
 rename {cwltest/tests => tests}/test_categories.py (77%)
 rename {cwltest/tests => tests}/test_compare.py (93%)
 rename {cwltest/tests => tests}/test_exclude_tags.py (90%)
 rename {cwltest/tests => tests}/test_integer_id.py (88%)
 rename {cwltest/tests => tests}/test_multi_lined_doc.py (93%)
 rename {cwltest/tests => tests}/test_prepare.py (95%)
 rename {cwltest/tests => tests}/test_short_names.py (79%)
 rename {cwltest/tests => tests}/test_string_id.py (92%)
 rename {cwltest/tests => tests}/test_timeout.py (53%)
 rename {cwltest/tests => tests}/util.py (65%)

diff --git a/.coveragerc b/.coveragerc
index 4a89de0..020763e 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,7 @@
 [run]
 branch = True
 source = cwltest
-omit = cwltest/tests/*
+omit = tests/*
 
 [report]
 exclude_lines =
@@ -10,5 +10,4 @@ exclude_lines =
     raise NotImplementedError
     if __name__ == .__main__.:
 ignore_errors = True
-omit =
-    cwltest/tests/*
+omit = tests/*
diff --git a/MANIFEST.in b/MANIFEST.in
index f902163..1eab7bf 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,8 +1,8 @@
 include Makefile gittaggers.py test-requirements.txt mypy-requirements.txt requirements.txt
 include cwltest/cwltest-schema.yml
-include cwltest/tests/*
-include cwltest/tests/test-data/*
-include cwltest/tests/test-data/v1.0/*
+include tests/*
+include tests/test-data/*
+include tests/test-data/v1.0/*
 recursive-include mypy-stubs *.py?
 global-exclude *~
 global-exclude *.pyc
diff --git a/Makefile b/Makefile
index 1e84799..c65f07b 100644
--- a/Makefile
+++ b/Makefile
@@ -102,10 +102,10 @@ codespell:
 
 ## format                 : check/fix all code indentation and formatting (runs black)
 format:
-	black setup.py cwltest setup.py mypy-stubs
+	black setup.py setup.py cwltest tests mypy-stubs
 
 format-check:
-	black --diff --check setup.py cwltest mypy-stubs
+	black --diff --check setup.py cwltest tests mypy-stubs
 
 ## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
diff --git a/mypy-stubs/defusedxml/ElementTree.pyi b/mypy-stubs/defusedxml/ElementTree.pyi
new file mode 100644
index 0000000..e6f2465
--- /dev/null
+++ b/mypy-stubs/defusedxml/ElementTree.pyi
@@ -0,0 +1,6 @@
+import xml.etree.ElementTree
+from pathlib import Path
+
+def parse(
+    source: Path = ..., parser: xml.etree.ElementTree.XMLParser = ...
+) -> xml.etree.ElementTree.ElementTree: ...
diff --git a/cwltest/tests/__init__.py b/mypy-stubs/defusedxml/__init__.py
similarity index 100%
rename from cwltest/tests/__init__.py
rename to mypy-stubs/defusedxml/__init__.py
diff --git a/setup.py b/setup.py
index cd9349d..e2b1528 100644
--- a/setup.py
+++ b/setup.py
@@ -5,6 +5,8 @@
 import setuptools.command.egg_info as egg_info_cmd
 from setuptools import setup
 
+import cwltest
+
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, "README.rst")
 
@@ -38,7 +40,8 @@
     python_requires=">=3.6, <4",
     setup_requires=[] + pytest_runner,
     packages=["cwltest", "cwltest.tests"],
-    package_data={"cwltest": ["py.typed"], "cwltest.tests": ["test-data/*"]},
+    package_dir={"cwltest.tests": "tests"},
+    package_data={"cwltest": ["py.typed"], "tests": ["test-data/*"]},
     include_package_data=True,
     install_requires=install_requires,
     test_suite="tests",
@@ -46,7 +49,6 @@
     entry_points={
         "console_scripts": [
             "cwltest=cwltest.main:main",
-            "mock-cwl-runner=cwltest.tests.mock_cwl_runner:main",
         ]
     },
     zip_safe=True,
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..198807d
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1 @@
+"""Tests for cwltest."""
diff --git a/cwltest/tests/test-data/cores.txt b/tests/test-data/cores.txt
similarity index 100%
rename from cwltest/tests/test-data/cores.txt
rename to tests/test-data/cores.txt
diff --git a/cwltest/tests/test-data/exclude-tags.yml b/tests/test-data/exclude-tags.yml
similarity index 100%
rename from cwltest/tests/test-data/exclude-tags.yml
rename to tests/test-data/exclude-tags.yml
diff --git a/cwltest/tests/test-data/integer-id.yml b/tests/test-data/integer-id.yml
similarity index 100%
rename from cwltest/tests/test-data/integer-id.yml
rename to tests/test-data/integer-id.yml
diff --git a/cwltest/tests/mock_cwl_runner.py b/tests/test-data/mock_cwl_runner.py
old mode 100644
new mode 100755
similarity index 91%
rename from cwltest/tests/mock_cwl_runner.py
rename to tests/test-data/mock_cwl_runner.py
index 478e504..d807203
--- a/cwltest/tests/mock_cwl_runner.py
+++ b/tests/test-data/mock_cwl_runner.py
@@ -1,3 +1,6 @@
+#!/usr/bin/env python3
+"""Mock implementation of the cwlref-runner command line."""
+
 import argparse
 import sys
 from time import sleep
diff --git a/cwltest/tests/test-data/multi-lined-doc.yml b/tests/test-data/multi-lined-doc.yml
similarity index 100%
rename from cwltest/tests/test-data/multi-lined-doc.yml
rename to tests/test-data/multi-lined-doc.yml
diff --git a/cwltest/tests/test-data/optional-error.yml b/tests/test-data/optional-error.yml
similarity index 100%
rename from cwltest/tests/test-data/optional-error.yml
rename to tests/test-data/optional-error.yml
diff --git a/cwltest/tests/test-data/optional-unsupported.yml b/tests/test-data/optional-unsupported.yml
similarity index 100%
rename from cwltest/tests/test-data/optional-unsupported.yml
rename to tests/test-data/optional-unsupported.yml
diff --git a/cwltest/tests/test-data/required-unsupported.yml b/tests/test-data/required-unsupported.yml
similarity index 100%
rename from cwltest/tests/test-data/required-unsupported.yml
rename to tests/test-data/required-unsupported.yml
diff --git a/cwltest/tests/test-data/return-0.cwl b/tests/test-data/return-0.cwl
similarity index 100%
rename from cwltest/tests/test-data/return-0.cwl
rename to tests/test-data/return-0.cwl
diff --git a/cwltest/tests/test-data/return-1.cwl b/tests/test-data/return-1.cwl
similarity index 100%
rename from cwltest/tests/test-data/return-1.cwl
rename to tests/test-data/return-1.cwl
diff --git a/cwltest/tests/test-data/return-unsupported.cwl b/tests/test-data/return-unsupported.cwl
similarity index 100%
rename from cwltest/tests/test-data/return-unsupported.cwl
rename to tests/test-data/return-unsupported.cwl
diff --git a/cwltest/tests/test-data/short-names.yml b/tests/test-data/short-names.yml
similarity index 100%
rename from cwltest/tests/test-data/short-names.yml
rename to tests/test-data/short-names.yml
diff --git a/cwltest/tests/test-data/string-id.yml b/tests/test-data/string-id.yml
similarity index 100%
rename from cwltest/tests/test-data/string-id.yml
rename to tests/test-data/string-id.yml
diff --git a/cwltest/tests/test-data/timeout.cwl b/tests/test-data/timeout.cwl
similarity index 100%
rename from cwltest/tests/test-data/timeout.cwl
rename to tests/test-data/timeout.cwl
diff --git a/cwltest/tests/test-data/timeout.yml b/tests/test-data/timeout.yml
similarity index 100%
rename from cwltest/tests/test-data/timeout.yml
rename to tests/test-data/timeout.yml
diff --git a/cwltest/tests/test-data/v1.0/cat-job.json b/tests/test-data/v1.0/cat-job.json
similarity index 100%
rename from cwltest/tests/test-data/v1.0/cat-job.json
rename to tests/test-data/v1.0/cat-job.json
diff --git a/cwltest/tests/test-data/v1.0/cat1-job.json b/tests/test-data/v1.0/cat1-job.json
similarity index 100%
rename from cwltest/tests/test-data/v1.0/cat1-job.json
rename to tests/test-data/v1.0/cat1-job.json
diff --git a/cwltest/tests/test-data/v1.0/cat2-job.json b/tests/test-data/v1.0/cat2-job.json
similarity index 100%
rename from cwltest/tests/test-data/v1.0/cat2-job.json
rename to tests/test-data/v1.0/cat2-job.json
diff --git a/cwltest/tests/test-data/v1.0/empty.json b/tests/test-data/v1.0/empty.json
similarity index 100%
rename from cwltest/tests/test-data/v1.0/empty.json
rename to tests/test-data/v1.0/empty.json
diff --git a/cwltest/tests/test-data/with-and-without-short-names.yml b/tests/test-data/with-and-without-short-names.yml
similarity index 100%
rename from cwltest/tests/test-data/with-and-without-short-names.yml
rename to tests/test-data/with-and-without-short-names.yml
diff --git a/cwltest/tests/test_argparse.py b/tests/test_argparse.py
similarity index 93%
rename from cwltest/tests/test_argparse.py
rename to tests/test_argparse.py
index 4234ba6..948ddd1 100644
--- a/cwltest/tests/test_argparse.py
+++ b/tests/test_argparse.py
@@ -1,7 +1,7 @@
 from cwltest.argparser import arg_parser
 
 
-def test_arg():
+def test_arg() -> None:
     """Basic test of the argparse."""
     parser = arg_parser()
     parsed = parser.parse_args(
diff --git a/cwltest/tests/test_categories.py b/tests/test_categories.py
similarity index 77%
rename from cwltest/tests/test_categories.py
rename to tests/test_categories.py
index 38461fc..28acb90 100644
--- a/cwltest/tests/test_categories.py
+++ b/tests/test_categories.py
@@ -3,13 +3,16 @@
 from os import linesep as n
 from os import sep as p
 from pathlib import Path
+from typing import cast
+from xml.etree.ElementTree import Element
 
 from .util import run_with_mock_cwl_runner, get_data
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
 
 
-def test_unsupported_with_required_tests():
+def test_unsupported_with_required_tests() -> None:
+    cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
     args = [
         "--test",
         schema_salad.ref_resolver.file_uri(
@@ -35,21 +38,23 @@ def test_unsupported_with_required_tests():
         "The `id` field is missing.{n}"
         "Test [1/2] Required test that is unsupported (without tags){n}"
         "{n}"
-        "Test 1 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        "Test 1 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
         "Required test that is unsupported (without tags){n}"
         "Does not support required feature{n}"
         "{n}"
         "Test [2/2] Required test that is unsupported (with tags){n}"
         "{n}"
-        "Test 2 failed: mock-cwl-runner --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        "Test 2 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
         "Required test that is unsupported (with tags){n}"
         "Does not support required feature{n}"
         "{n}"
-        "0 tests passed, 2 failures, 0 unsupported features{n}".format(n=n, p=p, q=q)
+        "0 tests passed, 2 failures, 0 unsupported features{n}".format(
+            cwl_runner=cwl_runner, n=n, p=p, q=q
+        )
     ) == stderr
 
 
-def test_unsupported_with_optional_tests():
+def test_unsupported_with_optional_tests() -> None:
     args = [
         "--test",
         schema_salad.ref_resolver.file_uri(
@@ -66,7 +71,7 @@ def test_unsupported_with_optional_tests():
     ) == stderr
 
 
-def test_error_with_optional_tests():
+def test_error_with_optional_tests() -> None:
     args = [
         "--test",
         schema_salad.ref_resolver.file_uri(
@@ -78,7 +83,7 @@ def test_error_with_optional_tests():
     assert "1 failures" in stderr
 
 
-def test_category_in_junit_xml(tmp_path: Path):
+def test_category_in_junit_xml(tmp_path: Path) -> None:
     junit_xml_report = tmp_path / "junit-report.xml"
     args = [
         "--test",
@@ -91,5 +96,7 @@ def test_category_in_junit_xml(tmp_path: Path):
     run_with_mock_cwl_runner(args)
     tree = ET.parse(junit_xml_report)
     root = tree.getroot()
-    category = root.find("testsuite").find("testcase").attrib["class"]
+    category = cast(
+        Element, cast(Element, root.find("testsuite")).find("testcase")
+    ).attrib["class"]
     assert category == "js, init_work_dir"
diff --git a/cwltest/tests/test_compare.py b/tests/test_compare.py
similarity index 93%
rename from cwltest/tests/test_compare.py
rename to tests/test_compare.py
index 826a253..aec983e 100644
--- a/cwltest/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -4,7 +4,7 @@
 import pytest
 
 
-def test_compare_file():
+def test_compare_file() -> None:
     expected = {
         "location": "cores.txt",
         "size": 2,
@@ -23,7 +23,7 @@ def test_compare_file():
     compare_file(expected, actual)
 
 
-def test_compare_contents_success():
+def test_compare_contents_success() -> None:
     expected = {
         "location": "cores.txt",
         "size": 2,
@@ -42,7 +42,7 @@ def test_compare_contents_success():
     compare(expected, actual)
 
 
-def test_compare_contents_failure():
+def test_compare_contents_failure() -> None:
     expected = {
         "location": "cores.txt",
         "size": 2,
diff --git a/cwltest/tests/test_exclude_tags.py b/tests/test_exclude_tags.py
similarity index 90%
rename from cwltest/tests/test_exclude_tags.py
rename to tests/test_exclude_tags.py
index 26283bd..f17ae48 100644
--- a/cwltest/tests/test_exclude_tags.py
+++ b/tests/test_exclude_tags.py
@@ -3,7 +3,7 @@
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_list_only_exclude():
+def test_list_only_exclude() -> None:
     args = [
         "--test",
         get_data("tests/test-data/exclude-tags.yml"),
@@ -16,7 +16,7 @@ def test_list_only_exclude():
     assert "opt-error3" not in stdout
 
 
-def test_list_include_and_exclude():
+def test_list_include_and_exclude() -> None:
     args = [
         "--test",
         get_data("tests/test-data/exclude-tags.yml"),
diff --git a/cwltest/tests/test_integer_id.py b/tests/test_integer_id.py
similarity index 88%
rename from cwltest/tests/test_integer_id.py
rename to tests/test_integer_id.py
index 7b0363f..64343e3 100644
--- a/cwltest/tests/test_integer_id.py
+++ b/tests/test_integer_id.py
@@ -1,7 +1,7 @@
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_warning_with_integer_id():
+def test_warning_with_integer_id() -> None:
     args = [
         "--test",
         get_data("tests/test-data/integer-id.yml"),
diff --git a/cwltest/tests/test_multi_lined_doc.py b/tests/test_multi_lined_doc.py
similarity index 93%
rename from cwltest/tests/test_multi_lined_doc.py
rename to tests/test_multi_lined_doc.py
index a5d8ea9..51ba2f9 100644
--- a/cwltest/tests/test_multi_lined_doc.py
+++ b/tests/test_multi_lined_doc.py
@@ -3,7 +3,7 @@
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_run():
+def test_run() -> None:
     args = ["--test", get_data("tests/test-data/multi-lined-doc.yml")]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     assert "The `label` field is deprecated. Use `id` field instead." in stderr
@@ -11,7 +11,7 @@ def test_run():
     assert f"Test [2/2] Test without label{n}" in stderr
 
 
-def test_list():
+def test_list() -> None:
     args = ["--test", get_data("tests/test-data/multi-lined-doc.yml"), "-l"]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     assert f"[1] opt-error: Test with label{n}" in stdout
diff --git a/cwltest/tests/test_prepare.py b/tests/test_prepare.py
similarity index 95%
rename from cwltest/tests/test_prepare.py
rename to tests/test_prepare.py
index f93a19b..9c3c3c1 100644
--- a/cwltest/tests/test_prepare.py
+++ b/tests/test_prepare.py
@@ -4,7 +4,7 @@
 from cwltest import utils
 
 
-def test_unix_relative_path():
+def test_unix_relative_path() -> None:
     """Confirm unix style to windows style path corrections."""
     command = utils.prepare_test_command(
         tool="cwl-runner",
diff --git a/cwltest/tests/test_short_names.py b/tests/test_short_names.py
similarity index 79%
rename from cwltest/tests/test_short_names.py
rename to tests/test_short_names.py
index d16c762..da87b6c 100644
--- a/cwltest/tests/test_short_names.py
+++ b/tests/test_short_names.py
@@ -1,18 +1,20 @@
 from os import linesep as n
 from pathlib import Path
+from typing import cast
+from xml.etree.ElementTree import Element
 
 import defusedxml.ElementTree as ET
 
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_stderr_output():
+def test_stderr_output() -> None:
     args = ["--test", get_data("tests/test-data/short-names.yml")]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     assert f"Test [1/1] opt-error: Test with a short name{n}" in stderr
 
 
-def test_run_by_short_name():
+def test_run_by_short_name() -> None:
     short_name = "opt-error"
     args = [
         "--test",
@@ -25,7 +27,7 @@ def test_run_by_short_name():
     assert "Test [1/2]" not in stderr
 
 
-def test_list_tests():
+def test_list_tests() -> None:
     args = [
         "--test",
         get_data("tests/test-data/with-and-without-short-names.yml"),
@@ -37,7 +39,7 @@ def test_list_tests():
     ) in stdout
 
 
-def test_short_name_in_junit_xml(tmp_path: Path):
+def test_short_name_in_junit_xml(tmp_path: Path) -> None:
     junit_xml_report = tmp_path / "junit-report.xml"
     args = [
         "--test",
@@ -48,5 +50,7 @@ def test_short_name_in_junit_xml(tmp_path: Path):
     run_with_mock_cwl_runner(args)
     tree = ET.parse(junit_xml_report)
     root = tree.getroot()
-    category = root.find("testsuite").find("testcase").attrib["file"]
+    category = cast(
+        Element, cast(Element, root.find("testsuite")).find("testcase")
+    ).attrib["file"]
     assert category == "opt-error"
diff --git a/cwltest/tests/test_string_id.py b/tests/test_string_id.py
similarity index 92%
rename from cwltest/tests/test_string_id.py
rename to tests/test_string_id.py
index 09e58c3..8a9eb1f 100644
--- a/cwltest/tests/test_string_id.py
+++ b/tests/test_string_id.py
@@ -3,7 +3,7 @@
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_list():
+def test_list() -> None:
     args = ["--test", get_data("tests/test-data/string-id.yml"), "-l"]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     assert f"[1] test-string-id: Test with a string label{n}" in stdout
diff --git a/cwltest/tests/test_timeout.py b/tests/test_timeout.py
similarity index 53%
rename from cwltest/tests/test_timeout.py
rename to tests/test_timeout.py
index bd27c86..bc01636 100644
--- a/cwltest/tests/test_timeout.py
+++ b/tests/test_timeout.py
@@ -1,4 +1,7 @@
 import os
+from pathlib import Path
+from typing import cast
+from xml.etree.ElementTree import Element
 
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
@@ -6,7 +9,7 @@
 from .util import get_data, run_with_mock_cwl_runner
 
 
-def test_timeout_stderr_stdout(tmp_path):
+def test_timeout_stderr_stdout(tmp_path: Path) -> None:
     junit_xml_report = tmp_path / "junit-report.xml"
 
     args = [
@@ -29,10 +32,20 @@ def test_timeout_stderr_stdout(tmp_path):
     tree = ET.parse(junit_xml_report)
     try:
         root = tree.getroot()
-        timeout_text = root.find("testsuite").find("testcase").find("failure").text
-        timeout_stderr = root.find("testsuite").find("testcase").find("system-err").text
-        assert "Test timed out" in timeout_text
-        assert "timeout stderr" in timeout_stderr
+        timeout_text = cast(
+            Element,
+            cast(Element, cast(Element, root.find("testsuite")).find("testcase")).find(
+                "failure"
+            ),
+        ).text
+        timeout_stderr = cast(
+            Element,
+            cast(Element, cast(Element, root.find("testsuite")).find("testcase")).find(
+                "system-err"
+            ),
+        ).text
+        assert timeout_text is not None and "Test timed out" in timeout_text
+        assert timeout_stderr is not None and "timeout stderr" in timeout_stderr
     except AttributeError as e:
         print(junit_xml_report.read_text())
         raise e
diff --git a/cwltest/tests/util.py b/tests/util.py
similarity index 65%
rename from cwltest/tests/util.py
rename to tests/util.py
index 25879bc..145d0b2 100644
--- a/cwltest/tests/util.py
+++ b/tests/util.py
@@ -1,15 +1,16 @@
 import os
-
 import subprocess  # nosec
+from typing import List, Tuple
 
 from pkg_resources import (
     Requirement,
-    ResolutionError,  # type: ignore
+    ResolutionError,
     resource_filename,
 )
 
 
-def get_data(filename):
+def get_data(filename: str) -> str:
+    """Return the absolute path starting from a file name."""
     filename = os.path.normpath(filename)
     # normalizing path depending on OS or else it will cause problem when
     # joining path
@@ -23,9 +24,11 @@ def get_data(filename):
     return filepath
 
 
-def run_with_mock_cwl_runner(args):
+def run_with_mock_cwl_runner(args: List[str]) -> Tuple[int, str, str]:
+    """Bind a mock cwlref-runner implementation to cwltest."""
+    cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
     process = subprocess.Popen(  # nosec
-        ["cwltest", "--tool", "mock-cwl-runner"] + args,
+        ["cwltest", "--tool", cwl_runner] + args,
         stdout=subprocess.PIPE,
         stderr=subprocess.PIPE,
     )
diff --git a/tox.ini b/tox.ini
index bd79838..5e47e6a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,8 +10,7 @@ envlist =
 skip_missing_interpreters = True
 
 [pytest]
-addopts = --pyargs cwltest
-testpaths = cwltest/tests
+testpaths = tests
 
 [gh-actions]
 python =
@@ -34,6 +33,7 @@ description =
 passenv =
   CI
   GITHUB_*
+
 deps =
   py{36,37,38,39,310,311}-{unit,mypy}: -rrequirements.txt
   py{36,37,38,39,310,311}-{unit,mypy}: -rtest-requirements.txt
@@ -48,7 +48,7 @@ setenv =
 commands =
   py{36,37,38,39,310,311}-unit: python -m pip install -U pip setuptools wheel
   py{36,37,38,39,310,311}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
-  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest --exclude cwltest/tests/*
+  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest --exclude tests/*
   py{36,37,38,39,310,311}-lint: make flake8
   py{36,37,38,39,310,311}-lint: make format-check
   py{37,38,39,310,311}-mypy: make mypy

From b80be607cffc488f997a78d50d6c3d2d33b1c3e0 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sat, 7 Jan 2023 14:49:18 +0100
Subject: [PATCH 054/165] build docs (#157)

---
 .readthedocs.yml         |  24 +++++++++
 Makefile                 |  33 +++++--------
 dev-requirements.txt     |  14 ++++++
 docs/Makefile            |  20 ++++++++
 docs/_static/favicon.ico | Bin 0 -> 15086 bytes
 docs/conf.py             | 102 +++++++++++++++++++++++++++++++++++++++
 docs/index.rst           |  17 +++++++
 docs/requirements.txt    |   6 +++
 release-test.sh          |   6 +--
 9 files changed, 198 insertions(+), 24 deletions(-)
 create mode 100644 .readthedocs.yml
 create mode 100644 dev-requirements.txt
 create mode 100644 docs/Makefile
 create mode 100644 docs/_static/favicon.ico
 create mode 100644 docs/conf.py
 create mode 100644 docs/index.rst
 create mode 100644 docs/requirements.txt

diff --git a/.readthedocs.yml b/.readthedocs.yml
new file mode 100644
index 0000000..5a74019
--- /dev/null
+++ b/.readthedocs.yml
@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+python:
+  install:
+   - requirements: docs/requirements.txt
+   - method: pip
+     path: .
diff --git a/Makefile b/Makefile
index c65f07b..9ff55a8 100644
--- a/Makefile
+++ b/Makefile
@@ -26,15 +26,13 @@ PACKAGE=cwltest
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=diff_cover black pylint pep257 pydocstyle flake8 tox tox-pyenv \
-	isort wheel autoflake flake8-bugbear pyupgrade bandit \
-	-rtest-requirements.txt -rmypy-requirements.txt
+DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
 VERSION=2.2.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 
-## all         : default task
+## all                    : default task (install in dev mode)
 all: dev
 
 ## help                   : print this help message and exit
@@ -61,13 +59,18 @@ install: FORCE
 
 ## dev                    : install the cwltest package in dev mode
 dev: install-dep
+	pip install -U pip setuptools wheel
 	pip install -e .
 
 ## dist                   : create a module package for distribution
 dist: dist/${MODULE}-$(VERSION).tar.gz
 
 dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
-	python setup.py sdist bdist_wheel
+	python -m build
+
+## docs                   : make the docs
+docs: FORCE
+	cd docs && $(MAKE) html
 
 ## clean                  : clean up all temporary / machine-generated files
 clean: FORCE
@@ -141,8 +144,8 @@ diff-cover.html: coverage.xml
 	diff-cover --compare-branch=main $^ --html-report $@
 
 ## test                   : run the cwltest test suite
-test: $(PYSOURCES) all
-	python setup.py test ${PYTEST_EXTRA}
+test: $(PYSOURCES)
+	python -m pytest -rs ${PYTEST_EXTRA}
 
 ## testcov                : run the cwltest test suite and collect coverage
 testcov: $(PYSOURCES)
@@ -161,21 +164,9 @@ list-author-emails:
 
 mypy3: mypy
 mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
-	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
-	then \
-		rm -Rf mypy-stubs/ruamel/yaml ; \
-		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			mypy-stubs/ruamel/ ; \
-	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 mypy_3.6: $(filter-out setup.py gittagger.py,$(PYSOURCES))
-	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
-	then \
-		rm -Rf mypy-stubs/ruamel/yaml ; \
-		ln -s $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			mypy-stubs/ruamel/ ; \
-	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy --python-version 3.6 $^
 
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
@@ -187,8 +178,8 @@ release-test: FORCE
 
 release: release-test
 	. testenv2/bin/activate && \
-		python testenv2/src/${PACKAGE}/setup.py sdist bdist_wheel
-	. testenv2/bin/activate && \
+		pip install build && \
+		python -m build testenv2/src/${PACKAGE} && \
 		pip install twine && \
 		twine upload testenv2/src/${PACKAGE}/dist/* && \
 		git tag ${VERSION} && git push --tags
diff --git a/dev-requirements.txt b/dev-requirements.txt
new file mode 100644
index 0000000..3b58070
--- /dev/null
+++ b/dev-requirements.txt
@@ -0,0 +1,14 @@
+diff_cover
+black
+pylint
+pep257
+pydocstyle
+flake8
+tox < 4
+tox-pyenv
+isort
+wheel
+autoflake
+flake8-bugbear
+pyupgrade
+bandit
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d4bb2cb
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/favicon.ico b/docs/_static/favicon.ico
new file mode 100644
index 0000000000000000000000000000000000000000..9fadc9a7c992f41b5c8730b34cf60871378c8f56
GIT binary patch
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diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..1271b5e
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,102 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import time
+from datetime import datetime
+
+sys.path.insert(0, os.path.abspath(".."))
+
+
+# -- Project information -----------------------------------------------------
+
+build_date = datetime.utcfromtimestamp(
+    int(os.environ.get("SOURCE_DATE_EPOCH", time.time()))
+)
+# -- Project information -----------------------------------------------------
+
+project = "cwltest"
+copyright = (
+    f"2016 - {build_date.year}, Common Workflow Language project and contributors"
+)
+author = "Common Workflow Language project and contributors"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.inheritance_diagram",
+    "autoapi.extension",
+    "sphinx_autodoc_typehints",
+    "sphinx_rtd_theme",
+    "sphinxcontrib.autoprogram",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "schema_salad": ("https://schema-salad.readthedocs.io/en/stable/", None),
+    "rdflib": ("https://rdflib.readthedocs.io/en/6.2.0/", None),
+    #"ruamel.yaml": ("https://yaml.readthedocs.io/en/stable/", None),
+}
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+
+from pkg_resources import get_distribution
+
+release = get_distribution("cwltest").version
+version = ".".join(release.split(".")[:2])
+
+autoapi_dirs = ["../cwltest"]
+autodoc_typehints = "description"
+autoapi_keep_files = True
+autoapi_ignore = ["*.pyi"]
+autoapi_options = [
+    "members",
+    "undoc-members",
+    "show-inheritance",
+    "show-inheritance-diagram",
+    "show-module-summary",
+    "imported-members",
+    "special-members",
+]
+# sphinx-autodoc-typehints
+always_document_param_types = True
+# If False, do not add type info for undocumented parameters.
+# If True, add stub documentation for undocumented parameters to be able to add type info.
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..45c2163
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,17 @@
+.. include:: ../README.rst
+
+.. toctree::
+   :maxdepth: 2
+
+Command Line Options
+====================
+
+.. autoprogram:: cwltest.argparser:arg_parser()
+   :prog: cwltest
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 0000000..b8611de
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1,6 @@
+sphinx >= 2.2
+sphinx-rtd-theme==1.1.1
+sphinx-autoapi
+sphinx-autodoc-typehints
+typed_ast;python_version<'3.8'
+sphinxcontrib-autoprogram
diff --git a/release-test.sh b/release-test.sh
index e840392..42684e0 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -19,7 +19,7 @@ else
 fi
 run_tests="bin/py.test --pyargs ${module}"
 pipver=20.3.3  # minimum required version of pip for Python 3.10
-setuptoolsver=50.0.0  # required for Python 3.10
+setuptoolsver=50.0.1  # required for Python 3.10
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
 rm -Rf testenv? || /bin/true
@@ -63,7 +63,7 @@ rm -f lib/python-wheels/setuptools* \
 # The following can fail if you haven't pushed your commits to ${repo}
 pip install -e "git+${repo}@${HEAD}#egg=${package}${extras}"
 pushd src/${package}
-pip install -rtest-requirements.txt
+pip install -rtest-requirements.txt build
 make dist
 make test
 cp dist/${package}*tar.gz ../../../testenv3/
@@ -84,7 +84,7 @@ rm -f lib/python-wheels/setuptools* \
 	&& pip install --force-reinstall -U pip==${pipver} \
         && pip install setuptools==${setuptoolsver} wheel
 package_tar=$(find . -name "${package}*tar.gz")
-pip install "-r${DIR}/test-requirements.txt"
+pip install "-r${DIR}/test-requirements.txt" build
 pip install "${package_tar}${extras}"
 mkdir out
 tar --extract --directory=out -z -f ${package}*.tar.gz

From af433f71f5236b8a57deb724a362a2e3e1a66af3 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sun, 8 Jan 2023 20:26:06 +0100
Subject: [PATCH 055/165] cwltest plugin for pytest (#74)

Co-authored-by: GlassOfWhiskey <iacopo.c92@gmail.com>
---
 .coveragerc                                   |  18 +-
 Makefile                                      |  14 +-
 README.rst                                    |  16 +-
 cwltest/__init__.py                           |   2 +-
 cwltest/argparser.py                          |   9 +-
 cwltest/compare.py                            | 164 +++++
 cwltest/hooks.py                              |  23 +
 cwltest/main.py                               | 342 +++-------
 cwltest/plugin.py                             | 393 ++++++++++++
 cwltest/utils.py                              | 587 ++++++++++++------
 docs/conf.py                                  |   4 +-
 docs/index.rst                                |  14 +-
 docs/pytest.rst                               | 174 ++++++
 gittaggers.py                                 |   1 +
 mypy-requirements.txt                         |   2 +
 .../defusedxml/{__init__.py => __init__.pyi}  |   0
 .../ruamel/{__init__.py => __init__.pyi}      |   0
 release-test.sh                               |   2 +-
 requirements.txt                              |   3 +-
 setup.py                                      |  27 +-
 test-requirements.txt                         |   5 +-
 .../conformance_test_v1.0.cwltest.yml         |  17 +
 .../conformance_test_v1.2.cwltest.yaml        |  15 +
 tests/test-data/cwltool-conftest.py           |  37 ++
 tests/test-data/v1.0/args.py                  |   7 +
 tests/test-data/v1.0/cat-job.json             |   6 +
 tests/test-data/v1.0/cat-n-job.json           |   7 +
 tests/test-data/v1.0/cat1-testcli.cwl         |  45 ++
 tests/test-data/v1.0/hello.txt                |   1 +
 tests/test_categories.py                      |   8 +-
 tests/test_compare.py                         | 413 +++++++++++-
 tests/test_plugin.py                          | 126 ++++
 tests/util.py                                 |   6 +-
 tox.ini                                       |  21 +-
 34 files changed, 1986 insertions(+), 523 deletions(-)
 create mode 100644 cwltest/compare.py
 create mode 100644 cwltest/hooks.py
 create mode 100644 cwltest/plugin.py
 create mode 100644 docs/pytest.rst
 rename mypy-stubs/defusedxml/{__init__.py => __init__.pyi} (100%)
 rename mypy-stubs/ruamel/{__init__.py => __init__.pyi} (100%)
 create mode 100644 tests/test-data/conformance_test_v1.0.cwltest.yml
 create mode 100644 tests/test-data/conformance_test_v1.2.cwltest.yaml
 create mode 100644 tests/test-data/cwltool-conftest.py
 create mode 100644 tests/test-data/v1.0/args.py
 create mode 100644 tests/test-data/v1.0/cat-n-job.json
 create mode 100644 tests/test-data/v1.0/cat1-testcli.cwl
 create mode 100644 tests/test-data/v1.0/hello.txt
 create mode 100644 tests/test_plugin.py

diff --git a/.coveragerc b/.coveragerc
index 020763e..6086f7f 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,7 +1,15 @@
+[paths]
+source =
+  cwltest
+  */site-packages/cwltest
+  */cwltest
+
 [run]
 branch = True
-source = cwltest
-omit = tests/*
+source_pkgs = cwltest
+omit =
+  tests/*
+  */site-packages/cwltest/tests/*
 
 [report]
 exclude_lines =
@@ -9,5 +17,9 @@ exclude_lines =
     pragma: no cover
     raise NotImplementedError
     if __name__ == .__main__.:
+    if TYPE_CHECKING:
+    \.\.\.
 ignore_errors = True
-omit = tests/*
+omit =
+  tests/*
+  */site-packages/cwltest/tests/*
diff --git a/Makefile b/Makefile
index 9ff55a8..2c7d049 100644
--- a/Makefile
+++ b/Makefile
@@ -76,7 +76,7 @@ docs: FORCE
 clean: FORCE
 	rm -f ${MODILE}/*.pyc tests/*.pyc
 	python setup.py clean --all || true
-	rm -Rf .coverage
+	rm -Rf .coverage\.* .coverage
 	rm -f diff-cover.html
 
 # Linting and code style related targets
@@ -104,11 +104,11 @@ codespell:
 	codespell -w $(shell git ls-files | grep -v mypy-stubs | grep -v gitignore)
 
 ## format                 : check/fix all code indentation and formatting (runs black)
-format:
-	black setup.py setup.py cwltest tests mypy-stubs
+format: $(PYSOURCES) mypy-stubs
+	black $^
 
-format-check:
-	black --diff --check setup.py cwltest tests mypy-stubs
+format-check: $(PYSOURCES) mypy-stubs
+	black --diff --check $^
 
 ## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
@@ -123,7 +123,9 @@ diff_pylint_report: pylint_report.txt
 	diff-quality --compare-branch=main --violations=pylint pylint_report.txt
 
 .coverage: $(PYSOURCES)
-	python setup.py test --addopts "--cov --cov-config=.coveragerc --cov-report= ${PYTEST_EXTRA}"
+	COV_CORE_SOURCE=cwltest COV_CORE_CONFIG=.coveragerc COV_CORE_DATAFILE=.coverage \
+		python -m pytest --cov --cov-append --cov-report=
+	# https://pytest-cov.readthedocs.io/en/latest/plugins.html#plugin-coverage
 
 coverage.xml: .coverage
 	coverage xml
diff --git a/README.rst b/README.rst
index 15066a6..f6e7e2e 100644
--- a/README.rst
+++ b/README.rst
@@ -1,6 +1,6 @@
-==========================================
+##########################################
 Common Workflow Language testing framework
-==========================================
+##########################################
 
 |Linux Build Status| |Code coverage|
 
@@ -34,8 +34,12 @@ conformance tests.
 
 This is written and tested for Python 3.6, 3.7, 3.8, 3.9, 3.10, and 3.11.
 
+.. contents:: Table of Contents
+   :local:
+
+*******
 Install
--------
+*******
 
 Installing the official package from PyPi
 
@@ -56,15 +60,17 @@ Or from source
   git clone https://github.com/common-workflow-language/cwltest.git
   cd cwltest && python setup.py install
 
+***********************
 Run on the command line
------------------------
+***********************
 
 Simple command::
 
   cwltest --test test-descriptions.yml --tool cwl-runner
 
+*****************************************
 Generate conformance badges using cwltest
------------------------------------------
+*****************************************
 
 To make badges that show the results of the conformance test,
 you can generate JSON files for https://badgen.net by using --badgedir option
diff --git a/cwltest/__init__.py b/cwltest/__init__.py
index 5b6419f..fa05598 100755
--- a/cwltest/__init__.py
+++ b/cwltest/__init__.py
@@ -1,4 +1,4 @@
-"""Common Workflow Language testing framework."""
+"""Run CWL descriptions with a cwl-runner, and look for expected output."""
 
 import logging
 import threading
diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index b567622..6cc616d 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -7,7 +7,7 @@
 from cwltest import DEFAULT_TIMEOUT
 
 
-def arg_parser():  # type: () -> argparse.ArgumentParser
+def arg_parser() -> argparse.ArgumentParser:
     """Generate a command Line argument parser for cwltest."""
     parser = argparse.ArgumentParser(
         description="Common Workflow Language testing framework"
@@ -60,7 +60,8 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument(
         "--junit-verbose",
         action="https://github.com/store_true",
-        help="Store more verbose output to JUnit xml file",
+        help="Store more verbose output to JUnit XML file by not passing "
+        "'--quiet' to the CWL runner.",
     )
     parser.add_argument(
         "--test-arg",
@@ -101,7 +102,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
         ),
     )
     parser.add_argument(
-        "--badgedir", type=str, help="Directory that stores JSON files for badges."
+        "--badgedir",
+        type=str,
+        help="Create JSON badges and store them in this directory.",
     )
 
     pkg = pkg_resources.require("cwltest")
diff --git a/cwltest/compare.py b/cwltest/compare.py
new file mode 100644
index 0000000..b56a7c3
--- /dev/null
+++ b/cwltest/compare.py
@@ -0,0 +1,164 @@
+"""Compare utilities for CWL objects."""
+
+import json
+from typing import Any, Dict, Set
+
+
+class CompareFail(Exception):
+    """Compared CWL objects are not equal."""
+
+    @classmethod
+    def format(cls, expected, actual, cause=None):
+        # type: (Any, Any, Any) -> CompareFail
+        """Load the difference details into the error message."""
+        message = "expected: {}\ngot: {}".format(
+            json.dumps(expected, indent=4, sort_keys=True),
+            json.dumps(actual, indent=4, sort_keys=True),
+        )
+        if cause:
+            message += "\ncaused by: %s" % cause
+        return cls(message)
+
+
+def _check_keys(keys, expected, actual):
+    # type: (Set[str], Dict[str,Any], Dict[str,Any]) -> None
+    for k in keys:
+        try:
+            compare(expected.get(k), actual.get(k))
+        except CompareFail as e:
+            raise CompareFail.format(
+                expected, actual, f"field '{k}' failed comparison: {str(e)}"
+            ) from e
+
+
+def _compare_contents(expected, actual):
+    # type: (Dict[str,Any], Dict[str,Any]) -> None
+    expected_contents = expected["contents"]
+    with open(actual["path"]) as f:
+        actual_contents = f.read()
+    if expected_contents != actual_contents:
+        raise CompareFail.format(
+            expected,
+            actual,
+            json.dumps(
+                "Output file contents do not match: actual '%s' is not equal to expected '%s'"
+                % (actual_contents, expected_contents)
+            ),
+        )
+
+
+def _compare_dict(expected, actual):
+    # type: (Dict[str,Any], Dict[str,Any]) -> None
+    for c in expected:
+        try:
+            compare(expected[c], actual.get(c))
+        except CompareFail as e:
+            raise CompareFail.format(
+                expected, actual, f"failed comparison for key '{c}': {e}"
+            ) from e
+    extra_keys = set(actual.keys()).difference(list(expected.keys()))
+    for k in extra_keys:
+        if actual[k] is not None:
+            raise CompareFail.format(expected, actual, "unexpected key '%s'" % k)
+
+
+def _compare_directory(expected, actual):
+    # type: (Dict[str,Any], Dict[str,Any]) -> None
+    if actual.get("class") != "Directory":
+        raise CompareFail.format(
+            expected, actual, "expected object with a class 'Directory'"
+        )
+    if "listing" not in actual:
+        raise CompareFail.format(
+            expected, actual, "'listing' is mandatory field in Directory object"
+        )
+    for i in expected["listing"]:
+        found = False
+        for j in actual["listing"]:
+            try:
+                compare(i, j)
+                found = True
+                break
+            except CompareFail:
+                pass
+        if not found:
+            raise CompareFail.format(
+                expected,
+                actual,
+                "%s not found" % json.dumps(i, indent=4, sort_keys=True),
+            )
+    _compare_file(expected, actual)
+
+
+def _compare_file(expected, actual):
+    # type: (Dict[str,Any], Dict[str,Any]) -> None
+    _compare_location(expected, actual)
+    if "contents" in expected:
+        _compare_contents(expected, actual)
+    other_keys = set(expected.keys()) - {"path", "location", "listing", "contents"}
+    _check_keys(other_keys, expected, actual)
+    _check_keys(other_keys, expected, actual)
+
+
+def _compare_location(expected, actual):
+    # type: (Dict[str,Any], Dict[str,Any]) -> None
+    if "path" in expected:
+        comp = "path"
+        if "path" not in actual:
+            actual["path"] = actual["location"]
+    elif "location" in expected:
+        comp = "location"
+    else:
+        return
+    if actual.get("class") == "Directory":
+        actual[comp] = actual[comp].rstrip("/")
+
+    if expected[comp] != "Any" and (
+        not (
+            actual[comp].endswith("/" + expected[comp])
+            or ("/" not in actual[comp] and expected[comp] == actual[comp])
+        )
+    ):
+        raise CompareFail.format(
+            expected,
+            actual,
+            f"{actual[comp]} does not end with {expected[comp]}",
+        )
+
+
+def compare(expected, actual):  # type: (Any, Any) -> None
+    """Compare two CWL objects."""
+    if expected == "Any":
+        return
+    if expected is not None and actual is None:
+        raise CompareFail.format(expected, actual)
+
+    try:
+        if isinstance(expected, dict):
+            if not isinstance(actual, dict):
+                raise CompareFail.format(expected, actual)
+
+            if expected.get("class") == "File":
+                _compare_file(expected, actual)
+            elif expected.get("class") == "Directory":
+                _compare_directory(expected, actual)
+            else:
+                _compare_dict(expected, actual)
+
+        elif isinstance(expected, list):
+            if not isinstance(actual, list):
+                raise CompareFail.format(expected, actual)
+
+            if len(expected) != len(actual):
+                raise CompareFail.format(expected, actual, "lengths don't match")
+            for c in range(0, len(expected)):
+                try:
+                    compare(expected[c], actual[c])
+                except CompareFail as e:
+                    raise CompareFail.format(expected, actual, e) from e
+        else:
+            if expected != actual:
+                raise CompareFail.format(expected, actual)
+
+    except Exception as e:
+        raise CompareFail(str(e)) from e
diff --git a/cwltest/hooks.py b/cwltest/hooks.py
new file mode 100644
index 0000000..9b3faae
--- /dev/null
+++ b/cwltest/hooks.py
@@ -0,0 +1,23 @@
+"""Hooks for pytest-cwl users."""
+
+from typing import Any, Dict, Optional, Tuple
+
+from cwltest import utils
+
+
+def pytest_cwl_execute_test(  # type: ignore[empty-body]
+    config: utils.CWLTestConfig, processfile: str, jobfile: Optional[str]
+) -> Tuple[int, Optional[Dict[str, Any]]]:
+    """
+    Execute CWL test using a Python function instead of a command line runner.
+
+    The return value is a tuple.
+     - status code
+        - 0 = success
+        - :py:attr:`cwltest.UNSUPPORTED_FEATURE` for an unsupported feature
+        - and any other number for failure
+     - CWL output object using plain Python objects.
+
+    :param processfile: a path to a CWL document
+    :param jobfile: an optionl path to JSON/YAML input object
+    """
diff --git a/cwltest/main.py b/cwltest/main.py
index 3652764..6c9d293 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -2,201 +2,71 @@
 """Entry point for cwltest."""
 
 import argparse
-import json
 import os
-import shlex
-import shutil
-import subprocess  # nosec
 import sys
-import time
 from collections import defaultdict
 from concurrent.futures import ThreadPoolExecutor
-from typing import Any, Dict, List, Optional, Set, Union
+from typing import Dict, List, Optional, Set, cast
 
 import junit_xml
-import pkg_resources
-import ruamel.yaml.scanner
 import schema_salad.avro
 import schema_salad.ref_resolver
 import schema_salad.schema
-from rdflib import Graph
-
-from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
 from cwltest.argparser import arg_parser
-from cwltest.utils import TestResult
+from cwltest.utils import CWLTestConfig, TestResult
+from schema_salad.exceptions import ValidationException
 
+from cwltest import logger, utils
 
-def _run_test(
-    args,  # type: argparse.Namespace
-    test,  # type: Dict[str, str]
-    test_number,  # type: int
-    total_tests,  # type: int
-    timeout,  # type: int
-    junit_verbose=False,  # type: bool
-    verbose=False,  # type: bool
-):  # type: (...) -> TestResult
-    out = {}  # type: Dict[str,Any]
-    outdir = outstr = outerr = ""
-    test_command = []  # type: List[str]
-    duration = 0.0
-    process = None  # type: Optional[subprocess.Popen[str]]
-    prefix = ""
-    suffix = ""
-    if sys.stderr.isatty():
-        prefix = "\r"
-    else:
-        suffix = "\n"
-    try:
-        cwd = os.getcwd()
-        test_command = utils.prepare_test_command(
-            args.tool, args.args, args.testargs, test, cwd, junit_verbose
-        )
+if sys.stderr.isatty():
+    PREFIX = "\r"
+    SUFFIX = ""
+else:
+    PREFIX = ""
+    SUFFIX = "\n"
 
-        if test.get("short_name"):
-            sys.stderr.write(
-                "%sTest [%i/%i] %s: %s%s\n"
-                % (
-                    prefix,
-                    test_number,
-                    total_tests,
-                    test.get("short_name"),
-                    test.get("doc", "").replace("\n", " ").strip(),
-                    suffix,
-                )
-            )
-        else:
-            sys.stderr.write(
-                "%sTest [%i/%i] %s%s\n"
-                % (
-                    prefix,
-                    test_number,
-                    total_tests,
-                    test.get("doc", "").replace("\n", " ").strip(),
-                    suffix,
-                )
-            )
-        if verbose:
-            sys.stderr.write(f"Running: {' '.join(test_command)}\n")
-        sys.stderr.flush()
 
-        start_time = time.time()
-        stderr = subprocess.PIPE if not args.verbose else None
-        process = subprocess.Popen(  # nosec
-            test_command,
-            stdout=subprocess.PIPE,
-            stderr=stderr,
-            universal_newlines=True,
-            cwd=cwd,
-        )
-        outstr, outerr = process.communicate(timeout=timeout)
-        return_code = process.poll()
-        duration = time.time() - start_time
-        if return_code:
-            raise subprocess.CalledProcessError(return_code, " ".join(test_command))
-
-        out = json.loads(outstr)
-    except ValueError as err:
-        logger.error(str(err))
-        logger.error(outstr)
-        logger.error(outerr)
-    except subprocess.CalledProcessError as err:
-        if err.returncode == UNSUPPORTED_FEATURE and REQUIRED not in test.get(
-            "tags", ["required"]
-        ):
-            return utils.TestResult(
-                UNSUPPORTED_FEATURE, outstr, outerr, duration, args.classname
+def _run_test(
+    args: argparse.Namespace,
+    test: Dict[str, str],
+    test_number: int,
+    total_tests: int,
+) -> TestResult:
+    if test.get("short_name"):
+        sys.stderr.write(
+            "%sTest [%i/%i] %s: %s%s\n"
+            % (
+                PREFIX,
+                test_number,
+                total_tests,
+                test.get("short_name"),
+                test.get("doc", "").replace("\n", " ").strip(),
+                SUFFIX,
             )
-        if test.get("should_fail", False):
-            return utils.TestResult(0, outstr, outerr, duration, args.classname)
-        logger.error(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
         )
-        logger.error(test.get("doc", "").replace("\n", " ").strip())
-        if err.returncode == UNSUPPORTED_FEATURE:
-            logger.error("Does not support required feature")
-        else:
-            logger.error("Returned non-zero")
-        logger.error(outerr)
-        return utils.TestResult(1, outstr, outerr, duration, args.classname, str(err))
-    except (ruamel.yaml.scanner.ScannerError, TypeError) as err:
-        logger.error(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
-        )
-        logger.error(outstr)
-        logger.error("Parse error %s", str(err))
-        logger.error(outerr)
-    except KeyboardInterrupt:
-        logger.error(
-            """Test %i interrupted: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
-        )
-        raise
-    except subprocess.TimeoutExpired:
-        logger.error(
-            """Test %i timed out: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
-        )
-        logger.error(test.get("doc", "").replace("\n", " ").strip())
-        # Kill and re-communicate to get the logs and reap the child, as
-        # instructed in the subprocess docs.
-        if process:
-            process.kill()
-            outstr, outerr = process.communicate()
-        return utils.TestResult(
-            2, outstr, outerr, timeout, args.classname, "Test timed out"
-        )
-    finally:
-        if process is not None and process.returncode is None:
-            logger.error("""Terminating lingering process""")
-            process.terminate()
-            for _ in range(0, 3):
-                time.sleep(1)
-                if process.poll() is not None:
-                    break
-            if process.returncode is None:
-                process.kill()
-
-    fail_message = ""
-
-    if test.get("should_fail", False):
-        logger.warning(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
-        )
-        logger.warning(test.get("doc", "").replace("\n", " ").strip())
-        logger.warning("Returned zero but it should be non-zero")
-        return utils.TestResult(1, outstr, outerr, duration, args.classname)
-
-    try:
-        utils.compare(test.get("output"), out)
-    except utils.CompareFail as ex:
-        logger.warning(
-            """Test %i failed: %s""",
-            test_number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+    else:
+        sys.stderr.write(
+            "%sTest [%i/%i] %s%s\n"
+            % (
+                PREFIX,
+                test_number,
+                total_tests,
+                test.get("doc", "").replace("\n", " ").strip(),
+                SUFFIX,
+            )
         )
-        logger.warning(test.get("doc", "").replace("\n", " ").strip())
-        logger.warning("Compare failure %s", ex)
-        fail_message = str(ex)
-
-    if outdir:
-        shutil.rmtree(outdir, True)
-
-    return utils.TestResult(
-        (1 if fail_message else 0),
-        outstr,
-        outerr,
-        duration,
-        args.classname,
-        fail_message,
+    sys.stderr.flush()
+    config = CWLTestConfig(
+        basedir=args.basedir,
+        classname=args.classname,
+        tool=args.tool,
+        args=args.args,
+        testargs=args.testargs,
+        timeout=args.timeout,
+        verbose=args.verbose,
+        runner_quiet=not args.junit_verbose,
     )
+    return utils.run_test_plain(config, test, test_number)
 
 
 def _expand_number_range(nr: str) -> List[int]:
@@ -226,34 +96,17 @@ def main() -> int:
         arg_parser().print_help()
         return 1
 
-    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
-    cache = {
-        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
-            "utf-8"
-        )
-    }  # type: Optional[Dict[str, Union[str, Graph, bool]]]
-    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
-        "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
-    )
-
-    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
-        print(avsc_names)
+    try:
+        tests, metadata = utils.load_and_validate_tests(args.test)
+    except ValidationException:
         return 1
 
-    tests, metadata = schema_salad.schema.load_and_validate(
-        document_loader, avsc_names, args.test, True
-    )
-
     failures = 0
     unsupported = 0
-    passed = 0
     suite_name, _ = os.path.splitext(os.path.basename(args.test))
-    report = junit_xml.TestSuite(suite_name, [])
+    report: Optional[junit_xml.TestSuite] = junit_xml.TestSuite(suite_name, [])
 
-    # the number of total tests, failed tests, unsupported tests and passed tests for each tag
     ntotal = defaultdict(int)  # type: Dict[str, int]
-    nfailures = defaultdict(int)  # type: Dict[str, int]
-    nunsupported = defaultdict(int)  # type: Dict[str, int]
     npassed = defaultdict(int)  # type: Dict[str, int]
 
     if args.only_tools:
@@ -269,22 +122,12 @@ def main() -> int:
                 raise Exception("Unexpected code path.")
 
     if args.tags:
-        alltests = tests
-        tests = []
-        tags = args.tags.split(",")
-        for t in alltests:
-            ts = t.get("tags", [])
-            if any(tag in ts for tag in tags):
-                tests.append(t)
+        tags = set(args.tags.split(","))
+        tests = [t for t in tests if tags.intersection(t.get("tags", []))]
 
     if args.exclude_tags:
-        ex_tests = []
-        tags = args.exclude_tags.split(",")
-        for t in tests:
-            ts = t.get("tags", [])
-            if all(tag not in ts for tag in tags):
-                ex_tests.append(t)
-        tests = ex_tests
+        tags = set(args.exclude_tags.split(","))
+        tests = [t for t in tests if not tags.intersection(t.get("tags", []))]
 
     for t in tests:
         if t.get("label"):
@@ -363,49 +206,23 @@ def main() -> int:
                 tests[i],
                 i + 1,
                 len(tests),
-                args.timeout,
-                args.junit_verbose,
-                args.verbose,
             )
             for i in ntest
         ]
         try:
-            for i, job in zip(ntest, jobs):
-                test_result = job.result()
-                test_case = test_result.create_test_case(tests[i])
-                test_case.url = f"cwltest:{suite_name}#{i + 1}"
-                total += 1
-                tags = tests[i].get("tags", [])
-                for t in tags:
-                    ntotal[t] += 1
-
-                return_code = test_result.return_code
-                category = test_case.category
-                if return_code == 0:
-                    passed += 1
-                    for t in tags:
-                        npassed[t] += 1
-                elif return_code != UNSUPPORTED_FEATURE:
-                    failures += 1
-                    for t in tags:
-                        nfailures[t] += 1
-                    test_case.add_failure_info(output=test_result.message)
-                elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
-                    failures += 1
-                    for t in tags:
-                        nfailures[t] += 1
-                    test_case.add_failure_info(output=test_result.message)
-                elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
-                    unsupported += 1
-                    for t in tags:
-                        nunsupported[t] += 1
-                    test_case.add_skipped_info("Unsupported")
-                else:
-                    raise Exception(
-                        "This is impossible, return_code: {}, category: "
-                        "{}".format(return_code, category)
-                    )
-                report.test_cases.append(test_case)
+            (
+                total,
+                passed,
+                failures,
+                unsupported,
+                ntotal,
+                npassed,
+                nfailures,
+                nunsupported,
+                report,
+            ) = utils.parse_results(
+                (job.result() for job in jobs), tests, suite_name, report
+            )
         except KeyboardInterrupt:
             for job in jobs:
                 job.cancel()
@@ -413,29 +230,10 @@ def main() -> int:
 
     if args.junit_xml:
         with open(args.junit_xml, "w") as xml:
-            junit_xml.to_xml_report_file(xml, [report])
+            junit_xml.to_xml_report_file(xml, [cast(junit_xml.TestSuite, report)])
 
     if args.badgedir:
-        os.mkdir(args.badgedir)
-        for t, v in ntotal.items():
-            percent = int((npassed[t] / float(v)) * 100)
-            if npassed[t] == v:
-                color = "green"
-            elif t == "required":
-                color = "red"
-            else:
-                color = "yellow"
-
-            with open(f"{args.badgedir}/{t}.json", "w") as out:
-                out.write(
-                    json.dumps(
-                        {
-                            "subject": f"{t}",
-                            "status": f"{percent}%",
-                            "color": color,
-                        }
-                    )
-                )
+        utils.generate_badges(args.badgedir, ntotal, npassed)
 
     if failures == 0 and unsupported == 0:
         logger.info("All tests passed")
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
new file mode 100644
index 0000000..c642519
--- /dev/null
+++ b/cwltest/plugin.py
@@ -0,0 +1,393 @@
+"""Discovers CWL test files and converts them to pytest.Items."""
+import argparse
+import json
+import os
+import time
+import traceback
+from io import StringIO
+from pathlib import Path
+from typing import (
+    Any,
+    Dict,
+    Iterator,
+    List,
+    Optional,
+    Set,
+    TYPE_CHECKING,
+    Tuple,
+    Union,
+    cast,
+)
+
+import pytest
+from typing_extensions import Protocol
+
+from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
+from cwltest.compare import CompareFail, compare
+
+if TYPE_CHECKING:
+    from _pytest._code.code import ExceptionInfo, _TracebackStyle
+    from _pytest.compat import LEGACY_PATH
+    from _pytest.config import Config
+    from _pytest.config import Config as PytestConfig
+    from _pytest.config import PytestPluginManager
+    from _pytest.config.argparsing import Parser as PytestParser
+    from _pytest.nodes import Node
+
+
+class TestRunner(Protocol):
+    """Protocol to type-check test runner functions via the pluggy hook."""
+
+    def __call__(
+        self, config: utils.CWLTestConfig, processfile: str, jobfile: Optional[str]
+    ) -> List[Optional[Dict[str, Any]]]:
+        """Type signature for pytest_cwl_execute_test hook results."""
+        ...
+
+
+def _get_comma_separated_option(config: "Config", name: str) -> List[str]:
+    options = config.getoption(name)
+    if options is None:
+        return []
+    elif "," in options:
+        return [opt.strip() for opt in options.split(",")]
+    else:
+        return [options.strip()]
+
+
+def _run_test_hook_or_plain(
+    test: Dict[str, str],
+    config: utils.CWLTestConfig,
+    hook: TestRunner,
+) -> utils.TestResult:
+    """Run tests using a provided pytest_cwl_execute_test hook or the --cwl-runner."""
+    processfile, jobfile = utils.prepare_test_paths(test, config.basedir)
+    start_time = time.time()
+    outerr = ""
+    hook_out = hook(config=config, processfile=processfile, jobfile=jobfile)
+    if not hook_out:
+        return utils.run_test_plain(config, test)
+    returncode, out = cast(Tuple[int, Optional[Dict[str, Any]]], hook_out[0])
+    duration = time.time() - start_time
+    outstr = json.dumps(out) if out is not None else "{}"
+    if returncode == UNSUPPORTED_FEATURE:
+        if REQUIRED not in test.get("tags", ["required"]):
+            return utils.TestResult(
+                UNSUPPORTED_FEATURE, outstr, "", duration, config.classname
+            )
+    elif returncode != 0:
+        if not bool(test.get("should_fail", False)):
+            logger.warning("Test failed unexpectedly: %s %s", processfile, jobfile)
+            logger.warning(test.get("doc"))
+            message = "Returned non-zero but it should be zero"
+            return utils.TestResult(
+                1, outstr, outerr, duration, config.classname, message
+            )
+        return utils.TestResult(0, outstr, outerr, duration, config.classname)
+    if bool(test.get("should_fail", False)):
+        return utils.TestResult(
+            1,
+            outstr,
+            outerr,
+            duration,
+            config.classname,
+            "Test should failed, but it did not.",
+        )
+
+    fail_message = ""
+
+    try:
+        compare(test.get("output"), out)
+    except CompareFail as ex:
+        logger.warning("""Test failed: %s %s""", processfile, jobfile)
+        logger.warning(test.get("doc"))
+        logger.warning("Compare failure %s", ex)
+        fail_message = str(ex)
+
+    return utils.TestResult(
+        (1 if fail_message else 0),
+        outstr,
+        outerr,
+        duration,
+        config.classname,
+        fail_message,
+    )
+
+
+class CWLTestException(Exception):
+    """custom exception for error reporting."""
+
+
+class CWLItem(pytest.Item):
+    """A CWL test Item."""
+
+    def __init__(
+        self,
+        name: str,
+        parent: Optional["Node"],
+        spec: Dict[str, Any],
+    ) -> None:
+        """Initialize this CWLItem."""
+        super().__init__(name, parent)
+        self.spec = spec
+
+    def runtest(self) -> None:
+        """Execute using cwltest."""
+        cwl_args = self.config.getoption("cwl_args")
+        config = utils.CWLTestConfig(
+            basedir=self.config.getoption("cwl_basedir"),
+            outdir=str(
+                self.config._tmp_path_factory.mktemp(  # type: ignore[attr-defined]
+                    self.spec.get("label", "unlabled_test")
+                )
+            ),
+            tool=self.config.getoption("cwl_runner"),
+            args=cwl_args.split(" ") if cwl_args else None,
+            testargs=self.config.getoption("cwl_test_arg"),
+            timeout=self.config.getoption("timeout", None),
+            verbose=self.config.getoption("verbose", 0) >= 1,
+            runner_quiet=not self.config.getoption("cwl_runner_verbose", False),
+        )
+        hook = self.config.hook.pytest_cwl_execute_test
+        result = _run_test_hook_or_plain(
+            self.spec,
+            config,
+            hook,
+        )
+        cwl_results = self.config.cwl_results  # type: ignore[attr-defined]
+        cast(List[Tuple[Dict[str, Any], utils.TestResult]], cwl_results).append(
+            (self.spec, result)
+        )
+        if result.return_code != 0:
+            raise CWLTestException(self, result)
+
+    def repr_failure(
+        self,
+        excinfo: "ExceptionInfo[BaseException]",
+        style: Optional["_TracebackStyle"] = None,
+    ) -> str:
+        """
+        Document failure reason.
+
+        Called when self.runtest() raises an exception.
+        """
+        if isinstance(excinfo.value, CWLTestException):
+            from ruamel.yaml.main import YAML
+
+            yaml = YAML()
+            result = excinfo.value.args[1]
+            stream = StringIO()
+            yaml.dump(self.spec, stream)
+            return "\n".join(
+                [
+                    "CWL test execution failed. ",
+                    result.message,
+                    f"Test: {stream.getvalue()}",
+                ]
+            )
+        else:
+            return (
+                f"{excinfo.type.__name__} occurred during CWL test execution:\n"
+                + "".join(
+                    traceback.format_exception(
+                        excinfo.type, excinfo.value, excinfo.traceback[0]._rawentry
+                    )
+                )
+            )
+
+    def reportinfo(self) -> Tuple[Union["os.PathLike[str]", str], Optional[int], str]:
+        """Status report."""
+        return self.fspath, 0, "cwl test: %s" % self.name
+
+
+class CWLYamlFile(pytest.File):
+    """A CWL test file."""
+
+    def _add_global_properties(self) -> None:
+        """Nonfunctional if xdist is installed and anything besides "-n 0" is used."""
+        from _pytest.junitxml import xml_key
+
+        xml = self.config._store.get(xml_key, None)
+        if xml:
+            xml.add_global_property("runner", self.config.getoption("cwl_runner"))
+            xml.add_global_property(
+                "runner_extra_args", self.config.getoption("cwl_args")
+            )
+
+    def collect(self) -> Iterator[CWLItem]:
+        """Load the cwltest file and yield parsed entries."""
+        include: Set[str] = set(_get_comma_separated_option(self.config, "cwl_include"))
+        exclude: Set[str] = set(_get_comma_separated_option(self.config, "cwl_exclude"))
+        tags: Set[str] = set(_get_comma_separated_option(self.config, "cwl_tags"))
+        exclude_tags: Set[str] = set(
+            _get_comma_separated_option(self.config, "cwl_exclude_tags")
+        )
+        tests, _ = utils.load_and_validate_tests(str(self.path))
+        self._add_global_properties()
+        for entry in tests:
+            entry_tags = entry.get("tags", [])
+            if "label" in entry:
+                name = entry["label"]
+            elif "id" in entry:
+                name = utils.shortname(entry["id"])
+            else:
+                name = entry.get("doc", "")
+            item = CWLItem.from_parent(self, name=name, spec=entry)
+            if include and name not in include:
+                item.add_marker(
+                    pytest.mark.skip(
+                        reason=f"Test '{name}' is not in the include list: {','.join(include)}."
+                    )
+                )
+            elif exclude and name in exclude:
+                item.add_marker(
+                    pytest.mark.skip(reason=f"Test '{name}' is in the exclude list.")
+                )
+            elif tags and not tags.intersection(entry_tags):
+                item.add_marker(
+                    pytest.mark.skip(
+                        reason=f"Test '{name}' with tags {','.join(entry_tags)}"
+                        f" doesn't have a tag on the allowed tag list: {','.join(tags)}."
+                    )
+                )
+            elif exclude_tags and exclude_tags.intersection(entry_tags):
+                item.add_marker(
+                    pytest.mark.skip(
+                        reason=f"Test '{name}' has one or more tags on the exclusion "
+                        f" tag list: {','.join(exclude_tags.intersection(entry_tags))}."
+                    )
+                )
+            yield item
+
+
+__OPTIONS: List[Tuple[str, Dict[str, Any]]] = [
+    (
+        "--cwl-runner",
+        {
+            "type": str,
+            "dest": "cwl_runner",
+            "default": "cwl-runner",
+            "help": "Name of the CWL runner to use.",
+        },
+    ),
+    (
+        "--cwl-runner-verbose",
+        {
+            "dest": "cwl_runner_verbose",
+            "default": False,
+            "action": "store_true",
+            "help": "If set, don't pass --quiet to the CWL runner.",
+        },
+    ),
+    (
+        "--cwl-badgedir",
+        {
+            "type": str,
+            "help": "Create badge JSON files and store them in this directory.",
+        },
+    ),
+    (
+        "--cwl-include",
+        {
+            "type": str,
+            "help": "Run specific CWL tests using their short names separated by comma",
+        },
+    ),
+    (
+        "--cwl-exclude",
+        {
+            "type": str,
+            "help": "Exclude specific CWL tests using their short names separated by comma",
+        },
+    ),
+    ("--cwl-tags", {"type": str, "help": "Tags to be tested."}),
+    ("--cwl-exclude-tags", {"type": str, "help": "Tags not to be tested."}),
+    (
+        "--cwl-args",
+        {
+            "type": str,
+            "help": "one or more arguments to pass first to tool runner (separated by spaces)",
+        },
+    ),
+    (
+        "--cwl-test-arg",
+        {
+            "type": str,
+            "help": "Additional argument given in test cases and required prefix for tool runner.",
+            "action": "append",
+        },
+    ),
+    (
+        "--cwl-basedir",
+        {
+            "help": "Basedir to use for tests",
+            "default": os.getcwd(),
+        },
+    ),
+]
+
+
+def pytest_addoption(parser: "PytestParser") -> None:
+    """Add our options to the pytest command line."""
+    for entry in __OPTIONS:
+        parser.addoption(entry[0], **entry[1])
+
+
+def _doc_options() -> argparse.ArgumentParser:
+    """Generate a stand-alone ArgumentParser to aid in documention."""
+    parser = argparse.ArgumentParser("cwltest options for pytest.", add_help=False)
+    for entry in __OPTIONS:
+        parser.add_argument(entry[0], **entry[1])
+    return parser
+
+
+def pytest_collect_file(
+    file_path: Path, path: "LEGACY_PATH", parent: pytest.Collector
+) -> Optional[pytest.Collector]:
+    """Is this file for us."""
+    if (
+        file_path.suffix == ".yml" or file_path.suffix == ".yaml"
+    ) and file_path.stem.endswith(".cwltest"):
+        return cast(
+            Optional[pytest.Collector],
+            CWLYamlFile.from_parent(parent, path=file_path),
+        )
+    return None
+
+
+def pytest_configure(config: "PytestConfig") -> None:
+    """Store the raw tests and the test results."""
+    cwl_results: List[Tuple[Dict[str, Any], utils.TestResult]] = []
+    config.cwl_results = cwl_results  # type: ignore[attr-defined]
+
+
+def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
+    """Generate badges."""
+    cwl_results = cast(
+        List[Tuple[Dict[str, Any], utils.TestResult]],
+        getattr(session.config, "cwl_results", None),
+    )
+    if not cwl_results:
+        return
+    tests, results = (list(item) for item in zip(*cwl_results))
+    (
+        total,
+        passed,
+        failures,
+        unsupported,
+        ntotal,
+        npassed,
+        nfailures,
+        nunsupported,
+        _,
+    ) = utils.parse_results(results, tests)
+    cwl_badgedir = session.config.getoption("cwl_badgedir")
+    if cwl_badgedir:
+        utils.generate_badges(cwl_badgedir, ntotal, npassed)
+
+
+def pytest_addhooks(pluginmanager: "PytestPluginManager") -> None:
+    """Register our cwl hooks."""
+    from cwltest import hooks
+
+    pluginmanager.add_hookspecs(hooks)
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 632e513..036fafb 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -1,14 +1,65 @@
 import json
 import os
 import re
+import shlex
+import shutil
+import subprocess  # nosec
 import sys
 import tempfile
-from typing import Any, Dict, List, Optional, Set, Text
+import time
+from collections import defaultdict
+from typing import (
+    Any,
+    Dict,
+    Iterable,
+    List,
+    MutableMapping,
+    MutableSequence,
+    Optional,
+    Tuple,
+    Union,
+    cast,
+)
 
 import junit_xml
+import pkg_resources
+import ruamel.yaml.scanner
+import schema_salad.avro
 import schema_salad.ref_resolver
+import schema_salad.schema
+from cwltest.compare import CompareFail, compare
+from rdflib import Graph
+from ruamel.yaml.scalarstring import ScalarString
+from schema_salad.exceptions import ValidationException
 
-from cwltest import REQUIRED, templock
+from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, templock
+
+
+class CWLTestConfig(object):
+    """Store configuration values for cwltest."""
+
+    def __init__(
+        self,
+        basedir: Optional[str] = None,
+        outdir: Optional[str] = None,
+        classname: Optional[str] = None,
+        tool: Optional[str] = None,
+        args: Optional[List[str]] = None,
+        testargs: Optional[List[str]] = None,
+        timeout: Optional[int] = None,
+        verbose: Optional[bool] = None,
+        runner_quiet: Optional[bool] = None,
+    ) -> None:
+        """Initialize test configuration."""
+        self.basedir: str = basedir or os.getcwd()
+        self.outdir: Optional[str] = outdir
+        self.classname: str = classname or ""
+        self.tool: str = tool or "cwl-runner"
+        self.args: List[str] = args or []
+        self.testargs: List[str] = testargs or []
+        self.timeout: Optional[int] = timeout
+        self.verbose: bool = verbose or False
+        self.runner_quiet: bool = runner_quiet or True
 
 
 class TestResult:
@@ -16,14 +67,13 @@ class TestResult:
 
     def __init__(
         self,
-        return_code,
-        standard_output,
-        error_output,
-        duration,
-        classname,
-        message="",
-    ):
-        # type: (int, Text, Text, float, Text, str) -> None
+        return_code: int,
+        standard_output: str,
+        error_output: str,
+        duration: float,
+        classname: str,
+        message: str = "",
+    ) -> None:
         """Initialize a TestResult object."""
         self.return_code = return_code
         self.standard_output = standard_output
@@ -32,8 +82,8 @@ def __init__(
         self.message = message
         self.classname = classname
 
-    def create_test_case(self, test):
-        # type: (Dict[Text, Any]) -> junit_xml.TestCase
+    def create_test_case(self, test: Dict[str, Any]) -> junit_xml.TestCase:
+        """Create a jUnit XML test case from this test result."""
         doc = test.get("doc", "N/A").strip()
         if test.get("tags"):
             category = ", ".join(test["tags"])
@@ -53,177 +103,186 @@ def create_test_case(self, test):
         return case
 
 
-class CompareFail(Exception):
-    @classmethod
-    def format(cls, expected, actual, cause=None):
-        # type: (Any, Any, Any) -> CompareFail
-        message = "expected: {}\ngot: {}".format(
-            json.dumps(expected, indent=4, sort_keys=True),
-            json.dumps(actual, indent=4, sort_keys=True),
-        )
-        if cause:
-            message += "\ncaused by: %s" % cause
-        return cls(message)
-
-
-def compare_location(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
-    if "path" in expected:
-        comp = "path"
-        if "path" not in actual:
-            actual["path"] = actual["location"]
-    elif "location" in expected:
-        comp = "location"
-    else:
-        return
-    if actual.get("class") == "Directory":
-        actual[comp] = actual[comp].rstrip("/")
-
-    if expected[comp] != "Any" and (
-        not (
-            actual[comp].endswith("/" + expected[comp])
-            or ("/" not in actual[comp] and expected[comp] == actual[comp])
-        )
-    ):
-        raise CompareFail.format(
-            expected,
-            actual,
-            f"{actual[comp]} does not end with {expected[comp]}",
-        )
-
-
-def compare_contents(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
-    expected_contents = expected["contents"]
-    with open(actual["path"]) as f:
-        actual_contents = f.read()
-    if expected_contents != actual_contents:
-        raise CompareFail.format(
-            expected,
-            actual,
-            json.dumps(
-                "Output file contents do not match: actual '%s' is not equal to expected '%s'"
-                % (actual_contents, expected_contents)
-            ),
-        )
-
+def _clean_ruamel(obj: Any) -> Any:
+    """Transform roundtrip loaded ruamel.yaml to plain objects."""
+    if isinstance(obj, MutableMapping):
+        new_dict = {}
+        for k, v in obj.items():
+            new_dict[str(k)] = _clean_ruamel(v)
+        return new_dict
+    if isinstance(obj, MutableSequence):
+        new_list = []
+        for entry in obj:
+            new_list.append(_clean_ruamel(entry))
+        return new_list
+    if isinstance(obj, ScalarString):
+        return str(obj)
+    for typ in int, float, bool, str:
+        if isinstance(obj, typ):
+            return typ(obj)
+    if obj is None:
+        return None
+    raise Exception(f"Unsupported type {type(obj)} of '{obj}'.")
+
+
+def generate_badges(
+    badgedir: str, ntotal: Dict[str, int], npassed: Dict[str, int]
+) -> None:
+    """Generate badges with conformance levels."""
+    os.mkdir(badgedir)
+    for t, v in ntotal.items():
+        percent = int((npassed[t] / float(v)) * 100)
+        if npassed[t] == v:
+            color = "green"
+        elif t == "required":
+            color = "red"
+        else:
+            color = "yellow"
+
+        with open(f"{badgedir}/{t}.json", "w") as out:
+            out.write(
+                json.dumps(
+                    {
+                        "subject": f"{t}",
+                        "status": f"{percent}%",
+                        "color": color,
+                    }
+                )
+            )
 
-def check_keys(keys, expected, actual):
-    # type: (Set[str], Dict[str,Any], Dict[str,Any]) -> None
-    for k in keys:
-        try:
-            compare(expected.get(k), actual.get(k))
-        except CompareFail as e:
-            raise CompareFail.format(
-                expected, actual, f"field '{k}' failed comparison: {str(e)}"
-            ) from e
 
+def get_test_number_by_key(
+    tests: List[Dict[str, str]], key: str, value: str
+) -> Optional[int]:
+    """Retrieve the test index from its name."""
+    for i, test in enumerate(tests):
+        if key in test and test[key] == value:
+            return i
+    return None
 
-def compare_file(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
-    compare_location(expected, actual)
-    if "contents" in expected:
-        compare_contents(expected, actual)
-    other_keys = set(expected.keys()) - {"path", "location", "listing", "contents"}
-    check_keys(other_keys, expected, actual)
 
+def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
+    """
+    Load and validate the given test file against the cwltest schema.
 
-def compare_directory(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
-    if actual.get("class") != "Directory":
-        raise CompareFail.format(
-            expected, actual, "expected object with a class 'Directory'"
+    This also processes $import directives.
+    """
+    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
+    cache: Optional[Dict[str, Union[str, Graph, bool]]] = {
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
+            "utf-8"
         )
-    if "listing" not in actual:
-        raise CompareFail.format(
-            expected, actual, "'listing' is mandatory field in Directory object"
+    }
+    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
+        "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
+    )
+
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        raise ValidationException(
+            "Wrong instance for avsc_names: {}".format(type(avsc_names))
         )
-    for i in expected["listing"]:
-        found = False
-        for j in actual["listing"]:
-            try:
-                compare(i, j)
-                found = True
-                break
-            except CompareFail:
-                pass
-        if not found:
-            raise CompareFail.format(
-                expected,
-                actual,
-                "%s not found" % json.dumps(i, indent=4, sort_keys=True),
-            )
-    compare_file(expected, actual)
-
-
-def compare_dict(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
-    for c in expected:
-        try:
-            compare(expected[c], actual.get(c))
-        except CompareFail as e:
-            raise CompareFail.format(
-                expected, actual, f"failed comparison for key '{c}': {e}"
-            ) from e
-    extra_keys = set(actual.keys()).difference(list(expected.keys()))
-    for k in extra_keys:
-        if actual[k] is not None:
-            raise CompareFail.format(expected, actual, "unexpected key '%s'" % k)
-
-
-def compare(expected, actual):  # type: (Any, Any) -> None
-    if expected == "Any":
-        return
-    if expected is not None and actual is None:
-        raise CompareFail.format(expected, actual)
-
-    try:
-        if isinstance(expected, dict):
-            if not isinstance(actual, dict):
-                raise CompareFail.format(expected, actual)
-
-            if expected.get("class") == "File":
-                compare_file(expected, actual)
-            elif expected.get("class") == "Directory":
-                compare_directory(expected, actual)
-            else:
-                compare_dict(expected, actual)
-
-        elif isinstance(expected, list):
-            if not isinstance(actual, list):
-                raise CompareFail.format(expected, actual)
-
-            if len(expected) != len(actual):
-                raise CompareFail.format(expected, actual, "lengths don't match")
-            for c in range(0, len(expected)):
-                try:
-                    compare(expected[c], actual[c])
-                except CompareFail as e:
-                    raise CompareFail.format(expected, actual, e) from e
-        else:
-            if expected != actual:
-                raise CompareFail.format(expected, actual)
-
-    except Exception as e:
-        raise CompareFail(str(e)) from e
 
+    tests, metadata = schema_salad.schema.load_and_validate(
+        document_loader, avsc_names, path, True
+    )
+    tests = cast(List[Dict[str, Any]], _clean_ruamel(tests))
+
+    return tests, metadata
+
+
+def parse_results(
+    results: Iterable[TestResult],
+    tests: List[Dict[str, Any]],
+    suite_name: Optional[str] = None,
+    report: Optional[junit_xml.TestSuite] = None,
+) -> Tuple[
+    int,  # total
+    int,  # passed
+    int,  # failures
+    int,  # unsupported
+    Dict[str, int],
+    Dict[str, int],
+    Dict[str, int],
+    Dict[str, int],
+    Optional[junit_xml.TestSuite],
+]:
+    """
+    Parse the results and return statistics and an optional report.
 
-def get_test_number_by_key(tests, key, value):
-    # type: (List[Dict[str, str]], str, str) -> Optional[int]
-    for i, test in enumerate(tests):
-        if key in test and test[key] == value:
-            return i
-    return None
+    Returns the total number of tests, dictionary of test counts
+    (total, passed, failed, unsupported) by tag, and a jUnit XML report.
+    """
+    total = 0
+    passed = 0
+    failures = 0
+    unsupported = 0
+    ntotal: Dict[str, int] = defaultdict(int)
+    nfailures: Dict[str, int] = defaultdict(int)
+    nunsupported: Dict[str, int] = defaultdict(int)
+    npassed: Dict[str, int] = defaultdict(int)
+
+    for i, test_result in enumerate(results):
+        test_case = test_result.create_test_case(tests[i])
+        test_case.url = (
+            f"cwltest:{suite_name}#{i + 1}"
+            if suite_name is not None
+            else "cwltest:#{i + 1}"
+        )
+        total += 1
+        tags = tests[i].get("tags", [])
+        for t in tags:
+            ntotal[t] += 1
+
+        return_code = test_result.return_code
+        category = test_case.category
+        if return_code == 0:
+            passed += 1
+            for t in tags:
+                npassed[t] += 1
+        elif return_code != 0 and return_code != UNSUPPORTED_FEATURE:
+            failures += 1
+            for t in tags:
+                nfailures[t] += 1
+            test_case.add_failure_info(output=test_result.message)
+        elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
+            failures += 1
+            for t in tags:
+                nfailures[t] += 1
+            test_case.add_failure_info(output=test_result.message)
+        elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
+            unsupported += 1
+            for t in tags:
+                nunsupported[t] += 1
+            test_case.add_skipped_info("Unsupported")
+        else:
+            raise Exception(
+                "This is impossible, return_code: {}, category: "
+                "{}".format(return_code, category)
+            )
+        if report:
+            report.test_cases.append(test_case)
+    return (
+        total,
+        passed,
+        failures,
+        unsupported,
+        ntotal,
+        npassed,
+        nfailures,
+        nunsupported,
+        report,
+    )
 
 
 def prepare_test_command(
-    tool,  # type: str
-    args,  # type: List[str]
-    testargs,  # type: Optional[List[str]]
-    test,  # type: Dict[str, Any]
-    cwd,  # type: str
-    verbose=False,  # type: bool
-):  # type: (...) -> List[str]
+    tool: str,
+    args: List[str],
+    testargs: Optional[List[str]],
+    test: Dict[str, Any],
+    cwd: str,
+    quiet: Optional[bool] = True,
+) -> List[str]:
     """Turn the test into a command line."""
     test_command = [tool]
     test_command.extend(args)
@@ -248,26 +307,182 @@ def prepare_test_command(
         else:
             outdir = tempfile.mkdtemp()
     test_command.extend([f"--outdir={outdir}"])
-    if not verbose:
+    if quiet:
         test_command.extend(["--quiet"])
+    processfile, jobfile = prepare_test_paths(test, cwd)
+    test_command.extend([os.path.normcase(processfile)])
+    if jobfile:
+        test_command.append(os.path.normcase(jobfile))
+    return test_command
 
+
+def prepare_test_paths(
+    test: Dict[str, str],
+    cwd: str,
+) -> Tuple[str, Optional[str]]:
+    """Determine the test path and the tool path."""
     cwd = schema_salad.ref_resolver.file_uri(cwd)
-    toolpath = test["tool"]
-    if toolpath.startswith(cwd):
-        toolpath = toolpath[len(cwd) + 1 :]
-    test_command.extend([os.path.normcase(toolpath)])
-
-    jobpath = test.get("job")
-    if jobpath:
-        if jobpath.startswith(cwd):
-            jobpath = jobpath[len(cwd) + 1 :]
-        test_command.append(os.path.normcase(jobpath))
-    return test_command
+    processfile = test["tool"]
+    if processfile.startswith(cwd):
+        processfile = processfile[len(cwd) + 1 :]
+
+    jobfile = test.get("job")
+    if jobfile:
+        if jobfile.startswith(cwd):
+            jobfile = jobfile[len(cwd) + 1 :]
+    return processfile, jobfile
+
+
+def run_test_plain(
+    config: CWLTestConfig,
+    test: Dict[str, str],
+    test_number: Optional[int] = None,
+) -> TestResult:
+    """Plain test runner."""
+    out: Dict[str, Any] = {}
+    outstr = outerr = ""
+    test_command: List[str] = []
+    duration = 0.0
+    number = "?"
+    if test_number is not None:
+        number = str(test_number)
+    process: Optional[subprocess.Popen[str]] = None
+    try:
+        cwd = os.getcwd()
+        test_command = prepare_test_command(
+            config.tool, config.args, config.testargs, test, cwd, config.runner_quiet
+        )
+        if config.verbose:
+            sys.stderr.write(f"Running: {' '.join(test_command)}\n")
+        sys.stderr.flush()
+        start_time = time.time()
+        stderr = subprocess.PIPE if not config.verbose else None
+        process = subprocess.Popen(  # nosec
+            test_command,
+            stdout=subprocess.PIPE,
+            stderr=stderr,
+            universal_newlines=True,
+            cwd=cwd,
+        )
+        outstr, outerr = process.communicate(timeout=config.timeout)
+        return_code = process.poll()
+        duration = time.time() - start_time
+        if return_code:
+            raise subprocess.CalledProcessError(return_code, " ".join(test_command))
+
+        logger.debug('outstr: "%s".', outstr)
+        out = json.loads(outstr) if outstr else {}
+    except subprocess.CalledProcessError as err:
+        if err.returncode == UNSUPPORTED_FEATURE and REQUIRED not in test.get(
+            "tags", ["required"]
+        ):
+            return TestResult(
+                UNSUPPORTED_FEATURE, outstr, outerr, duration, config.classname
+            )
+        if test.get("should_fail", False):
+            return TestResult(0, outstr, outerr, duration, config.classname)
+        if test_number:
+            logger.error(
+                """Test %i failed: %s""",
+                test_number,
+                " ".join([shlex.quote(tc) for tc in test_command]),
+            )
+        else:
+            logger.error(
+                """Test failed: %s""",
+                " ".join([shlex.quote(tc) for tc in test_command]),
+            )
+        logger.error(test.get("doc", "").replace("\n", " ").strip())
+        if err.returncode == UNSUPPORTED_FEATURE:
+            logger.error("Does not support required feature")
+        else:
+            logger.error("Returned non-zero")
+        return TestResult(1, outstr, outerr, duration, config.classname, str(err))
+    except (ruamel.yaml.scanner.ScannerError, TypeError) as err:
+        logger.error(
+            """Test %s failed: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(outstr)
+        logger.error("Parse error %s", str(err))
+        logger.error(outerr)
+    except KeyboardInterrupt:
+        logger.error(
+            """Test %s interrupted: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        raise
+    except subprocess.TimeoutExpired:
+        logger.error(
+            """Test %s timed out: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(test.get("doc", "").replace("\n", " ").strip())
+        # Kill and re-communicate to get the logs and reap the child, as
+        # instructed in the subprocess docs.
+        if process:
+            process.kill()
+            outstr, outerr = process.communicate()
+        return TestResult(
+            2,
+            outstr,
+            outerr,
+            float(cast(int, config.timeout)),
+            config.classname,
+            "Test timed out",
+        )
+    finally:
+        if process is not None and process.returncode is None:
+            logger.error("""Terminating lingering process""")
+            process.terminate()
+            for _ in range(0, 3):
+                time.sleep(1)
+                if process.poll() is not None:
+                    break
+            if process.returncode is None:
+                process.kill()
+
+    fail_message = ""
+
+    if test.get("should_fail", False):
+        logger.warning(
+            """Test %s failed: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.warning(test.get("doc", "").replace("\n", " ").strip())
+        logger.warning("Returned zero but it should be non-zero")
+        return TestResult(1, outstr, outerr, duration, config.classname)
+
+    try:
+        compare(test.get("output"), out)
+    except CompareFail as ex:
+        logger.warning(
+            """Test %s failed: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.warning(test.get("doc", "").replace("\n", " ").strip())
+        logger.warning("Compare failure %s", ex)
+        fail_message = str(ex)
+
+    if config.outdir:
+        shutil.rmtree(config.outdir, True)
+
+    return TestResult(
+        (1 if fail_message else 0),
+        outstr,
+        outerr,
+        duration,
+        config.classname,
+        fail_message,
+    )
 
 
-def shortname(
-    name,  # type: str
-):  # type: (...) -> str
+def shortname(name: str) -> str:
     """
     Return the short name of a given name.
 
diff --git a/docs/conf.py b/docs/conf.py
index 1271b5e..a598182 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -51,7 +51,9 @@
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "schema_salad": ("https://schema-salad.readthedocs.io/en/stable/", None),
-    "rdflib": ("https://rdflib.readthedocs.io/en/6.2.0/", None),
+    #"rdflib": ("https://rdflib.readthedocs.io/en/6.2.0/", None),
+    #"pytest": ("https://docs.pytest.org/en/7.2.x/", None),
+    "pytest_xdist": ("https://pytest-xdist.readthedocs.io/en/latest/", None),
     #"ruamel.yaml": ("https://yaml.readthedocs.io/en/stable/", None),
 }
 
diff --git a/docs/index.rst b/docs/index.rst
index 45c2163..4466152 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -1,16 +1,20 @@
 .. include:: ../README.rst
 
-.. toctree::
-   :maxdepth: 2
-
+********************
 Command Line Options
-====================
+********************
 
 .. autoprogram:: cwltest.argparser:arg_parser()
    :prog: cwltest
 
+.. toctree::
+   :maxdepth: 2
+
+   pytest
+
+******************
 Indices and tables
-==================
+******************
 
 * :ref:`genindex`
 * :ref:`modindex`
diff --git a/docs/pytest.rst b/docs/pytest.rst
new file mode 100644
index 0000000..195d392
--- /dev/null
+++ b/docs/pytest.rst
@@ -0,0 +1,174 @@
+*************
+Pytest plugin
+*************
+
+``cwltest`` can also be used as a Pytest plugin. The CWL test filename must
+end with ``.cwltest.yml`` or ``.cwltest.yaml``.
+
+In this case, the simple command::
+
+  cwltest --test conformance_xxx.cwltest.yml --tool cwl-runner
+
+becomes::
+
+  pytest conformance_xxx.cwltest.yml --cwl-runner cwl-runner
+
+Command Line Options
+====================
+
+.. autoprogram:: cwltest.plugin:_doc_options()
+   :prog: pytest
+
+Converting ``cwltest`` options to ``pytest`` options
+====================================================
+
+The table below details all the available command conversions between the two formats.
+
+.. list-table::
+   :widths: 40 30 30
+   :header-rows: 1
+
+   * - Feature
+     - ``cwltest``
+     - ``pytest``
+   * - YAML file describing test cases
+     - ``--test conformance_xxx.cwltest.yml``
+     - ``conformance_xxx.cwltest.yml``
+   * - CWL runner executable to use
+     - ``--tool CWL_RUNNER``
+     - :option:`--cwl-runner CWL_RUNNER`
+   * - Specifies the number of tests
+
+       to run simultaneously
+     - ``-j CORES``
+     - ``-n CORES`` [#f1]_
+   * - Automatically scale the number of tests
+
+       to run simultaneously
+     - **UNSUPPORTED**
+     - ``-n auto`` [#f1]_
+   * - Only run one test at a time
+
+       (good for debugging cwltest itself)
+     - ``-j 1``
+
+       (or leave out ``-j``)
+     - ``-n 0 -s`` [#f1]_
+   * - Time of execution in seconds
+
+       after which the test will be skipped
+     - ``--timeout TIMEOUT``
+     - ``--timeout TIMEOUT`` [#f3]_
+   * - List tests then exit
+     - ``-l``
+     - ``--collect-only``
+   * - Run specific tests using their short names
+     - ``-s TEST_NAME[,TEST_NAME…]``
+     - :option:`--cwl-include TEST_NAME[,TEST_NAME…]`
+   * - Exclude specific tests by short names
+     - ``-S TEST_NAME[,TEST_NAME…]``
+     - :option:`--cwl-exclude TEST_NAME[,TEST_NAME…]`
+   * - Tags to be tested
+     - ``--tags TAG[,TAG…]``
+     - :option:`--cwl-tags TAG[,TAG…]`
+   * - Tags not to be tested
+     - ``--exclude-tags TAG[,TAG…]``
+     - :option:`--cwl-exclude-tags TAG[,TAG…]`
+   * - Path to JUnit xml file
+     - ``--junit-xml PATH``
+     - ``--junit-xml=PATH`` [#f4]_
+   * - More verbose output during test run
+     - ``--verbose``
+     - ``-v[vv]``
+   * - Additional argument given in test cases
+
+       and required prefix for tool runner
+     - ``--test-arg ARG_NAME==ARG_PREFIX``
+     - :option:`--cwl-test-arg ARG_NAME==ARG_PREFIX`
+   * - Arguments to pass first to tool runner
+     - ``cwltest -- ARG [ARG …]``
+     - :option:`--cwl-args "ARG [ARG …]"`
+   * - Only test CommandLineTools
+     - ``--only-tools``
+     - **UNSUPPORTED**
+   * - Show all tags
+     - ``--show-tags``
+     - **UNSUPPORTED**
+   * - Store more verbose output to JUnit xml file
+     - ``--junit-verbose``
+     - :option:`--cwl-runner-verbose` [#f4]_
+   * - Specify classname for the Test Suite
+     - ``--classname CLASS_NAME``
+     - **UNSUPPORTED**
+
+.. [#f1] Requires `pytest-xdist <https://pypi.org/project/pytest-xdist/>`_.
+         See :ref:`pytest_xdist:parallelization`.
+.. [#f2] ``-s`` is a shortcut for ``--capture=no``, also helps with debugging
+         ``cwltest`` or the cwltest plugin to ``pytest``.
+.. [#f3] Requires `pytest-timeout <https://pypi.org/project/pytest-timeout/>`_.
+         Note: even if ``pytest-timeout`` is installed, there is no default
+         timeout. This is different than ``cwltest``'s default timeout of 10
+         minutes.
+
+Differences in the XML output
+=============================
+
+``cwltest --junit-xml`` output
+
+* top-level ``<testsuites>`` element has the elapsed time, and counts (errors,
+  failures, skipped, and total)
+* singular ``<testsuite>`` sub-element the same attributes as the top-level
+  ``<testsuites>`` plus ``name`` which is the basename of the YAML test file
+* each ``<testcase>`` element has the follow attributes
+
+  * ``name``: the doc string
+  * ``class``: the tags
+  * ``file``: the test ID
+  * ``url``: like "cwltest:conformance_tests#1"
+    (contains the basename of the YAML test file)
+  * ``time``: the elapsed time
+
+* ``<testcase>`` elements always contain the following sub-elements,
+  regardless of outcome
+
+  * ``<system-out>``: the output object
+  * ``<system-err>``: stderr (docker pull, other warnings, and errors)
+
+* ``<testcase>`` elements for failed test cases do not have a ``<failure>`` sub-element
+
+``pytest`` with ``cwltest`` plugin XML output
+
+* top-level ``<testsuites>`` element has no attributes
+* singular ``<testsuite>`` sub-element has the same attributes as the ``cwltest``
+  XML version along with these additional attributes
+
+  * ``name``: default is ``pytest``
+    (can be customized with the pytest INI option ``junit_suite_name``)
+  * ``timestamp="2023-01-08T11:39:07.425159"``
+  * ``hostname``: the hostname of the machine where the tests ran
+* inside the ``<testsuite>`` is a ``<properties>..</properties>`` element
+  with two ``<property name="…" value="…" />`` elements. But this
+  `does not work with pytest-xdist <https://github.com/pytest-dev/pytest/issues/7767>`_.
+
+  * ``runner``: the name of the CWL runner
+  * ``runner_extra_args``: the value of `--cwl-args``
+
+* each ``<testcase>`` element has the following attributes
+
+  * ``classname``: always the name of the YAML file (``conformance_test_v1.2.cwltest.yaml``)
+  * ``name``: the test ID
+  * ``time``: the elapsed time
+
+* ``<testcase>`` elements for failed test cases **do** have a ``<failure>`` sub-element
+  with a ``message`` attribute containing the :py:meth:`cwltest.plugin.CWLItem.repr_failure`
+  output. This text is repeated as the content of the ``<failure>`` element.
+  The presensce of ``<system-out>`` and ``<system-err>`` sub-elements varies. [#f4]_
+
+ .. [#f4] Depending on the value of the pytest INI option ``junit_logging``,
+         then ``<system-out>`` and ``<system-err>`` sub-elements will be generated.
+         However the default value for ``junit_logging`` is ``no``, so to get
+         either of these pick one from `the full list
+         <https://docs.pytest.org/en/stable/reference/reference.html#confval-junit_logging>`_.
+         You can set ``junit_logging`` in `a configuration file
+         <https://docs.pytest.org/en/stable/reference/customize.html#configuration-file-formats>`_
+         or on the command line: ``pytest -o junit_logging=out-err``.
diff --git a/gittaggers.py b/gittaggers.py
index e91cf0f..39e79f7 100644
--- a/gittaggers.py
+++ b/gittaggers.py
@@ -1,5 +1,6 @@
 import subprocess
 import time
+
 import pkg_resources
 from setuptools.command.egg_info import egg_info
 
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f620fb9..381abed 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,3 +1,5 @@
 mypy==0.991
 types-setuptools
 types-requests
+types-PyYAML
+cwltool
diff --git a/mypy-stubs/defusedxml/__init__.py b/mypy-stubs/defusedxml/__init__.pyi
similarity index 100%
rename from mypy-stubs/defusedxml/__init__.py
rename to mypy-stubs/defusedxml/__init__.pyi
diff --git a/mypy-stubs/ruamel/__init__.py b/mypy-stubs/ruamel/__init__.pyi
similarity index 100%
rename from mypy-stubs/ruamel/__init__.py
rename to mypy-stubs/ruamel/__init__.pyi
diff --git a/release-test.sh b/release-test.sh
index 42684e0..d7010b0 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -17,7 +17,7 @@ else
     repo=https://github.com/common-workflow-language/cwltest.git
     HEAD=$(git rev-parse HEAD)
 fi
-run_tests="bin/py.test --pyargs ${module}"
+run_tests="bin/py.test -p pytester --pyargs ${module}"
 pipver=20.3.3  # minimum required version of pip for Python 3.10
 setuptoolsver=50.0.1  # required for Python 3.10
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
diff --git a/requirements.txt b/requirements.txt
index a51fd20..a15d1b3 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,5 @@
 schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
-pytest < 8
+pytest >= 7, < 8
 defusedxml
+typing-extensions
diff --git a/setup.py b/setup.py
index e2b1528..2a32a17 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,11 @@
 #!/usr/bin/env python3
 import os
+import pathlib
 import sys
 
 import setuptools.command.egg_info as egg_info_cmd
 from setuptools import setup
 
-import cwltest
-
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, "README.rst")
 
@@ -17,12 +16,6 @@
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = [
-    "schema-salad >= 5.0.20200220195218, < 9",
-    "junit-xml >= 1.8",
-    "defusedxml",
-]
-
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 8", "pytest-runner"] if needs_pytest else []
 
@@ -43,13 +36,25 @@
     package_dir={"cwltest.tests": "tests"},
     package_data={"cwltest": ["py.typed"], "tests": ["test-data/*"]},
     include_package_data=True,
-    install_requires=install_requires,
+    install_requires=open(
+        os.path.join(pathlib.Path(__file__).parent, "requirements.txt")
+    )
+    .read()
+    .splitlines(),
     test_suite="tests",
-    tests_require=["pytest<8"],
+    tests_require=open(
+        os.path.join(pathlib.Path(__file__).parent, "test-requirements.txt")
+    )
+    .read()
+    .splitlines(),
+    extras_require={"pytest-plugin": ["pytest"]},
     entry_points={
         "console_scripts": [
             "cwltest=cwltest.main:main",
-        ]
+        ],
+        "pytest11": [
+            "cwl = cwltest.plugin [pytest-plugin]",
+        ],
     },
     zip_safe=True,
     cmdclass={"egg_info": tagger},
diff --git a/test-requirements.txt b/test-requirements.txt
index e5540ed..6f0a196 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,2 +1,5 @@
-pytest >= 6.2, < 7.3
+cwlref-runner
+cwltool
+pytest >= 7, < 8
 pytest-cov
+pytest-xdist
diff --git a/tests/test-data/conformance_test_v1.0.cwltest.yml b/tests/test-data/conformance_test_v1.0.cwltest.yml
new file mode 100644
index 0000000..75f7086
--- /dev/null
+++ b/tests/test-data/conformance_test_v1.0.cwltest.yml
@@ -0,0 +1,17 @@
+- output:
+    args: [cat, hello.txt]
+  job: v1.0/cat-job.json
+  tool: v1.0/cat1-testcli.cwl
+  label: cl_optional_inputs_missing
+  id: 4
+  doc: Test command line with optional input (missing)
+  tags: [ required, command_line_tool ]
+
+- output:
+    args: [cat, -n, hello.txt]
+  job: v1.0/cat-n-job.json
+  tool: v1.0/cat1-testcli.cwl
+  label: cl_optional_bindings_provided
+  id: 5
+  doc: Test command line with optional input (provided)
+  tags: [ command_line_tool ]
\ No newline at end of file
diff --git a/tests/test-data/conformance_test_v1.2.cwltest.yaml b/tests/test-data/conformance_test_v1.2.cwltest.yaml
new file mode 100644
index 0000000..0b78da9
--- /dev/null
+++ b/tests/test-data/conformance_test_v1.2.cwltest.yaml
@@ -0,0 +1,15 @@
+- output:
+    args: [cat, hello.txt]
+  job: v1.0/cat-job.json
+  tool: v1.0/cat1-testcli.cwl
+  id: cl_optional_inputs_missing
+  doc: Test command line with optional input (missing)
+  tags: [ required, command_line_tool ]
+
+- output:
+    args: [cat, -n, hello.txt]
+  job: v1.0/cat-n-job.json
+  tool: v1.0/cat1-testcli.cwl
+  id: cl_optional_bindings_provided
+  doc: Test command line with optional input (provided)
+  tags: [ command_line_tool ]
\ No newline at end of file
diff --git a/tests/test-data/cwltool-conftest.py b/tests/test-data/cwltool-conftest.py
new file mode 100644
index 0000000..061b994
--- /dev/null
+++ b/tests/test-data/cwltool-conftest.py
@@ -0,0 +1,37 @@
+"""
+Example configuration for pytest-cwl plugin using cwltool directly.
+
+Calls cwltool via Python, instead of a subprocess via `--cwl-runner cwltool`.
+"""
+import json
+from io import StringIO
+from typing import Any, Dict, List, Optional, Tuple
+
+from cwltest import utils
+
+
+def pytest_cwl_execute_test(
+        config: utils.CWLTestConfig,
+        processfile: str,
+        jobfile: Optional[str]
+) -> Tuple[int, Optional[Dict[str, Any]]]:
+    """Use the CWL reference runner (cwltool) to execute tests."""
+    from cwltool import main
+    from cwltool.errors import WorkflowException
+
+    stdout = StringIO()
+    argsl: List[str] = [f"--outdir={config.outdir}"]
+    if config.runner_quiet:
+        argsl.append("--quiet")
+    elif config.verbose:
+        argsl.append("--debug")
+    argsl.extend(config.args)
+    argsl.append(processfile)
+    if jobfile:
+        argsl.append(jobfile)
+    try:
+        result = main.main(argsl=argsl, stdout=stdout)
+    except WorkflowException:
+        return 1, {}
+    out = stdout.getvalue()
+    return result, json.loads(out) if out else {}
diff --git a/tests/test-data/v1.0/args.py b/tests/test-data/v1.0/args.py
new file mode 100644
index 0000000..190fd5c
--- /dev/null
+++ b/tests/test-data/v1.0/args.py
@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+import sys
+import json
+import os
+args = [os.path.basename(a) for a in sys.argv[1:]]
+with open("cwl.output.json", "w") as f:
+    json.dump({"args": args}, f)
\ No newline at end of file
diff --git a/tests/test-data/v1.0/cat-job.json b/tests/test-data/v1.0/cat-job.json
index e69de29..b4b3b6b 100644
--- a/tests/test-data/v1.0/cat-job.json
+++ b/tests/test-data/v1.0/cat-job.json
@@ -0,0 +1,6 @@
+{
+    "file1": {
+        "class": "File",
+        "location": "hello.txt"
+    }
+}
\ No newline at end of file
diff --git a/tests/test-data/v1.0/cat-n-job.json b/tests/test-data/v1.0/cat-n-job.json
new file mode 100644
index 0000000..77e3537
--- /dev/null
+++ b/tests/test-data/v1.0/cat-n-job.json
@@ -0,0 +1,7 @@
+{
+    "file1": {
+        "class": "File",
+        "location": "hello.txt"
+    },
+    "numbering": true
+}
\ No newline at end of file
diff --git a/tests/test-data/v1.0/cat1-testcli.cwl b/tests/test-data/v1.0/cat1-testcli.cwl
new file mode 100644
index 0000000..311cd86
--- /dev/null
+++ b/tests/test-data/v1.0/cat1-testcli.cwl
@@ -0,0 +1,45 @@
+#!/usr/bin/env cwl-runner
+{
+    "class": "CommandLineTool",
+    "cwlVersion": "v1.0",
+    "doc": "Print the contents of a file to stdout using 'cat' running in a docker container.",
+    "hints": [
+        {
+            "class": "DockerRequirement",
+            "dockerPull": "python:2-slim"
+        },
+        {
+            "class": "ResourceRequirement",
+            "ramMin": 128
+        }
+    ],
+    "inputs": [
+        {
+            "id": "file1",
+            "type": "File",
+            "inputBinding": {"position": 1}
+        },
+        {
+            "id": "numbering",
+            "type": ["null", "boolean"],
+            "inputBinding": {
+                "position": 0,
+                "prefix": "-n"
+            }
+        },
+        {
+        id: "args.py",
+        type: File,
+        default: {
+          class: File,
+          location: args.py
+        },
+        inputBinding: {
+          position: -1
+        }
+      }
+    ],
+    "outputs": [{"id": "args", "type": "string[]"}],
+    "baseCommand": "python",
+    "arguments": ["cat"]
+}
\ No newline at end of file
diff --git a/tests/test-data/v1.0/hello.txt b/tests/test-data/v1.0/hello.txt
new file mode 100644
index 0000000..6769dd6
--- /dev/null
+++ b/tests/test-data/v1.0/hello.txt
@@ -0,0 +1 @@
+Hello world!
\ No newline at end of file
diff --git a/tests/test_categories.py b/tests/test_categories.py
index 28acb90..c6461e9 100644
--- a/tests/test_categories.py
+++ b/tests/test_categories.py
@@ -1,15 +1,16 @@
-import re
 import os
+import re
 from os import linesep as n
 from os import sep as p
 from pathlib import Path
 from typing import cast
 from xml.etree.ElementTree import Element
 
-from .util import run_with_mock_cwl_runner, get_data
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
 
+from .util import get_data, run_with_mock_cwl_runner
+
 
 def test_unsupported_with_required_tests() -> None:
     cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
@@ -41,13 +42,11 @@ def test_unsupported_with_required_tests() -> None:
         "Test 1 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
         "Required test that is unsupported (without tags){n}"
         "Does not support required feature{n}"
-        "{n}"
         "Test [2/2] Required test that is unsupported (with tags){n}"
         "{n}"
         "Test 2 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
         "Required test that is unsupported (with tags){n}"
         "Does not support required feature{n}"
-        "{n}"
         "0 tests passed, 2 failures, 0 unsupported features{n}".format(
             cwl_runner=cwl_runner, n=n, p=p, q=q
         )
@@ -62,6 +61,7 @@ def test_unsupported_with_optional_tests() -> None:
         ),
     ]
     error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    stderr = re.sub(r" '?--outdir=[^ ]*", "", stderr)
     assert error_code == 0
     assert (
         "The `id` field is missing.{n}"
diff --git a/tests/test_compare.py b/tests/test_compare.py
index aec983e..86d456e 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -1,26 +1,34 @@
-from .util import get_data
-from cwltest.utils import CompareFail, compare_file, compare
+from typing import Any, Dict
 
 import pytest
+from cwltest.compare import CompareFail, compare
+
+from .util import get_data
+
+
+def test_compare_any_success() -> None:
+    expected = "Any"
+    actual: Dict[str, Any] = {}
+    compare(expected, actual)
 
 
-def test_compare_file() -> None:
+def test_compare_contents_failure() -> None:
     expected = {
         "location": "cores.txt",
         "size": 2,
         "class": "File",
-        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+        "contents": "2",
     }
-
     actual = {
         "basename": "cores.txt",
         "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
         "class": "File",
         "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-        "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": get_data("tests/test-data/cores.txt"),
         "size": 2,
     }
-    compare_file(expected, actual)
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
 
 
 def test_compare_contents_success() -> None:
@@ -30,7 +38,6 @@ def test_compare_contents_success() -> None:
         "class": "File",
         "contents": "2\n",
     }
-
     actual = {
         "basename": "cores.txt",
         "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
@@ -42,21 +49,403 @@ def test_compare_contents_success() -> None:
     compare(expected, actual)
 
 
-def test_compare_contents_failure() -> None:
+def test_compare_directory_success() -> None:
+    expected = {
+        "stuff": {
+            "class": "Directory",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "listing": [
+                        {
+                            "basename": "bar.txt",
+                            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                            "class": "File",
+                            "size": 0,
+                        }
+                    ],
+                },
+            ],
+        }
+    }
+    actual = {
+        "stuff": {
+            "class": "Directory",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "listing": [
+                        {
+                            "basename": "bar.txt",
+                            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                            "class": "File",
+                            "size": 0,
+                        }
+                    ],
+                },
+            ],
+        }
+    }
+    compare(expected, actual)
+
+
+def test_compare_directory_failure_different_listing() -> None:
+    expected = {
+        "stuff": {
+            "class": "Directory",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "listing": [
+                        {
+                            "basename": "bar.txt",
+                            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                            "class": "File",
+                            "size": 0,
+                        }
+                    ],
+                },
+            ],
+        }
+    }
+    actual = {
+        "stuff": {
+            "class": "Directory",
+            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff",
+            "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
+                    "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
+                    "listing": [
+                        {
+                            "basename": "bar.txt",
+                            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80775",
+                            "class": "File",
+                            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
+                            "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
+                            "size": 0,
+                        }
+                    ],
+                },
+            ],
+        }
+    }
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
+
+
+def test_compare_directory_failure_no_listing() -> None:
+    expected = {
+        "stuff": {
+            "class": "Directory",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "listing": [
+                        {
+                            "basename": "bar.txt",
+                            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                            "class": "File",
+                            "size": 0,
+                        }
+                    ],
+                },
+            ],
+        }
+    }
+    actual = {
+        "stuff": {
+            "class": "Directory",
+            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff",
+            "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff",
+            "listing": [
+                {
+                    "basename": "baz.txt",
+                    "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                    "class": "File",
+                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "size": 0,
+                },
+                {
+                    "basename": "foo",
+                    "class": "Directory",
+                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
+                    "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
+                },
+            ],
+        }
+    }
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
+
+
+def test_compare_file_failure_different() -> None:
     expected = {
         "location": "cores.txt",
         "size": 2,
         "class": "File",
-        "contents": "2",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7b",
+    }
+    actual = {
+        "basename": "cores.txt",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+        "class": "File",
+        "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "size": 2,
     }
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
+
+
+def test_compare_file_failure_none() -> None:
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7b",
+    }
+    actual: Dict[str, Any] = {}
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
 
+
+def test_compare_file_success() -> None:
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+    }
     actual = {
         "basename": "cores.txt",
         "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
         "class": "File",
         "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
-        "path": get_data("tests/test-data/cores.txt"),
+        "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
         "size": 2,
     }
+    compare(expected, actual)
+
+
+def test_compare_list_failure_missing() -> None:
+    expected = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "--min-seq-length",
+            "20",
+            "map2",
+            "--min-seq-length",
+            "20",
+            "stage2",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+        ]
+    }
+    actual = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "stage2",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+        ]
+    }
     with pytest.raises(CompareFail):
-        compare_file(expected, actual)
+        compare(expected, actual)
+
+
+def test_compare_list_failure_order() -> None:
+    expected = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "--min-seq-length",
+            "20",
+            "map2",
+            "--min-seq-length",
+            "20",
+            "stage2",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+        ]
+    }
+    actual = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "--min-seq-length",
+            "20",
+            "map2",
+            "--min-seq-length",
+            "20",
+            "stage2",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+        ]
+    }
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
+
+
+def test_compare_list_failure_type() -> None:
+    expected = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "--min-seq-length",
+            "20",
+            "map2",
+            "--min-seq-length",
+            "20",
+            "stage2",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+        ]
+    }
+    actual: Dict[str, Any] = {"args": {}}
+    with pytest.raises(CompareFail):
+        compare(expected, actual)
+
+
+def test_compare_list_success() -> None:
+    expected = {
+        "args": [
+            "tmap",
+            "mapall",
+            "stage1",
+            "map1",
+            "--min-seq-length",
+            "20",
+            "map2",
+            "--min-seq-length",
+            "20",
+            "stage2",
+            "map1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+            "--seed-length",
+            "16",
+            "map2",
+            "--max-seed-hits",
+            "-1",
+            "--max-seq-length",
+            "20",
+            "--min-seq-length",
+            "10",
+        ]
+    }
+    compare(expected, expected)
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
new file mode 100644
index 0000000..4951c3f
--- /dev/null
+++ b/tests/test_plugin.py
@@ -0,0 +1,126 @@
+import os
+import shutil
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from .util import get_data
+
+if TYPE_CHECKING:
+    from _pytest.pytester import Pytester
+
+
+def _load_v1_0_dir(path: Path) -> None:
+    inner_dir = os.path.join(path.parent, "v1.0")
+    os.mkdir(inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/cat1-testcli.cwl"), inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/cat-job.json"), inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/cat-n-job.json"), inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/hello.txt"), inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/args.py"), inner_dir)
+
+
+def test_include(pytester: "Pytester") -> None:
+    """Test the pytest plugin using cwltool as cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest(
+        "-k",
+        "conformance_test_v1.0.cwltest.yml",
+        "--cwl-include",
+        "cl_optional_inputs_missing",
+    )
+    result.assert_outcomes(passed=1, skipped=1)
+
+
+def test_exclude(pytester: "Pytester") -> None:
+    """Test the pytest plugin using cwltool as cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest(
+        "-k",
+        "conformance_test_v1.0.cwltest.yml",
+        "--cwl-exclude",
+        "cl_optional_inputs_missing,cl_optional_bindings_provided",
+    )
+    result.assert_outcomes(passed=0, skipped=2)
+
+
+def test_tags(pytester: "Pytester") -> None:
+    """Test the pytest plugin using cwltool as cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest(
+        "-k", "conformance_test_v1.0.cwltest.yml", "--cwl-tags", "required"
+    )
+    result.assert_outcomes(passed=1, skipped=1)
+
+
+def test_exclude_tags(pytester: "Pytester") -> None:
+    """Test the pytest plugin using cwltool as cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest(
+        "-k",
+        "conformance_test_v1.0.cwltest.yml",
+        "--cwl-exclude-tags",
+        "command_line_tool",
+    )
+    result.assert_outcomes(skipped=2)
+
+
+def test_badgedir(pytester: "Pytester") -> None:
+    """Test the pytest plugin creates the badges directory."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    assert not os.path.exists("cwl-badges")
+    pytester.runpytest(
+        "-k", "conformance_test_v1.0.cwltest.yml", "--cwl-badgedir", "cwl-badges"
+    )
+    assert os.path.exists("cwl-badges")
+
+
+def test_no_label(pytester: "Pytester") -> None:
+    """Test the pytest plugin correctly extracts test names from the id field when label is missing."""
+    path = pytester.copy_example("conformance_test_v1.2.cwltest.yaml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest(
+        "-k", "conformance_test_v1.2.cwltest.yaml", "--cwl-tags", "required"
+    )
+    result.assert_outcomes(passed=1, skipped=1)
+
+
+def test_cwltool_hook(pytester: "Pytester") -> None:
+    """Test the pytest plugin using cwltool as cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    result = pytester.runpytest("-k", "conformance_test_v1.0.cwltest.yml")
+    result.assert_outcomes(passed=2)
+
+
+def test_no_hook(pytester: "Pytester") -> None:
+    """Test the pytest plugin using the default cwl-runner."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    _load_v1_0_dir(path)
+    result = pytester.runpytest("-k", "conformance_test_v1.0.cwltest.yml")
+    result.assert_outcomes(passed=2)
diff --git a/tests/util.py b/tests/util.py
index 145d0b2..002fa53 100644
--- a/tests/util.py
+++ b/tests/util.py
@@ -2,11 +2,7 @@
 import subprocess  # nosec
 from typing import List, Tuple
 
-from pkg_resources import (
-    Requirement,
-    ResolutionError,
-    resource_filename,
-)
+from pkg_resources import Requirement, ResolutionError, resource_filename
 
 
 def get_data(filename: str) -> str:
diff --git a/tox.ini b/tox.ini
index 5e47e6a..b0b4234 100644
--- a/tox.ini
+++ b/tox.ini
@@ -10,6 +10,8 @@ envlist =
 skip_missing_interpreters = True
 
 [pytest]
+addopts = -p pytester -n auto
+pytester_example_dir = tests/test-data
 testpaths = tests
 
 [gh-actions]
@@ -22,6 +24,9 @@ python =
   3.11: py311
 
 [testenv]
+skipsdist =
+  py3{6,7,8,9,10,11}-!{unit,mypy,lintreadme} = True
+
 description =
   py{36,37,38,39,310,311}-unit: Run the unit tests
   py{36,37,38,39,310,311}-lint: Lint the Python code
@@ -44,10 +49,15 @@ deps =
 
 setenv =
   py{36,37,38,39,310,311}-unit: LC_ALL = C.UTF-8
+  COV_CORE_SOURCE=cwltest
+  COV_CORE_CONFIG={toxinidir}/.coveragerc
+  COV_CORE_DATAFILE={toxinidir}/.coverage.eager
+
 
 commands =
   py{36,37,38,39,310,311}-unit: python -m pip install -U pip setuptools wheel
-  py{36,37,38,39,310,311}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py{36,37,38,39,310,311}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py{36,37,38,39,310,311}-unit: coverage xml
   py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest --exclude tests/*
   py{36,37,38,39,310,311}-lint: make flake8
   py{36,37,38,39,310,311}-lint: make format-check
@@ -75,11 +85,10 @@ skip_install = true
 [testenv:py310-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
-  python setup.py sdist
-  python setup.py bdist_wheel
-  twine check dist/*
+  python -m build --outdir {distdir}
+  twine check {distdir}/*
 deps =
     twine
-    wheel
-    readme_renderer[md]
+    build
+    readme_renderer[rst]
 skip_install = true

From de7f1ad0e67893dea622856dfc5c74b3d9d92f41 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Sun, 8 Jan 2023 20:36:15 +0100
Subject: [PATCH 056/165] Prepare for the release of 2.3.x

---
 Makefile | 2 +-
 setup.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index 2c7d049..ced0a68 100644
--- a/Makefile
+++ b/Makefile
@@ -29,7 +29,7 @@ PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.2.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.3.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 
 ## all                    : default task (install in dev mode)
diff --git a/setup.py b/setup.py
index 2a32a17..5b9c52f 100644
--- a/setup.py
+++ b/setup.py
@@ -21,7 +21,7 @@
 
 setup(
     name="cwltest",
-    version="2.2",  # update the VERSION prefix in the Makefile as well 🙂
+    version="2.3",  # update the VERSION prefix in the Makefile as well 🙂
     description="Common Workflow Language testing framework",
     long_description=open(README).read(),
     long_description_content_type="text/x-rst",

From 7152c432b110f2c64905aac8eed09330dfa05f97 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Mon, 9 Jan 2023 10:35:31 +0100
Subject: [PATCH 057/165] CodeQL: limit scans

---
 .github/workflows/codeql-analysis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 7993d84..292544f 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -2,7 +2,9 @@ name: "Code scanning - action"
 
 on:
   push:
+      branches: [main]
   pull_request:
+      branches: [main]
   schedule:
     - cron: '0 17 * * 0'
 

From 657872b89308b0bb05e1abfa7cc30d5572b1905e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 9 Jan 2023 10:42:01 +0100
Subject: [PATCH 058/165] Update tox requirement from <4 to <5 (#159)

Updates the requirements on [tox](https://github.com/tox-dev/tox) to permit the latest version.
- [Release notes](https://github.com/tox-dev/tox/releases)
- [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst)
- [Commits](https://github.com/tox-dev/tox/compare/0.5...4.2.6)

---
updated-dependencies:
- dependency-name: tox
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 3b58070..5af12b2 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -4,7 +4,7 @@ pylint
 pep257
 pydocstyle
 flake8
-tox < 4
+tox < 5
 tox-pyenv
 isort
 wheel

From 7061207c818d2c77bac86305c70dcf60ed56b58d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Mon, 30 Jan 2023 15:23:16 +0100
Subject: [PATCH 059/165] use CODECOV_TOKEN to avoid CI fails (#160)

---
 .github/workflows/ci-tests.yml | 34 ++++++++++++++++------------------
 1 file changed, 16 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 3738b7b..ddd8e49 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -39,12 +39,11 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
-
-      - name: Cache for pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt', 'tox.ini') }}
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+            test-requirements.txt
+            mypy-requirements.txt
 
       - name: Upgrade setuptools and install tox
         run: |
@@ -66,6 +65,7 @@ jobs:
         uses: codecov/codecov-action@v3
         with:
           fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   tox-style:
     name: CI linters via Tox
@@ -89,12 +89,11 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
-
-      - name: Cache for pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.step }}-${{ hashFiles('requirements.txt') }}
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+            test-requirements.txt
+            mypy-requirements.txt
 
       - name: Upgrade setuptools and install tox
         run: |
@@ -120,12 +119,11 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
-
-      - name: Cache for pip
-        uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-release-${{ hashFiles('requirements.txt', 'test-requirements.txt') }}
+          cache: pip
+          cache-dependency-path: |
+            requirements.txt
+            test-requirements.txt
+            mypy-requirements.txt
 
       - name: Install packages
         run: |

From d3532f3487d921726fae26c7815488b1b99b95f0 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com>
Date: Tue, 31 Jan 2023 11:51:15 +0100
Subject: [PATCH 060/165] readthedocs: install graphviz (#161)

---
 .readthedocs.yml | 2 ++
 docs/index.rst   | 1 +
 2 files changed, 3 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5a74019..cd1f440 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -16,6 +16,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  apt_packages:
+    - graphviz
 
 python:
   install:
diff --git a/docs/index.rst b/docs/index.rst
index 4466152..ce7ab8a 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -11,6 +11,7 @@ Command Line Options
    :maxdepth: 2
 
    pytest
+   autoapi/index
 
 ******************
 Indices and tables

From 3a290cb8ddb764e78cdaa22f555b906ec1068355 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 7 Feb 2023 00:02:19 +0000
Subject: [PATCH 061/165] Bump mypy from 0.991 to 1.0.0

Bumps [mypy](https://github.com/python/mypy) from 0.991 to 1.0.0.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v0.991...v1.0.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 381abed..671641f 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==0.991
+mypy==1.0.0
 types-setuptools
 types-requests
 types-PyYAML

From 343562963673af2b239f773c89ede956482d6c2f Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 13 Feb 2023 18:05:17 +0100
Subject: [PATCH 062/165] upgrade black & format

---
 cwltest/compare.py   | 29 +++++++++++++----------------
 cwltest/main.py      |  2 +-
 cwltest/plugin.py    |  4 ++--
 cwltest/utils.py     | 11 ++++++++---
 dev-requirements.txt |  2 +-
 tox.ini              |  2 +-
 6 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/cwltest/compare.py b/cwltest/compare.py
index b56a7c3..2278a86 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -1,15 +1,16 @@
 """Compare utilities for CWL objects."""
 
 import json
-from typing import Any, Dict, Set
+from typing import Any, Dict, Optional, Set
 
 
 class CompareFail(Exception):
     """Compared CWL objects are not equal."""
 
     @classmethod
-    def format(cls, expected, actual, cause=None):
-        # type: (Any, Any, Any) -> CompareFail
+    def format(
+        cls, expected: Any, actual: Any, cause: Optional[Any] = None
+    ) -> "CompareFail":
         """Load the difference details into the error message."""
         message = "expected: {}\ngot: {}".format(
             json.dumps(expected, indent=4, sort_keys=True),
@@ -20,8 +21,9 @@ def format(cls, expected, actual, cause=None):
         return cls(message)
 
 
-def _check_keys(keys, expected, actual):
-    # type: (Set[str], Dict[str,Any], Dict[str,Any]) -> None
+def _check_keys(
+    keys: Set[str], expected: Dict[str, Any], actual: Dict[str, Any]
+) -> None:
     for k in keys:
         try:
             compare(expected.get(k), actual.get(k))
@@ -31,8 +33,7 @@ def _check_keys(keys, expected, actual):
             ) from e
 
 
-def _compare_contents(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
+def _compare_contents(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     expected_contents = expected["contents"]
     with open(actual["path"]) as f:
         actual_contents = f.read()
@@ -47,8 +48,7 @@ def _compare_contents(expected, actual):
         )
 
 
-def _compare_dict(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
+def _compare_dict(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     for c in expected:
         try:
             compare(expected[c], actual.get(c))
@@ -62,8 +62,7 @@ def _compare_dict(expected, actual):
             raise CompareFail.format(expected, actual, "unexpected key '%s'" % k)
 
 
-def _compare_directory(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
+def _compare_directory(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     if actual.get("class") != "Directory":
         raise CompareFail.format(
             expected, actual, "expected object with a class 'Directory'"
@@ -90,8 +89,7 @@ def _compare_directory(expected, actual):
     _compare_file(expected, actual)
 
 
-def _compare_file(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
+def _compare_file(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     _compare_location(expected, actual)
     if "contents" in expected:
         _compare_contents(expected, actual)
@@ -100,8 +98,7 @@ def _compare_file(expected, actual):
     _check_keys(other_keys, expected, actual)
 
 
-def _compare_location(expected, actual):
-    # type: (Dict[str,Any], Dict[str,Any]) -> None
+def _compare_location(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     if "path" in expected:
         comp = "path"
         if "path" not in actual:
@@ -126,7 +123,7 @@ def _compare_location(expected, actual):
         )
 
 
-def compare(expected, actual):  # type: (Any, Any) -> None
+def compare(expected: Any, actual: Any) -> None:
     """Compare two CWL objects."""
     if expected == "Any":
         return
diff --git a/cwltest/main.py b/cwltest/main.py
index 6c9d293..f93a279 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -144,7 +144,7 @@ def main() -> int:
             logger.warning("The `id` field is missing.")
 
     if args.show_tags:
-        alltags = set()  # type: Set[str]
+        alltags: Set[str] = set()
         for t in tests:
             ts = t.get("tags", [])
             alltags |= set(ts)
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index c642519..d59c2f5 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -7,23 +7,23 @@
 from io import StringIO
 from pathlib import Path
 from typing import (
+    TYPE_CHECKING,
     Any,
     Dict,
     Iterator,
     List,
     Optional,
     Set,
-    TYPE_CHECKING,
     Tuple,
     Union,
     cast,
 )
 
 import pytest
+from cwltest.compare import CompareFail, compare
 from typing_extensions import Protocol
 
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
-from cwltest.compare import CompareFail, compare
 
 if TYPE_CHECKING:
     from _pytest._code.code import ExceptionInfo, _TracebackStyle
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 036fafb..d47f376 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -35,7 +35,7 @@
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, templock
 
 
-class CWLTestConfig(object):
+class CWLTestConfig:
     """Store configuration values for cwltest."""
 
     def __init__(
@@ -173,14 +173,19 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
             "utf-8"
         )
     }
-    (document_loader, avsc_names, _, _,) = schema_salad.schema.load_schema(
+    (
+        document_loader,
+        avsc_names,
+        _,
+        _,
+    ) = schema_salad.schema.load_schema(
         "https://w3id.org/cwl/cwltest/cwltest-schema.yml", cache=cache
     )
 
     if not isinstance(avsc_names, schema_salad.avro.schema.Names):
         print(avsc_names)
         raise ValidationException(
-            "Wrong instance for avsc_names: {}".format(type(avsc_names))
+            f"Wrong instance for avsc_names: {type(avsc_names)}"
         )
 
     tests, metadata = schema_salad.schema.load_and_validate(
diff --git a/dev-requirements.txt b/dev-requirements.txt
index 5af12b2..4ac7321 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black
+black ~= 23.1
 pylint
 pep257
 pydocstyle
diff --git a/tox.ini b/tox.ini
index b0b4234..0ac4e44 100644
--- a/tox.ini
+++ b/tox.ini
@@ -43,7 +43,7 @@ deps =
   py{36,37,38,39,310,311}-{unit,mypy}: -rrequirements.txt
   py{36,37,38,39,310,311}-{unit,mypy}: -rtest-requirements.txt
   py{36,37,38,39,310,311}-lint: flake8-bugbear
-  py{36,37,38,39,310,311}-lint: black
+  py{36,37,38,39,310,311}-lint: black~=23.1
   py{36,37,38,39,310,311}-bandit: bandit
   py{37,38,39,310,311}-mypy: -rmypy-requirements.txt
 

From f0bae2d3ca894fb09f4856ba9a66892fd82b4244 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 13 Feb 2023 18:16:44 +0100
Subject: [PATCH 063/165] flake8 config upgrade

---
 .flake8               |  9 ++++++---
 cwltest/compare.py    |  4 ++--
 cwltest/plugin.py     |  8 ++++----
 cwltest/utils.py      |  6 ++----
 setup.cfg             |  5 -----
 tests/test_compare.py | 15 ++++++++++-----
 6 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/.flake8 b/.flake8
index 35967ff..ed7277f 100644
--- a/.flake8
+++ b/.flake8
@@ -1,4 +1,7 @@
 [flake8]
-ignore = E203, E266, E501, W503, E211, E731
-max-line-length = 88
-select = B,C,E,F,W,T4,B9
+ignore = E203,W503
+max-line-length = 100
+select = B,C,E,F,W,T4
+extend-ignore = E501,B905
+# when Python 3.10 is the minimum version, re-enable check B905 for zip + strict
+extend-select = B9
diff --git a/cwltest/compare.py b/cwltest/compare.py
index 2278a86..5374202 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -29,7 +29,7 @@ def _check_keys(
             compare(expected.get(k), actual.get(k))
         except CompareFail as e:
             raise CompareFail.format(
-                expected, actual, f"field '{k}' failed comparison: {str(e)}"
+                expected, actual, f"field {k!r} failed comparison: {str(e)}"
             ) from e
 
 
@@ -54,7 +54,7 @@ def _compare_dict(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
             compare(expected[c], actual.get(c))
         except CompareFail as e:
             raise CompareFail.format(
-                expected, actual, f"failed comparison for key '{c}': {e}"
+                expected, actual, f"failed comparison for key {c!r}: {e}"
             ) from e
     extra_keys = set(actual.keys()).difference(list(expected.keys()))
     for k in extra_keys:
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index d59c2f5..c3c0c6b 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -236,24 +236,24 @@ def collect(self) -> Iterator[CWLItem]:
             if include and name not in include:
                 item.add_marker(
                     pytest.mark.skip(
-                        reason=f"Test '{name}' is not in the include list: {','.join(include)}."
+                        reason=f"Test {name!r} is not in the include list: {','.join(include)}."
                     )
                 )
             elif exclude and name in exclude:
                 item.add_marker(
-                    pytest.mark.skip(reason=f"Test '{name}' is in the exclude list.")
+                    pytest.mark.skip(reason=f"Test {name!r} is in the exclude list.")
                 )
             elif tags and not tags.intersection(entry_tags):
                 item.add_marker(
                     pytest.mark.skip(
-                        reason=f"Test '{name}' with tags {','.join(entry_tags)}"
+                        reason=f"Test {name!r} with tags {','.join(entry_tags)}"
                         f" doesn't have a tag on the allowed tag list: {','.join(tags)}."
                     )
                 )
             elif exclude_tags and exclude_tags.intersection(entry_tags):
                 item.add_marker(
                     pytest.mark.skip(
-                        reason=f"Test '{name}' has one or more tags on the exclusion "
+                        reason=f"Test {name!r} has one or more tags on the exclusion "
                         f" tag list: {','.join(exclude_tags.intersection(entry_tags))}."
                     )
                 )
diff --git a/cwltest/utils.py b/cwltest/utils.py
index d47f376..60413ad 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -122,7 +122,7 @@ def _clean_ruamel(obj: Any) -> Any:
             return typ(obj)
     if obj is None:
         return None
-    raise Exception(f"Unsupported type {type(obj)} of '{obj}'.")
+    raise Exception(f"Unsupported type {type(obj)} of {obj!r}.")
 
 
 def generate_badges(
@@ -184,9 +184,7 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
 
     if not isinstance(avsc_names, schema_salad.avro.schema.Names):
         print(avsc_names)
-        raise ValidationException(
-            f"Wrong instance for avsc_names: {type(avsc_names)}"
-        )
+        raise ValidationException(f"Wrong instance for avsc_names: {type(avsc_names)}")
 
     tests, metadata = schema_salad.schema.load_and_validate(
         document_loader, avsc_names, path, True
diff --git a/setup.cfg b/setup.cfg
index aae8e39..cf9fe0a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,8 +1,3 @@
-[flake8]
-ignore = E124,E128,E129,E201,E202,E225,E226,E231,E265,E271,E302,E303,F401,E402,E501,W503,E731,F811,F821,F841
-max-line-length = 88
-extend-ignore = E203, W503
-
 [aliases]
 test=pytest
 
diff --git a/tests/test_compare.py b/tests/test_compare.py
index 86d456e..687f177 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -139,22 +139,26 @@ def test_compare_directory_failure_different_listing() -> None:
                     "basename": "baz.txt",
                     "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                     "class": "File",
-                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "location": "file:///var/folders/8x/"
+                    "2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
                     "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
                     "size": 0,
                 },
                 {
                     "basename": "foo",
                     "class": "Directory",
-                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
+                    "location": "file:///var/folders/8x/"
+                    "2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
                     "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo",
                     "listing": [
                         {
                             "basename": "bar.txt",
                             "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80775",
                             "class": "File",
-                            "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
-                            "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
+                            "location": "file:///var/folders/8x/"
+                            "2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
+                            "path": "/var/folders/8x/"
+                            "2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/foo/bar.txt",
                             "size": 0,
                         }
                     ],
@@ -202,7 +206,8 @@ def test_compare_directory_failure_no_listing() -> None:
                     "basename": "baz.txt",
                     "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                     "class": "File",
-                    "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
+                    "location": "file:///var/folders/8x/"
+                    "2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
                     "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/stuff/baz.txt",
                     "size": 0,
                 },

From 8b23a7b878c71fd75a6e15af105990baf8b9cca5 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 13 Feb 2023 18:18:38 +0100
Subject: [PATCH 064/165] ci: skip linting on py3.6

---
 .github/workflows/ci-tests.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index ddd8e49..22e4357 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -27,6 +27,9 @@ jobs:
           - py-ver-major: 3
             py-ver-minor: 6
             step: mypy
+          - py-ver-major: 3
+            py-ver-minor: 6
+            step: lint
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
@@ -34,6 +37,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
       - name: Set up Python
         uses: actions/setup-python@v4
@@ -48,7 +53,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install tox tox-gh-actions
+          pip install "tox<4" "tox-gh-actions<3"
 
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
@@ -77,8 +82,8 @@ jobs:
         step: [lintreadme, pydocstyle]
 
     env:
-      py-semver: "3.10"
-      TOXENV: ${{ format('py310-{0}', matrix.step) }}
+      py-semver: "3.11"
+      TOXENV: ${{ format('py311-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v3
@@ -98,7 +103,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install tox tox-gh-actions
+          pip install "tox<4" "tox-gh-actions<3"
 
       - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
         name: Create local branch for diff-quality for PRs
@@ -118,7 +123,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.10"  # quoted, otherwise that turns into the number 3.1
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: |
             requirements.txt

From 00e011bb92a5b32880ee5dd4c943c303c05756b6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Feb 2023 17:27:12 +0000
Subject: [PATCH 065/165] Bump sphinx-rtd-theme from 1.1.1 to 1.2.0

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.1.1 to 1.2.0.
- [Release notes](https://github.com/readthedocs/sphinx_rtd_theme/releases)
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.1.1...1.2.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index b8611de..d4fbc5d 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==1.1.1
+sphinx-rtd-theme==1.2.0
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 65736b9745ef417ccff27cb1dbcef1596d004c45 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 20 Feb 2023 01:31:48 +0000
Subject: [PATCH 066/165] Bump mypy from 1.0.0 to 1.0.1

Bumps [mypy](https://github.com/python/mypy) from 1.0.0 to 1.0.1.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v1.0.0...v1.0.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 671641f..f405f74 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.0.0
+mypy==1.0.1
 types-setuptools
 types-requests
 types-PyYAML

From 821f4e91a0a2a6fe8f2152ac457932759912b450 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 8 Mar 2023 00:58:31 +0000
Subject: [PATCH 067/165] Bump mypy from 1.0.1 to 1.1.1

Bumps [mypy](https://github.com/python/mypy) from 1.0.1 to 1.1.1.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v1.0.1...v1.1.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f405f74..d5593cc 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.0.1
+mypy==1.1.1
 types-setuptools
 types-requests
 types-PyYAML

From d9910739486bf037a7d483c6c8ef4c1747e88194 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 30 Mar 2023 00:58:03 +0000
Subject: [PATCH 068/165] Update black requirement from ~=23.1 to ~=23.3

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.1.0...23.3.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 4ac7321..75c59ca 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.1
+black ~= 23.3
 pylint
 pep257
 pydocstyle

From 6a7cf28fb0b9cb6b0ffeecaaff8b7d0c9d2aa6d9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 7 Apr 2023 00:57:43 +0000
Subject: [PATCH 069/165] Bump mypy from 1.1.1 to 1.2.0

Bumps [mypy](https://github.com/python/mypy) from 1.1.1 to 1.2.0.
- [Release notes](https://github.com/python/mypy/releases)
- [Commits](https://github.com/python/mypy/compare/v1.1.1...v1.2.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index d5593cc..93518b7 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.1.1
+mypy==1.2.0
 types-setuptools
 types-requests
 types-PyYAML

From 6b4a7bc3bb95460ebb4a3dfa9d00ea8bfe908c64 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 11 May 2023 00:57:49 +0000
Subject: [PATCH 070/165] Bump mypy from 1.2.0 to 1.3.0

Bumps [mypy](https://github.com/python/mypy) from 1.2.0 to 1.3.0.
- [Commits](https://github.com/python/mypy/compare/v1.2.0...v1.3.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 93518b7..f26d55f 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.2.0
+mypy==1.3.0
 types-setuptools
 types-requests
 types-PyYAML

From 5cd65d552df4673f3269f5bf3a8b9e8a5280cc8e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 24 May 2023 00:57:57 +0000
Subject: [PATCH 071/165] Bump sphinx-rtd-theme from 1.2.0 to 1.2.1

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.0 to 1.2.1.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.0...1.2.1)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index d4fbc5d..be677f9 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==1.2.0
+sphinx-rtd-theme==1.2.1
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 4c57396b9063988a296dc99fac5ecf03b2c44302 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 27 May 2023 11:12:12 +0200
Subject: [PATCH 072/165] Validate actual file properties such as `checksum`

A re-do of https://github.com/common-workflow-language/cwltest/pull/146

Co-Authored-By: Michael R. Crusoe <michael.crusoe@gmail.com>
---
 cwltest/compare.py    | 136 +++++++++++++++++++++++++++++++++++-------
 tests/test_compare.py | 123 +++++++++++++++++++++++++++++++++++++-
 tox.ini               |   4 +-
 3 files changed, 236 insertions(+), 27 deletions(-)

diff --git a/cwltest/compare.py b/cwltest/compare.py
index 5374202..8a4e89e 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -1,7 +1,10 @@
 """Compare utilities for CWL objects."""
 
+import hashlib
 import json
-from typing import Any, Dict, Optional, Set
+import os.path
+import urllib.parse
+from typing import Any, Callable, Dict, Optional, Set
 
 
 class CompareFail(Exception):
@@ -22,11 +25,11 @@ def format(
 
 
 def _check_keys(
-    keys: Set[str], expected: Dict[str, Any], actual: Dict[str, Any]
+    keys: Set[str], expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
 ) -> None:
     for k in keys:
         try:
-            compare(expected.get(k), actual.get(k))
+            compare(expected.get(k), actual.get(k), skip_details)
         except CompareFail as e:
             raise CompareFail.format(
                 expected, actual, f"field {k!r} failed comparison: {str(e)}"
@@ -48,10 +51,12 @@ def _compare_contents(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
         )
 
 
-def _compare_dict(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+def _compare_dict(
+    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+) -> None:
     for c in expected:
         try:
-            compare(expected[c], actual.get(c))
+            compare(expected[c], actual.get(c), skip_details)
         except CompareFail as e:
             raise CompareFail.format(
                 expected, actual, f"failed comparison for key {c!r}: {e}"
@@ -62,7 +67,9 @@ def _compare_dict(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
             raise CompareFail.format(expected, actual, "unexpected key '%s'" % k)
 
 
-def _compare_directory(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+def _compare_directory(
+    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+) -> None:
     if actual.get("class") != "Directory":
         raise CompareFail.format(
             expected, actual, "expected object with a class 'Directory'"
@@ -75,7 +82,7 @@ def _compare_directory(expected: Dict[str, Any], actual: Dict[str, Any]) -> None
         found = False
         for j in actual["listing"]:
             try:
-                compare(i, j)
+                compare(i, j, skip_details)
                 found = True
                 break
             except CompareFail:
@@ -86,19 +93,32 @@ def _compare_directory(expected: Dict[str, Any], actual: Dict[str, Any]) -> None
                 actual,
                 "%s not found" % json.dumps(i, indent=4, sort_keys=True),
             )
-    _compare_file(expected, actual)
+    _compare_file(expected, actual, skip_details)
 
 
-def _compare_file(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
-    _compare_location(expected, actual)
+def _compare_file(
+    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+) -> None:
+    _compare_location(expected, actual, skip_details)
     if "contents" in expected:
         _compare_contents(expected, actual)
-    other_keys = set(expected.keys()) - {"path", "location", "listing", "contents"}
-    _check_keys(other_keys, expected, actual)
-    _check_keys(other_keys, expected, actual)
-
-
-def _compare_location(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+    if actual.get("class") == "File" and not skip_details:
+        _compare_checksum(expected, actual)
+        _compare_size(expected, actual)
+    other_keys = set(expected.keys()) - {
+        "path",
+        "location",
+        "listing",
+        "contents",
+        "checksum",
+        "size",
+    }
+    _check_keys(other_keys, expected, actual, skip_details)
+
+
+def _compare_location(
+    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+) -> None:
     if "path" in expected:
         comp = "path"
         if "path" not in actual:
@@ -109,7 +129,19 @@ def _compare_location(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
         return
     if actual.get("class") == "Directory":
         actual[comp] = actual[comp].rstrip("/")
-
+        exist_fun: Callable[[str], bool] = os.path.isdir
+    else:
+        exist_fun = os.path.isfile
+    if "path" in actual:
+        path = urllib.parse.urlparse(actual["path"]).path
+    else:
+        path = urllib.parse.urlparse(actual["location"]).path
+    if not exist_fun(path) and not skip_details:
+        raise CompareFail.format(
+            expected,
+            actual,
+            f"{actual[comp]} does not exist",
+        )
     if expected[comp] != "Any" and (
         not (
             actual[comp].endswith("/" + expected[comp])
@@ -123,7 +155,67 @@ def _compare_location(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
         )
 
 
-def compare(expected: Any, actual: Any) -> None:
+def _compare_checksum(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+    if "path" in actual:
+        path = urllib.parse.urlparse(actual["path"]).path
+    else:
+        path = urllib.parse.urlparse(actual["location"]).path
+    checksum = hashlib.sha1()  # nosec
+    with open(path, "rb") as f:
+        contents = f.read(1024 * 1024)
+        while contents != b"":
+            checksum.update(contents)
+            contents = f.read(1024 * 1024)
+    actual_checksum_on_disk = f"sha1${checksum.hexdigest()}"
+    if "checksum" in actual:
+        actual_checksum_declared = actual["checksum"]
+        if actual_checksum_on_disk != actual_checksum_declared:
+            raise CompareFail.format(
+                expected,
+                actual,
+                "Output file checksums do not match: actual "
+                f"{actual_checksum_on_disk!r} on disk is not equal to actual "
+                f"{actual_checksum_declared!r} in the output object",
+            )
+    if "checksum" in expected:
+        expected_checksum = expected["checksum"]
+        if expected_checksum != actual_checksum_on_disk:
+            raise CompareFail.format(
+                expected,
+                actual,
+                "Output file checksums do not match: actual "
+                f"{actual_checksum_on_disk!r} is not equal to expected {expected_checksum!r}",
+            )
+
+
+def _compare_size(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+    if "path" in actual:
+        path = urllib.parse.urlparse(actual["path"]).path
+    else:
+        path = urllib.parse.urlparse(actual["location"]).path
+    actual_size_on_disk = os.path.getsize(path)
+    if "size" in actual:
+        actual_size_declared = actual["size"]
+        if actual_size_on_disk != actual_size_declared:
+            raise CompareFail.format(
+                expected,
+                actual,
+                "Output file sizes do not match: actual "
+                f"{actual_size_on_disk!r} on disk is not equal to actual "
+                f"{actual_size_declared!r}' in the output object",
+            )
+    if "size" in expected:
+        expected_size = expected["size"]
+        if expected_size != actual_size_on_disk:
+            raise CompareFail.format(
+                expected,
+                actual,
+                "Output file sizes do not match: actual "
+                f"{actual_size_on_disk!r} is not equal to expected {expected_size!r}",
+            )
+
+
+def compare(expected: Any, actual: Any, skip_details: bool = False) -> None:
     """Compare two CWL objects."""
     if expected == "Any":
         return
@@ -136,11 +228,11 @@ def compare(expected: Any, actual: Any) -> None:
                 raise CompareFail.format(expected, actual)
 
             if expected.get("class") == "File":
-                _compare_file(expected, actual)
+                _compare_file(expected, actual, skip_details)
             elif expected.get("class") == "Directory":
-                _compare_directory(expected, actual)
+                _compare_directory(expected, actual, skip_details)
             else:
-                _compare_dict(expected, actual)
+                _compare_dict(expected, actual, skip_details)
 
         elif isinstance(expected, list):
             if not isinstance(actual, list):
@@ -150,7 +242,7 @@ def compare(expected: Any, actual: Any) -> None:
                 raise CompareFail.format(expected, actual, "lengths don't match")
             for c in range(0, len(expected)):
                 try:
-                    compare(expected[c], actual[c])
+                    compare(expected[c], actual[c], skip_details)
                 except CompareFail as e:
                     raise CompareFail.format(expected, actual, e) from e
         else:
diff --git a/tests/test_compare.py b/tests/test_compare.py
index 687f177..6491f8d 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -1,7 +1,9 @@
+import os
+from pathlib import Path
 from typing import Any, Dict
 
 import pytest
-from cwltest.compare import CompareFail, compare
+from cwltest.compare import CompareFail, _compare_directory, _compare_file, compare
 
 from .util import get_data
 
@@ -37,6 +39,7 @@ def test_compare_contents_success() -> None:
         "size": 2,
         "class": "File",
         "contents": "2\n",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
     }
     actual = {
         "basename": "cores.txt",
@@ -49,6 +52,120 @@ def test_compare_contents_success() -> None:
     compare(expected, actual)
 
 
+def test_compare_contents_not_exist() -> None:
+    expected = {
+        "location": "cores.txt",
+        "class": "File",
+    }
+    actual = {
+        "basename": "cores.txt",
+        "class": "File",
+        "location": "file:///var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
+        "path": "/none/exist/path/to/cores.txt",
+        "size": 2,
+    }
+    with pytest.raises(CompareFail):
+        _compare_file(expected, actual, False)
+
+
+def test_compare_file_different_size(tmp_path: Path) -> None:
+    expected = {
+        "location": "cores.txt",
+        "size": 2,
+        "class": "File",
+    }
+
+    path = tmp_path / "cores.txt"
+    with open(path, "w") as f:
+        f.write("hello")
+
+    actual = {
+        "basename": "cores.txt",
+        "class": "File",
+        "location": str(path),
+    }
+    with pytest.raises(CompareFail):
+        _compare_file(expected, actual, False)
+
+
+def test_compare_file_different_checksum(tmp_path: Path) -> None:
+    expected = {
+        "location": "cores.txt",
+        "class": "File",
+        "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7a",
+    }
+
+    path = tmp_path / "cores.txt"
+    with open(path, "w") as f:
+        f.write("hello")
+
+    actual = {
+        "basename": "cores.txt",
+        "class": "File",
+        "location": str(path),
+    }
+    with pytest.raises(CompareFail):
+        _compare_file(expected, actual, False)
+
+
+def test_compare_file_inconsistent_size(tmp_path: Path) -> None:
+    expected = {
+        "location": "cores.txt",
+        "class": "File",
+    }
+
+    path = tmp_path / "cores.txt"
+    with open(path, "w") as f:
+        f.write("hello")
+
+    actual = {
+        "basename": "cores.txt",
+        "class": "File",
+        "location": str(path),
+        "size": 65535,
+    }
+    with pytest.raises(CompareFail):
+        _compare_file(expected, actual, False)
+
+
+def test_compare_file_inconsistent_checksum(tmp_path: Path) -> None:
+    expected = {
+        "location": "cores.txt",
+        "class": "File",
+    }
+
+    path = tmp_path / "cores.txt"
+    with open(path, "w") as f:
+        f.write("hello")
+
+    actual = {
+        "basename": "cores.txt",
+        "checksum": "inconsistent-checksum",
+        "class": "File",
+        "location": str(path),
+    }
+    with pytest.raises(CompareFail):
+        _compare_file(expected, actual, False)
+
+
+def test_compare_directory(tmp_path: Path) -> None:
+    expected = {
+        "location": "dir",
+        "class": "Directory",
+        "listing": [],
+    }
+
+    path = tmp_path / "dir"
+    os.makedirs(path)
+
+    actual = {
+        "class": "Directory",
+        "location": str(path),
+        "listing": [],
+    }
+    _compare_directory(expected, actual, False)
+
+
 def test_compare_directory_success() -> None:
     expected = {
         "stuff": {
@@ -100,7 +217,7 @@ def test_compare_directory_success() -> None:
             ],
         }
     }
-    compare(expected, actual)
+    compare(expected, actual, skip_details=True)
 
 
 def test_compare_directory_failure_different_listing() -> None:
@@ -270,7 +387,7 @@ def test_compare_file_success() -> None:
         "path": "/var/folders/8x/2df05_7j20j6r8y81w4qf43r0000gn/T/tmpG0EkrS/cores.txt",
         "size": 2,
     }
-    compare(expected, actual)
+    compare(expected, actual, skip_details=True)
 
 
 def test_compare_list_failure_missing() -> None:
diff --git a/tox.ini b/tox.ini
index 0ac4e44..a841a1e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,6 @@
 [tox]
 envlist =
-  py{36,37,38,39,310,311}-lint,
+  py{37,38,39,310,311}-lint,
   py{36,37,38,39,310,311}-unit,
   py{36,37,38,39,310,311}-bandit,
   py{37,38,39,310,311}-mypy,
@@ -58,7 +58,7 @@ commands =
   py{36,37,38,39,310,311}-unit: python -m pip install -U pip setuptools wheel
   py{36,37,38,39,310,311}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
   py{36,37,38,39,310,311}-unit: coverage xml
-  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest --exclude tests/*
+  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest
   py{36,37,38,39,310,311}-lint: make flake8
   py{36,37,38,39,310,311}-lint: make format-check
   py{37,38,39,310,311}-mypy: make mypy

From 4b106d3d2188c342604096cad3079ee9cd4a3f99 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 7 Jun 2023 15:06:09 +0100
Subject: [PATCH 073/165] include missing files in sdist

---
 MANIFEST.in | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index 1eab7bf..3aec21c 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,7 @@
-include Makefile gittaggers.py test-requirements.txt mypy-requirements.txt requirements.txt
-include cwltest/cwltest-schema.yml
+include Makefile gittaggers.py test-requirements.txt mypy-requirements.txt requirements.txt tox.ini mypy.ini
+include dev-requirements.txt .flake8 .coveragerc release-test.sh
+include docs/Makefile docs/conf.py docs/requirements.txt docs/_static/favicon.ico docs/*.rst
+include cwltest/*.yml
 include tests/*
 include tests/test-data/*
 include tests/test-data/v1.0/*

From 0f9117efaa811494135983f732bf55266d4b4ccb Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <crusoe@debian.org>
Date: Wed, 7 Jun 2023 16:50:06 +0100
Subject: [PATCH 074/165] test_catories path fixes

---
 tests/test_categories.py | 37 +++++++++++++++----------------------
 1 file changed, 15 insertions(+), 22 deletions(-)

diff --git a/tests/test_categories.py b/tests/test_categories.py
index c6461e9..ceb2f3b 100644
--- a/tests/test_categories.py
+++ b/tests/test_categories.py
@@ -14,15 +14,10 @@
 
 def test_unsupported_with_required_tests() -> None:
     cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
-    args = [
-        "--test",
-        schema_salad.ref_resolver.file_uri(
-            get_data("tests/test-data/required-unsupported.yml")
-        ),
-    ]
     cwd = os.getcwd()
+    os.chdir(get_data("tests/test-data/"))
+    args = ["--test", "required-unsupported.yml"]
     try:
-        os.chdir(get_data("tests/test-data/"))
         error_code, stdout, stderr = run_with_mock_cwl_runner(args)
     finally:
         os.chdir(cwd)
@@ -35,21 +30,19 @@ def test_unsupported_with_required_tests() -> None:
     else:
         q = ""
     assert (
-        "The `id` field is missing.{n}"
-        "The `id` field is missing.{n}"
-        "Test [1/2] Required test that is unsupported (without tags){n}"
-        "{n}"
-        "Test 1 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
-        "Required test that is unsupported (without tags){n}"
-        "Does not support required feature{n}"
-        "Test [2/2] Required test that is unsupported (with tags){n}"
-        "{n}"
-        "Test 2 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
-        "Required test that is unsupported (with tags){n}"
-        "Does not support required feature{n}"
-        "0 tests passed, 2 failures, 0 unsupported features{n}".format(
-            cwl_runner=cwl_runner, n=n, p=p, q=q
-        )
+        f"The `id` field is missing.{n}"
+        f"The `id` field is missing.{n}"
+        f"Test [1/2] Required test that is unsupported (without tags){n}"
+        f"{n}"
+        f"Test 1 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        f"Required test that is unsupported (without tags){n}"
+        f"Does not support required feature{n}"
+        f"Test [2/2] Required test that is unsupported (with tags){n}"
+        f"{n}"
+        f"Test 2 failed: {cwl_runner} --quiet return-unsupported.cwl {q}v1.0{p}cat-job.json{q}{n}"
+        f"Required test that is unsupported (with tags){n}"
+        f"Does not support required feature{n}"
+        f"0 tests passed, 2 failures, 0 unsupported features{n}"
     ) == stderr
 
 

From 120ca38a07ab8c17af5f92633eaf5c15ce96cbb5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 8 Jun 2023 00:58:03 +0000
Subject: [PATCH 075/165] Bump sphinx-rtd-theme from 1.2.1 to 1.2.2

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.1...1.2.2)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index be677f9..4820ced 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==1.2.1
+sphinx-rtd-theme==1.2.2
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 1e60b9ecacd3041114788500dda0493046e564b1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 21 Jun 2023 00:58:07 +0000
Subject: [PATCH 076/165] Bump mypy from 1.3.0 to 1.4.0

Bumps [mypy](https://github.com/python/mypy) from 1.3.0 to 1.4.0.
- [Commits](https://github.com/python/mypy/compare/v1.3.0...v1.4.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f26d55f..e4ebae2 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.3.0
+mypy==1.4.0
 types-setuptools
 types-requests
 types-PyYAML

From e0e7b4d1ff5e00255b6580e884d40a4fce2c6e79 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 26 Jun 2023 01:06:13 +0000
Subject: [PATCH 077/165] Bump mypy from 1.4.0 to 1.4.1

Bumps [mypy](https://github.com/python/mypy) from 1.4.0 to 1.4.1.
- [Commits](https://github.com/python/mypy/compare/v1.4.0...v1.4.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index e4ebae2..b5de881 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.4.0
+mypy==1.4.1
 types-setuptools
 types-requests
 types-PyYAML

From cf6586673fa8deee9740b15b5aa84039bfc3e359 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 11 Jul 2023 00:37:48 +0000
Subject: [PATCH 078/165] Update black requirement from ~=23.3 to ~=23.7

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.3.0...23.7.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 75c59ca..a44e618 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.3
+black ~= 23.7
 pylint
 pep257
 pydocstyle

From c6b8baf70b9568d3ca1ede0da66396b9c85c85a9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 00:34:09 +0000
Subject: [PATCH 079/165] Bump sphinx-rtd-theme from 1.2.2 to 1.3.0

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.2 to 1.3.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.2...1.3.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 4820ced..bd71cd1 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==1.2.2
+sphinx-rtd-theme==1.3.0
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 1a1a5ff03b5c14476ace4d5867867c95257da0fb Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 22 Aug 2023 08:13:08 +0000
Subject: [PATCH 080/165] Bump mypy from 1.4.1 to 1.5.1

Bumps [mypy](https://github.com/python/mypy) from 1.4.1 to 1.5.1.
- [Commits](https://github.com/python/mypy/compare/v1.4.1...v1.5.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index b5de881..e28b381 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.4.1
+mypy==1.5.1
 types-setuptools
 types-requests
 types-PyYAML

From fc8cf0bcf0f67b60760b26a6f94ee498d1b664ee Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 25 Aug 2023 14:46:46 +0200
Subject: [PATCH 081/165] testing: drop Python 3.7, add 3.12

---
 .github/workflows/ci-tests.yml |  5 ++-
 setup.py                       |  2 +-
 tox.ini                        | 70 +++++++++++++++++-----------------
 3 files changed, 39 insertions(+), 38 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 22e4357..55e7434 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -21,7 +21,7 @@ jobs:
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [6, 7, 8, 9, 10, 11]
+        py-ver-minor: [6, 8, 9, 10, 11, 12]
         step: [lint, unit, mypy, bandit]
         exclude:
           - py-ver-major: 3
@@ -44,6 +44,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
+          allow-prereleases: true
           cache: pip
           cache-dependency-path: |
             requirements.txt
@@ -75,7 +76,7 @@ jobs:
   tox-style:
     name: CI linters via Tox
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
diff --git a/setup.py b/setup.py
index 5b9c52f..60e258f 100644
--- a/setup.py
+++ b/setup.py
@@ -65,11 +65,11 @@
         "Operating System :: MacOS :: MacOS X",
         "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Typing :: Typed",
     ],
 )
diff --git a/tox.ini b/tox.ini
index a841a1e..690fe66 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,11 +1,11 @@
 [tox]
 envlist =
-  py{37,38,39,310,311}-lint,
-  py{36,37,38,39,310,311}-unit,
-  py{36,37,38,39,310,311}-bandit,
-  py{37,38,39,310,311}-mypy,
-  py310-lintreadme,
-  py310-pydocstyle
+  py3{8,9,10,11,12}-lint,
+  py3{6,8,9,10,11,12}-unit,
+  py3{6,8,9,10,11,12}-bandit,
+  py3{8,9,10,11,12}-mypy,
+  py311-lintreadme,
+  py311-pydocstyle
 
 skip_missing_interpreters = True
 
@@ -17,64 +17,64 @@ testpaths = tests
 [gh-actions]
 python =
   3.6: py36
-  3.7: py37
   3.8: py38
   3.9: py39
   3.10: py310
   3.11: py311
+  3.12: py312
 
 [testenv]
 skipsdist =
   py3{6,7,8,9,10,11}-!{unit,mypy,lintreadme} = True
 
 description =
-  py{36,37,38,39,310,311}-unit: Run the unit tests
-  py{36,37,38,39,310,311}-lint: Lint the Python code
-  py{36,37,38,39,310,311}-bandit: Search for common security issues
-  py{37,38,39,310,311}-mypy: Check for type safety
-  py310-pydocstyle: docstring style checker
-  py310-lintreadme: Lint the README.rst->.md conversion
+  py3{6,8,9,10,11,12}-unit: Run the unit tests
+  py3{6,8,9,10,11,12}-lint: Lint the Python code
+  py3{6,8,9,10,11,12}-bandit: Search for common security issues
+  py3{8,9,10,11,12}-mypy: Check for type safety
+  py311-pydocstyle: docstring style checker
+  py311-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 
 deps =
-  py{36,37,38,39,310,311}-{unit,mypy}: -rrequirements.txt
-  py{36,37,38,39,310,311}-{unit,mypy}: -rtest-requirements.txt
-  py{36,37,38,39,310,311}-lint: flake8-bugbear
-  py{36,37,38,39,310,311}-lint: black~=23.1
-  py{36,37,38,39,310,311}-bandit: bandit
-  py{37,38,39,310,311}-mypy: -rmypy-requirements.txt
+  py3{6,8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
+  py3{6,8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
+  py3{6,8,9,10,11,12}-lint: flake8-bugbear
+  py3{6,8,9,10,11,12}-lint: black~=23.1
+  py3{6,8,9,10,11,12}-bandit: bandit
+  py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
 
 setenv =
-  py{36,37,38,39,310,311}-unit: LC_ALL = C.UTF-8
+  py3{6,8,3,10,11,12}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
 
 commands =
-  py{36,37,38,39,310,311}-unit: python -m pip install -U pip setuptools wheel
-  py{36,37,38,39,310,311}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
-  py{36,37,38,39,310,311}-unit: coverage xml
-  py{36,37,38,39,310,311}-bandit: bandit --recursive cwltest
-  py{36,37,38,39,310,311}-lint: make flake8
-  py{36,37,38,39,310,311}-lint: make format-check
-  py{37,38,39,310,311}-mypy: make mypy
-  py37-mypy: make mypy_3.6
+  py3{6,8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
+  py3{6,8,9,10,11,12}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py3{6,8,9,10,11,12}-unit: coverage xml
+  py3{6,8,9,10,11,12}-bandit: bandit --recursive cwltest
+  py3{6,8,9,10,11,12}-lint: make flake8
+  py3{6,8,9,10,11,12}-lint: make format-check
+  py3{8,9,10,11,12}-mypy: make mypy
+  py38-mypy: make mypy_3.6
 
 allowlist_externals =
-  py{36,37,38,39,310,311}-lint: flake8
-  py{36,37,38,39,310,311}-lint: black
-  py{36,37,38,39,310,311}-{mypy,shellcheck,lint,unit}: make
+  py3{6,8,9,10,11,12}-lint: flake8
+  py3{6,8,9,10,11,12}-lint: black
+  py3{6,8,9,10,11,12}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py{36,37,38,39,310,311}-lint: true
-  py{36,37,38,39,310,311}-bandit: true
+  py3{6,8,9,10,11,12}-lint: true
+  py3{6,8,9,10,11,12}-bandit: true
 
 
-[testenv:py310-pydocstyle]
+[testenv:py311-pydocstyle]
 allowlist_externals = make
 commands = make diff_pydocstyle_report
 deps =
@@ -82,7 +82,7 @@ deps =
     diff-cover
 skip_install = true
 
-[testenv:py310-lintreadme]
+[testenv:py311-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
   python -m build --outdir {distdir}

From 44c0ad84ed2637c574f085fb5a575240b9c1d198 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 5 Sep 2023 00:06:48 +0000
Subject: [PATCH 082/165] Bump actions/checkout from 3 to 4

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml        | 6 +++---
 .github/workflows/codeql-analysis.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 55e7434..2bb6680 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -36,7 +36,7 @@ jobs:
       TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -87,7 +87,7 @@ jobs:
       TOXENV: ${{ format('py311-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -119,7 +119,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v4
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 292544f..8c5fc31 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -15,7 +15,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.

From f8e68b865d453611523a25596dc2ae4936f0e81e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Sep 2023 00:24:45 +0000
Subject: [PATCH 083/165] Update black requirement from ~=23.7 to ~=23.9

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.7.0...23.9.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index a44e618..8be2342 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.7
+black ~= 23.9
 pylint
 pep257
 pydocstyle

From 3a36d096ba9dfa9077aef8190e0e0f0a3294652e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 11 Oct 2023 00:30:49 +0000
Subject: [PATCH 084/165] Bump mypy from 1.5.1 to 1.6.0

Bumps [mypy](https://github.com/python/mypy) from 1.5.1 to 1.6.0.
- [Commits](https://github.com/python/mypy/compare/v1.5.1...v1.6.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index e28b381..357d788 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.5.1
+mypy==1.6.0
 types-setuptools
 types-requests
 types-PyYAML

From f9c8f1c459df4f976a4dd7ee4145548293432f0d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 11 Oct 2023 09:21:58 +0200
Subject: [PATCH 085/165] Drop Python 3.6 testing

This is now a Python 3.8+ codebase

Default to Python 3.12 for release testing and others
---
 .github/workflows/ci-tests.yml | 16 +++------
 Makefile                       |  6 ++--
 README.rst                     |  2 +-
 cwltest/argparser.py           |  3 +-
 cwltest/compare.py             |  3 +-
 cwltest/plugin.py              |  8 ++---
 dev-requirements.txt           |  1 +
 release-test.sh                |  4 +--
 requirements.txt               |  1 -
 setup.py                       |  3 +-
 tox.ini                        | 60 ++++++++++++++++------------------
 11 files changed, 45 insertions(+), 62 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 2bb6680..9222ed9 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -21,15 +21,8 @@ jobs:
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [6, 8, 9, 10, 11, 12]
+        py-ver-minor: [8, 9, 10, 11, 12]
         step: [lint, unit, mypy, bandit]
-        exclude:
-          - py-ver-major: 3
-            py-ver-minor: 6
-            step: mypy
-          - py-ver-major: 3
-            py-ver-minor: 6
-            step: lint
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
@@ -44,7 +37,6 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ env.py-semver }}
-          allow-prereleases: true
           cache: pip
           cache-dependency-path: |
             requirements.txt
@@ -83,8 +75,8 @@ jobs:
         step: [lintreadme, pydocstyle]
 
     env:
-      py-semver: "3.11"
-      TOXENV: ${{ format('py311-{0}', matrix.step) }}
+      py-semver: "3.12"
+      TOXENV: ${{ format('py312-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v4
@@ -124,7 +116,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache: pip
           cache-dependency-path: |
             requirements.txt
diff --git a/Makefile b/Makefile
index ced0a68..0e5889e 100644
--- a/Makefile
+++ b/Makefile
@@ -168,11 +168,9 @@ mypy3: mypy
 mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
-mypy_3.6: $(filter-out setup.py gittagger.py,$(PYSOURCES))
-	MYPYPATH=$$MYPYPATH:mypy-stubs mypy --python-version 3.6 $^
-
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
-	pyupgrade --exit-zero-even-if-changed --py36-plus $^
+	pyupgrade --exit-zero-even-if-changed --py38-plus $^
+	auto-walrus $^
 
 release-test: FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
diff --git a/README.rst b/README.rst
index f6e7e2e..a20438f 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.6, 3.7, 3.8, 3.9, 3.10, and 3.11.
+This is written and tested for Python 3.8, 3.9, 3.10, 3.11, and 3.12.
 
 .. contents:: Table of Contents
    :local:
diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index 6cc616d..819c553 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -107,8 +107,7 @@ def arg_parser() -> argparse.ArgumentParser:
         help="Create JSON badges and store them in this directory.",
     )
 
-    pkg = pkg_resources.require("cwltest")
-    if pkg:
+    if pkg := pkg_resources.require("cwltest"):
         ver = f"{sys.argv[0]} {pkg[0].version}"
     else:
         ver = "{} {}".format(sys.argv[0], "unknown version")
diff --git a/cwltest/compare.py b/cwltest/compare.py
index 8a4e89e..f392239 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -37,10 +37,9 @@ def _check_keys(
 
 
 def _compare_contents(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
-    expected_contents = expected["contents"]
     with open(actual["path"]) as f:
         actual_contents = f.read()
-    if expected_contents != actual_contents:
+    if (expected_contents := expected["contents"]) != actual_contents:
         raise CompareFail.format(
             expected,
             actual,
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index c3c0c6b..40da5f5 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -13,6 +13,7 @@
     Iterator,
     List,
     Optional,
+    Protocol,
     Set,
     Tuple,
     Union,
@@ -21,7 +22,6 @@
 
 import pytest
 from cwltest.compare import CompareFail, compare
-from typing_extensions import Protocol
 
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
 
@@ -207,8 +207,7 @@ def _add_global_properties(self) -> None:
         """Nonfunctional if xdist is installed and anything besides "-n 0" is used."""
         from _pytest.junitxml import xml_key
 
-        xml = self.config._store.get(xml_key, None)
-        if xml:
+        if xml := self.config._store.get(xml_key, None):
             xml.add_global_property("runner", self.config.getoption("cwl_runner"))
             xml.add_global_property(
                 "runner_extra_args", self.config.getoption("cwl_args")
@@ -381,8 +380,7 @@ def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
         nunsupported,
         _,
     ) = utils.parse_results(results, tests)
-    cwl_badgedir = session.config.getoption("cwl_badgedir")
-    if cwl_badgedir:
+    if cwl_badgedir := session.config.getoption("cwl_badgedir"):
         utils.generate_badges(cwl_badgedir, ntotal, npassed)
 
 
diff --git a/dev-requirements.txt b/dev-requirements.txt
index 8be2342..c77c4c6 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -12,3 +12,4 @@ autoflake
 flake8-bugbear
 pyupgrade
 bandit
+auto-walrus
diff --git a/release-test.sh b/release-test.sh
index d7010b0..1eb6004 100755
--- a/release-test.sh
+++ b/release-test.sh
@@ -18,8 +18,8 @@ else
     HEAD=$(git rev-parse HEAD)
 fi
 run_tests="bin/py.test -p pytester --pyargs ${module}"
-pipver=20.3.3  # minimum required version of pip for Python 3.10
-setuptoolsver=50.0.1  # required for Python 3.10
+pipver=23.1  # minimum required version of pip for Python 3.12
+setuptoolsver=67.6.1  # required for Python 3.12
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
 
 rm -Rf testenv? || /bin/true
diff --git a/requirements.txt b/requirements.txt
index a15d1b3..bce0adf 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,4 +2,3 @@ schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
 pytest >= 7, < 8
 defusedxml
-typing-extensions
diff --git a/setup.py b/setup.py
index 60e258f..1e19380 100644
--- a/setup.py
+++ b/setup.py
@@ -30,7 +30,7 @@
     url="https://github.com/common-workflow-language/cwltest",
     download_url="https://github.com/common-workflow-language/cwltest",
     license="Apache 2.0",
-    python_requires=">=3.6, <4",
+    python_requires=">=3.8, <4",
     setup_requires=[] + pytest_runner,
     packages=["cwltest", "cwltest.tests"],
     package_dir={"cwltest.tests": "tests"},
@@ -64,7 +64,6 @@
         "Operating System :: POSIX",
         "Operating System :: MacOS :: MacOS X",
         "Development Status :: 5 - Production/Stable",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
diff --git a/tox.ini b/tox.ini
index 690fe66..a41f0f0 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,11 +1,11 @@
 [tox]
 envlist =
   py3{8,9,10,11,12}-lint,
-  py3{6,8,9,10,11,12}-unit,
-  py3{6,8,9,10,11,12}-bandit,
+  py3{8,9,10,11,12}-unit,
+  py3{8,9,10,11,12}-bandit,
   py3{8,9,10,11,12}-mypy,
-  py311-lintreadme,
-  py311-pydocstyle
+  py312-lintreadme,
+  py312-pydocstyle
 
 skip_missing_interpreters = True
 
@@ -16,7 +16,6 @@ testpaths = tests
 
 [gh-actions]
 python =
-  3.6: py36
   3.8: py38
   3.9: py39
   3.10: py310
@@ -25,56 +24,55 @@ python =
 
 [testenv]
 skipsdist =
-  py3{6,7,8,9,10,11}-!{unit,mypy,lintreadme} = True
+  py3{8,9,10,11,12}-!{unit,mypy,lintreadme} = True
 
 description =
-  py3{6,8,9,10,11,12}-unit: Run the unit tests
-  py3{6,8,9,10,11,12}-lint: Lint the Python code
-  py3{6,8,9,10,11,12}-bandit: Search for common security issues
+  py3{8,9,10,11,12}-unit: Run the unit tests
+  py3{8,9,10,11,12}-lint: Lint the Python code
+  py3{8,9,10,11,12}-bandit: Search for common security issues
   py3{8,9,10,11,12}-mypy: Check for type safety
-  py311-pydocstyle: docstring style checker
-  py311-lintreadme: Lint the README.rst->.md conversion
+  py312-pydocstyle: docstring style checker
+  py312-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 
 deps =
-  py3{6,8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
-  py3{6,8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
-  py3{6,8,9,10,11,12}-lint: flake8-bugbear
-  py3{6,8,9,10,11,12}-lint: black~=23.1
-  py3{6,8,9,10,11,12}-bandit: bandit
+  py3{8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
+  py3{8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
+  py3{8,9,10,11,12}-lint: flake8-bugbear
+  py3{8,9,10,11,12}-lint: black~=23.1
+  py3{8,9,10,11,12}-bandit: bandit
   py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
 
 setenv =
-  py3{6,8,3,10,11,12}-unit: LC_ALL = C.UTF-8
+  py3{8,3,10,11,12}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
 
 commands =
-  py3{6,8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
-  py3{6,8,9,10,11,12}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
-  py3{6,8,9,10,11,12}-unit: coverage xml
-  py3{6,8,9,10,11,12}-bandit: bandit --recursive cwltest
-  py3{6,8,9,10,11,12}-lint: make flake8
-  py3{6,8,9,10,11,12}-lint: make format-check
+  py3{8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
+  py3{8,9,10,11,12}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py3{8,9,10,11,12}-unit: coverage xml
+  py3{8,9,10,11,12}-bandit: bandit --recursive cwltest
+  py3{8,9,10,11,12}-lint: make flake8
+  py3{8,9,10,11,12}-lint: make format-check
   py3{8,9,10,11,12}-mypy: make mypy
-  py38-mypy: make mypy_3.6
 
 allowlist_externals =
-  py3{6,8,9,10,11,12}-lint: flake8
-  py3{6,8,9,10,11,12}-lint: black
-  py3{6,8,9,10,11,12}-{mypy,shellcheck,lint,unit}: make
+  py3{8,9,10,11,12}-lint: flake8
+  py3{8,9,10,11,12}-lint: black
+  py3{8,9,10,11,12}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py3{6,8,9,10,11,12}-lint: true
-  py3{6,8,9,10,11,12}-bandit: true
+  py3{8,9,10,11,12}-lint: true
+  py3{8,9,10,11,12}-bandit: true
 
 
-[testenv:py311-pydocstyle]
+[testenv:py312-pydocstyle]
 allowlist_externals = make
 commands = make diff_pydocstyle_report
 deps =
@@ -82,7 +80,7 @@ deps =
     diff-cover
 skip_install = true
 
-[testenv:py311-lintreadme]
+[testenv:py312-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
   python -m build --outdir {distdir}

From 70d5cd87b875823aa7983e320a165ce44d3d0a31 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 11 Oct 2023 09:38:29 +0200
Subject: [PATCH 086/165] gh-actions: codeql cancel out of date actions

---
 .github/workflows/codeql-analysis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 8c5fc31..e759476 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -8,6 +8,10 @@ on:
   schedule:
     - cron: '0 17 * * 0'
 
+concurrency:
+  group: scan-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   CodeQL-Build:
 

From 9770ae3b628c5ca6681da379909d98833a2c6da5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 18 Oct 2023 01:00:50 +0000
Subject: [PATCH 087/165] Update black requirement from ~=23.9 to ~=23.10

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.9.0...23.10.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index c77c4c6..789ecd2 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.9
+black ~= 23.10
 pylint
 pep257
 pydocstyle

From 774a8c465a9c3fe4de588826772d8573a7322126 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 19 Oct 2023 00:31:06 +0000
Subject: [PATCH 088/165] Bump mypy from 1.6.0 to 1.6.1

Bumps [mypy](https://github.com/python/mypy) from 1.6.0 to 1.6.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.6.0...v1.6.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 357d788..1019b08 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.6.0
+mypy==1.6.1
 types-setuptools
 types-requests
 types-PyYAML

From 952d95197173cbb5f759036bb99a48bb09934797 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 31 Oct 2023 14:35:04 +0100
Subject: [PATCH 089/165] favor "path" over "location" when testing

Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
---
 cwltest/compare.py    | 28 ++++++++++++++++------------
 tests/test_compare.py | 28 +++++++++++++++++++++++-----
 2 files changed, 39 insertions(+), 17 deletions(-)

diff --git a/cwltest/compare.py b/cwltest/compare.py
index f392239..18452ed 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -119,38 +119,42 @@ def _compare_location(
     expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
 ) -> None:
     if "path" in expected:
-        comp = "path"
+        expected_comp = "path"
         if "path" not in actual:
             actual["path"] = actual["location"]
     elif "location" in expected:
-        comp = "location"
+        expected_comp = "location"
     else:
         return
+    if "path" in actual:
+        actual_comp = "path"
+    else:
+        actual_comp = "location"
+    path = urllib.parse.urlparse(actual[actual_comp]).path
     if actual.get("class") == "Directory":
-        actual[comp] = actual[comp].rstrip("/")
+        actual[actual_comp] = actual[actual_comp].rstrip("/")
         exist_fun: Callable[[str], bool] = os.path.isdir
     else:
         exist_fun = os.path.isfile
-    if "path" in actual:
-        path = urllib.parse.urlparse(actual["path"]).path
-    else:
-        path = urllib.parse.urlparse(actual["location"]).path
     if not exist_fun(path) and not skip_details:
         raise CompareFail.format(
             expected,
             actual,
-            f"{actual[comp]} does not exist",
+            f"{actual[actual_comp]} does not exist",
         )
-    if expected[comp] != "Any" and (
+    if expected[expected_comp] != "Any" and (
         not (
-            actual[comp].endswith("/" + expected[comp])
-            or ("/" not in actual[comp] and expected[comp] == actual[comp])
+            actual[actual_comp].endswith("/" + expected[expected_comp])
+            or (
+                "/" not in actual[actual_comp]
+                and expected[expected_comp] == actual[actual_comp]
+            )
         )
     ):
         raise CompareFail.format(
             expected,
             actual,
-            f"{actual[comp]} does not end with {expected[comp]}",
+            f"{actual[actual_comp]} does not end with {expected[expected_comp]}",
         )
 
 
diff --git a/tests/test_compare.py b/tests/test_compare.py
index 6491f8d..b26c074 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -82,7 +82,7 @@ def test_compare_file_different_size(tmp_path: Path) -> None:
     actual = {
         "basename": "cores.txt",
         "class": "File",
-        "location": str(path),
+        "location": path.as_uri(),
     }
     with pytest.raises(CompareFail):
         _compare_file(expected, actual, False)
@@ -102,7 +102,7 @@ def test_compare_file_different_checksum(tmp_path: Path) -> None:
     actual = {
         "basename": "cores.txt",
         "class": "File",
-        "location": str(path),
+        "location": path.as_uri(),
     }
     with pytest.raises(CompareFail):
         _compare_file(expected, actual, False)
@@ -121,7 +121,7 @@ def test_compare_file_inconsistent_size(tmp_path: Path) -> None:
     actual = {
         "basename": "cores.txt",
         "class": "File",
-        "location": str(path),
+        "location": path.as_uri(),
         "size": 65535,
     }
     with pytest.raises(CompareFail):
@@ -142,7 +142,7 @@ def test_compare_file_inconsistent_checksum(tmp_path: Path) -> None:
         "basename": "cores.txt",
         "checksum": "inconsistent-checksum",
         "class": "File",
-        "location": str(path),
+        "location": path.as_uri(),
     }
     with pytest.raises(CompareFail):
         _compare_file(expected, actual, False)
@@ -160,7 +160,25 @@ def test_compare_directory(tmp_path: Path) -> None:
 
     actual = {
         "class": "Directory",
-        "location": str(path),
+        "location": path.as_uri(),
+        "listing": [],
+    }
+    _compare_directory(expected, actual, False)
+
+
+def test_compare_directory_path(tmp_path: Path) -> None:
+    expected = {
+        "location": "dir",
+        "class": "Directory",
+        "listing": [],
+    }
+
+    path = tmp_path / "dir"
+    os.makedirs(path)
+
+    actual = {
+        "class": "Directory",
+        "path": str(path),
         "listing": [],
     }
     _compare_directory(expected, actual, False)

From 6dd17148e8a6b3fd31e235e834764a8aae2ea337 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 31 Oct 2023 15:18:27 +0100
Subject: [PATCH 090/165] Switch to setuptools_scm

---
 .gitignore    |  2 ++
 MANIFEST.in   |  2 +-
 Makefile      | 18 ++++++++++--------
 gittaggers.py | 37 -------------------------------------
 setup.py      | 18 +++++-------------
 5 files changed, 18 insertions(+), 59 deletions(-)
 delete mode 100644 gittaggers.py

diff --git a/.gitignore b/.gitignore
index 27e2aac..613149a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,5 @@
 *.egg-info
 build
 dist
+
+cwltest/_version.py
diff --git a/MANIFEST.in b/MANIFEST.in
index 3aec21c..40bd4c8 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,4 @@
-include Makefile gittaggers.py test-requirements.txt mypy-requirements.txt requirements.txt tox.ini mypy.ini
+include Makefile test-requirements.txt mypy-requirements.txt requirements.txt tox.ini mypy.ini
 include dev-requirements.txt .flake8 .coveragerc release-test.sh
 include docs/Makefile docs/conf.py docs/requirements.txt docs/_static/favicon.ico docs/*.rst
 include cwltest/*.yml
diff --git a/Makefile b/Makefile
index 0e5889e..16b3c52 100644
--- a/Makefile
+++ b/Makefile
@@ -29,7 +29,7 @@ PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.3.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.4.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 
 ## all                    : default task (install in dev mode)
@@ -105,10 +105,10 @@ codespell:
 
 ## format                 : check/fix all code indentation and formatting (runs black)
 format: $(PYSOURCES) mypy-stubs
-	black $^
+	black --exclude cwltest/_version.py $^
 
 format-check: $(PYSOURCES) mypy-stubs
-	black --diff --check $^
+	black --diff --check --exclude cwltest/_version.py $^
 
 ## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
@@ -151,7 +151,7 @@ test: $(PYSOURCES)
 
 ## testcov                : run the cwltest test suite and collect coverage
 testcov: $(PYSOURCES)
-	python setup.py test --addopts "--cov" ${PYTEST_EXTRA}
+	pytest --cov ${PYTEST_EXTRA}
 
 sloccount.sc: $(PYSOURCES) Makefile
 	sloccount --duplicates --wide --details $^ > $@
@@ -165,7 +165,7 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: $(filter-out setup.py gittagger.py,$(PYSOURCES))
+mypy: $(filter-out setup.py,$(PYSOURCES))
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
@@ -176,7 +176,9 @@ release-test: FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
 	./release-test.sh
 
-release: release-test
+release:
+	export SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION} && \
+	./release-test.sh && \
 	. testenv2/bin/activate && \
 		pip install build && \
 		python -m build testenv2/src/${PACKAGE} && \
@@ -184,8 +186,8 @@ release: release-test
 		twine upload testenv2/src/${PACKAGE}/dist/* && \
 		git tag ${VERSION} && git push --tags
 
-flake8: $(PYSOURCES)
-	flake8 $^
+flake8: FORCE
+	flake8 $(PYSOURCES)
 
 FORCE:
 
diff --git a/gittaggers.py b/gittaggers.py
deleted file mode 100644
index 39e79f7..0000000
--- a/gittaggers.py
+++ /dev/null
@@ -1,37 +0,0 @@
-import subprocess
-import time
-
-import pkg_resources
-from setuptools.command.egg_info import egg_info
-
-SETUPTOOLS_VER = pkg_resources.get_distribution(
-    "setuptools").version.split('.')
-
-RECENT_SETUPTOOLS = int(SETUPTOOLS_VER[0]) > 40 or (
-    int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) > 0) or (
-        int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) == 0 and
-        int(SETUPTOOLS_VER[2]) > 0)
-
-class EggInfoFromGit(egg_info):
-    """Tag the build with git commit timestamp.
-
-    If a build tag has already been set (e.g., "egg_info -b", building
-    from source package), leave it alone.
-    """
-
-    def git_timestamp_tag(self):
-        gitinfo = subprocess.check_output(
-            ['git', 'log', '--first-parent', '--max-count=1',
-             '--format=format:%ct', '.']).strip()
-        return time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo)))
-
-    def tags(self):
-        if self.tag_build is None:
-            try:
-                self.tag_build = self.git_timestamp_tag()
-            except subprocess.CalledProcessError:
-                pass
-        return egg_info.tags(self)
-
-    if RECENT_SETUPTOOLS:
-        vtags = property(tags)
diff --git a/setup.py b/setup.py
index 1e19380..13bd5ec 100644
--- a/setup.py
+++ b/setup.py
@@ -2,26 +2,18 @@
 import os
 import pathlib
 import sys
+from typing import List
 
-import setuptools.command.egg_info as egg_info_cmd
 from setuptools import setup
 
 SETUP_DIR = os.path.dirname(__file__)
 README = os.path.join(SETUP_DIR, "README.rst")
 
-try:
-    import gittaggers
-
-    tagger = gittaggers.EggInfoFromGit
-except ImportError:
-    tagger = egg_info_cmd.egg_info
-
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
-pytest_runner = ["pytest < 8", "pytest-runner"] if needs_pytest else []
+pytest_runner: List[str] = ["pytest < 8", "pytest-runner"] if needs_pytest else []
 
 setup(
     name="cwltest",
-    version="2.3",  # update the VERSION prefix in the Makefile as well 🙂
     description="Common Workflow Language testing framework",
     long_description=open(README).read(),
     long_description_content_type="text/x-rst",
@@ -30,8 +22,9 @@
     url="https://github.com/common-workflow-language/cwltest",
     download_url="https://github.com/common-workflow-language/cwltest",
     license="Apache 2.0",
-    python_requires=">=3.8, <4",
-    setup_requires=[] + pytest_runner,
+    python_requires=">=3.8,<3.13",
+    use_scm_version=True,
+    setup_requires=pytest_runner + ["setuptools_scm>=8.0.4,<9"],
     packages=["cwltest", "cwltest.tests"],
     package_dir={"cwltest.tests": "tests"},
     package_data={"cwltest": ["py.typed"], "tests": ["test-data/*"]},
@@ -57,7 +50,6 @@
         ],
     },
     zip_safe=True,
-    cmdclass={"egg_info": tagger},
     classifiers=[
         "Environment :: Console",
         "License :: OSI Approved :: Apache Software License",

From a2da92aefbbda29afe1107ed064320f9a57a87db Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Nov 2023 00:59:44 +0000
Subject: [PATCH 091/165] Bump mypy from 1.6.1 to 1.7.0

Bumps [mypy](https://github.com/python/mypy) from 1.6.1 to 1.7.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.6.1...v1.7.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 1019b08..b37a768 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.6.1
+mypy==1.7.0
 types-setuptools
 types-requests
 types-PyYAML

From 1987ca25d76975e41974bea3a34591051ece6379 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Nov 2023 07:08:54 +0000
Subject: [PATCH 092/165] Update black requirement from ~=23.10 to ~=23.11

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.10.0...23.11.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 789ecd2..efaf2fa 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.10
+black ~= 23.11
 pylint
 pep257
 pydocstyle

From bb3e2e116c50977cfad97cc54a4a1a04f216218a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 24 Nov 2023 00:13:17 +0000
Subject: [PATCH 093/165] Bump mypy from 1.7.0 to 1.7.1

Bumps [mypy](https://github.com/python/mypy) from 1.7.0 to 1.7.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.7.0...v1.7.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index b37a768..988f5d4 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.7.0
+mypy==1.7.1
 types-setuptools
 types-requests
 types-PyYAML

From e927b1d13b39dc11da65053ce738326cbd7be2a5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 29 Nov 2023 00:30:16 +0000
Subject: [PATCH 094/165] Bump sphinx-rtd-theme from 1.3.0 to 2.0.0

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.3.0 to 2.0.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.3.0...2.0.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index bd71cd1..1cdb96e 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==1.3.0
+sphinx-rtd-theme==2.0.0
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 80348edd96e5bc68e9f16ca57e5caa204c08b27a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 7 Dec 2023 00:30:51 +0000
Subject: [PATCH 095/165] Bump actions/setup-python from 4 to 5

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 9222ed9..08df513 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -34,7 +34,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -84,7 +84,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -114,7 +114,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.12"
           cache: pip

From 304270098defe5d3e55dbb309a715ff1e5ff2c73 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 8 Dec 2023 15:58:05 +0100
Subject: [PATCH 096/165] remove use of deprecated pkg-resources

---
 cwltest/argparser.py | 13 ++++++-------
 cwltest/utils.py     | 19 ++++++++++++-------
 docs/conf.py         |  4 ++--
 requirements.txt     |  1 +
 tests/util.py        | 17 ++++++++++++-----
 5 files changed, 33 insertions(+), 21 deletions(-)

diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index 819c553..2f7c7d9 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -1,8 +1,7 @@
 """Command line argument parsing for cwltest."""
 import argparse
 import sys
-
-import pkg_resources
+from importlib.metadata import PackageNotFoundError, version
 
 from cwltest import DEFAULT_TIMEOUT
 
@@ -107,10 +106,10 @@ def arg_parser() -> argparse.ArgumentParser:
         help="Create JSON badges and store them in this directory.",
     )
 
-    if pkg := pkg_resources.require("cwltest"):
-        ver = f"{sys.argv[0]} {pkg[0].version}"
-    else:
-        ver = "{} {}".format(sys.argv[0], "unknown version")
-    parser.add_argument("--version", action="https://github.com/version", version=ver)
+    try:
+        ver = version("cwltest")
+    except PackageNotFoundError:
+        ver = "unknown version"
+    parser.add_argument("--version", action="https://github.com/version", version=f"{sys.argv[0]} {ver}")
 
     return parser
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 60413ad..d4c0570 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -22,7 +22,6 @@
 )
 
 import junit_xml
-import pkg_resources
 import ruamel.yaml.scanner
 import schema_salad.avro
 import schema_salad.ref_resolver
@@ -32,8 +31,15 @@
 from ruamel.yaml.scalarstring import ScalarString
 from schema_salad.exceptions import ValidationException
 
+if sys.version_info >= (3, 9):
+    from importlib.resources import as_file, files
+else:
+    from importlib_resources import as_file, files
+
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, templock
 
+__all__ = ["files", "as_file"]
+
 
 class CWLTestConfig:
     """Store configuration values for cwltest."""
@@ -167,12 +173,11 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
 
     This also processes $import directives.
     """
-    schema_resource = pkg_resources.resource_stream(__name__, "cwltest-schema.yml")
-    cache: Optional[Dict[str, Union[str, Graph, bool]]] = {
-        "https://w3id.org/cwl/cwltest/cwltest-schema.yml": schema_resource.read().decode(
-            "utf-8"
-        )
-    }
+    schema_resource = files("cwltest").joinpath("cwltest-schema.yml")
+    with schema_resource.open("r", encoding="utf-8") as fp:
+        cache: Optional[Dict[str, Union[str, Graph, bool]]] = {
+            "https://w3id.org/cwl/cwltest/cwltest-schema.yml": fp.read()
+        }
     (
         document_loader,
         avsc_names,
diff --git a/docs/conf.py b/docs/conf.py
index a598182..f5a7a2e 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -80,9 +80,9 @@
 html_static_path = ["_static"]
 
 
-from pkg_resources import get_distribution
+from importlib.metadata import version as metadata_version
 
-release = get_distribution("cwltest").version
+release = metadata_version("cwltest")
 version = ".".join(release.split(".")[:2])
 
 autoapi_dirs = ["../cwltest"]
diff --git a/requirements.txt b/requirements.txt
index bce0adf..b6c5a46 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,3 +2,4 @@ schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
 pytest >= 7, < 8
 defusedxml
+importlib_resources>=1.4;python_version<'3.9'
diff --git a/tests/util.py b/tests/util.py
index 002fa53..20cd99a 100644
--- a/tests/util.py
+++ b/tests/util.py
@@ -1,8 +1,12 @@
+"""Test functions."""
+import atexit
 import os
 import subprocess  # nosec
+from contextlib import ExitStack
+from pathlib import Path
 from typing import List, Tuple
 
-from pkg_resources import Requirement, ResolutionError, resource_filename
+from cwltest.utils import as_file, files
 
 
 def get_data(filename: str) -> str:
@@ -12,12 +16,15 @@ def get_data(filename: str) -> str:
     # joining path
     filepath = None
     try:
-        filepath = resource_filename(Requirement.parse("cwltest"), filename)
-    except ResolutionError:
+        file_manager = ExitStack()
+        atexit.register(file_manager.close)
+        traversable = files("cwltest") / filename
+        filepath = file_manager.enter_context(as_file(traversable))
+    except ModuleNotFoundError:
         pass
     if not filepath or not os.path.isfile(filepath):
-        filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
-    return filepath
+        filepath = Path(os.path.dirname(__file__)) / ".." / filename
+    return str(filepath.resolve())
 
 
 def run_with_mock_cwl_runner(args: List[str]) -> Tuple[int, str, str]:

From aade76aa2bd66ff4f63763e6b14dc5d35582588b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 8 Dec 2023 17:13:24 +0100
Subject: [PATCH 097/165] cleanup

---
 mypy-stubs/rdflib/query.pyi | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mypy-stubs/rdflib/query.pyi b/mypy-stubs/rdflib/query.pyi
index 73f4008..981fe12 100644
--- a/mypy-stubs/rdflib/query.pyi
+++ b/mypy-stubs/rdflib/query.pyi
@@ -31,12 +31,12 @@ class Result:
         source: IO[Any] | None = ...,
         format: str | None = ...,
         content_type: str | None = ...,
-        **kwargs: Any
+        **kwargs: Any,
     ) -> Result: ...
     def serialize(
         self,
         destination: str | IO[Any] | None = ...,
         encoding: str = ...,
         format: str = ...,
-        **args: Any
+        **args: Any,
     ) -> Optional[bytes]: ...

From 555a5b513bf5c6433b40d066a655309373b0d48b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 8 Dec 2023 16:19:04 +0100
Subject: [PATCH 098/165] covert setup.py to setup.cfg

Thank you https://pypi.org/project/setuptools-py2cfg/ !
---
 .github/workflows/ci-tests.yml |  4 +--
 Makefile                       | 15 ++++----
 README.rst                     |  2 +-
 dev-requirements.txt           |  5 +--
 pyproject.toml                 |  9 +++++
 setup.cfg                      | 47 +++++++++++++++++++++++-
 setup.py                       | 66 ----------------------------------
 tox.ini                        |  4 +--
 8 files changed, 70 insertions(+), 82 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 08df513..d52fa4f 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -46,7 +46,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install "tox<4" "tox-gh-actions<3"
+          pip install "tox>4,<5" "tox-gh-actions>3"
 
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
@@ -96,7 +96,7 @@ jobs:
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
-          pip install "tox<4" "tox-gh-actions<3"
+          pip install "tox>4,<5" "tox-gh-actions>3"
 
       - if: ${{ matrix.step == 'pydocstyle' && github.event_name == 'pull_request'}}
         name: Create local branch for diff-quality for PRs
diff --git a/Makefile b/Makefile
index 16b3c52..c5771b5 100644
--- a/Makefile
+++ b/Makefile
@@ -25,7 +25,7 @@ PACKAGE=cwltest
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
-PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
+PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py)
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
@@ -75,7 +75,6 @@ docs: FORCE
 ## clean                  : clean up all temporary / machine-generated files
 clean: FORCE
 	rm -f ${MODILE}/*.pyc tests/*.pyc
-	python setup.py clean --all || true
 	rm -Rf .coverage\.* .coverage
 	rm -f diff-cover.html
 
@@ -93,7 +92,7 @@ pydocstyle: $(PYSOURCES)
 	pydocstyle --add-ignore=D100,D101,D102,D103 $^ || true
 
 pydocstyle_report.txt: $(PYSOURCES)
-	pydocstyle setup.py $^ > $@ 2>&1 || true
+	pydocstyle $^ > $@ 2>&1 || true
 
 ## diff_pydocstyle_report : check Python docstring style for changed files only
 diff_pydocstyle_report: pydocstyle_report.txt
@@ -104,11 +103,11 @@ codespell:
 	codespell -w $(shell git ls-files | grep -v mypy-stubs | grep -v gitignore)
 
 ## format                 : check/fix all code indentation and formatting (runs black)
-format: $(PYSOURCES) mypy-stubs
-	black --exclude cwltest/_version.py $^
+format: $(filter-out cwltest/_version.py,$(PYSOURCES)) mypy-stubs
+	black $^
 
-format-check: $(PYSOURCES) mypy-stubs
-	black --diff --check --exclude cwltest/_version.py $^
+format-check: $(filter-out cwltest/_version.py,$(PYSOURCES)) mypy-stubs
+	black --diff --check $^
 
 ## pylint                 : run static code analysis on Python code
 pylint: $(PYSOURCES)
@@ -165,7 +164,7 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: $(filter-out setup.py,$(PYSOURCES))
+mypy: $(PYSOURCES)
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
diff --git a/README.rst b/README.rst
index a20438f..c4c50dd 100644
--- a/README.rst
+++ b/README.rst
@@ -58,7 +58,7 @@ Or from source
 .. code:: bash
 
   git clone https://github.com/common-workflow-language/cwltest.git
-  cd cwltest && python setup.py install
+  cd cwltest && pip install  .
 
 ***********************
 Run on the command line
diff --git a/dev-requirements.txt b/dev-requirements.txt
index efaf2fa..14263d6 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -4,8 +4,8 @@ pylint
 pep257
 pydocstyle
 flake8
-tox < 5
-tox-pyenv
+tox >4, < 5
+virtualenv-pyenv
 isort
 wheel
 autoflake
@@ -13,3 +13,4 @@ flake8-bugbear
 pyupgrade
 bandit
 auto-walrus
+build
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..81d4f6e
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,9 @@
+[build-system]
+requires = [
+    "setuptools>=45",
+    "setuptools_scm[toml]>=8.0.4,<9",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "cwltest/_version.py"
diff --git a/setup.cfg b/setup.cfg
index cf9fe0a..d61885f 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,39 @@
 [aliases]
-test=pytest
+test = pytest
+
+[metadata]
+name = cwltest
+author = Common workflow language working group
+author_email = common-workflow-language@googlegroups.com
+license = Apache 2.0
+description = Common Workflow Language testing framework
+url = https://github.com/common-workflow-language/cwltest
+download_url = https://github.com/common-workflow-language/cwltest
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+classifiers =
+    Environment :: Console
+    License :: OSI Approved :: Apache Software License
+    Operating System :: POSIX
+    Operating System :: MacOS :: MacOS X
+    Development Status :: 5 - Production/Stable
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Typing :: Typed
+
+[options]
+package_dir =
+    cwltest.tests = tests
+packages = cwltest, cwltest.tests
+zip_safe = True
+setup_requires = setuptools_scm>=8.0.4,<9
+install_requires = file: requirements.txt
+include_package_data = True
+python_requires = >=3.8,<3.13
+test_suite = tests
 
 [tool:isort]
 multi_line_output = 3
@@ -7,3 +41,14 @@ include_trailing_comma = True
 force_grid_wrap = 0
 use_parentheses = True
 line_length = 88
+
+[options.entry_points]
+console_scripts = cwltest=cwltest.main:main
+pytest11 = cwl = cwltest.plugin [pytest-plugin]
+
+[options.extras_require]
+pytest-plugin = pytest
+
+[options.package_data]
+cwltest = py.typed
+tests = test-data/*
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 13bd5ec..0000000
--- a/setup.py
+++ /dev/null
@@ -1,66 +0,0 @@
-#!/usr/bin/env python3
-import os
-import pathlib
-import sys
-from typing import List
-
-from setuptools import setup
-
-SETUP_DIR = os.path.dirname(__file__)
-README = os.path.join(SETUP_DIR, "README.rst")
-
-needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
-pytest_runner: List[str] = ["pytest < 8", "pytest-runner"] if needs_pytest else []
-
-setup(
-    name="cwltest",
-    description="Common Workflow Language testing framework",
-    long_description=open(README).read(),
-    long_description_content_type="text/x-rst",
-    author="Common workflow language working group",
-    author_email="common-workflow-language@googlegroups.com",
-    url="https://github.com/common-workflow-language/cwltest",
-    download_url="https://github.com/common-workflow-language/cwltest",
-    license="Apache 2.0",
-    python_requires=">=3.8,<3.13",
-    use_scm_version=True,
-    setup_requires=pytest_runner + ["setuptools_scm>=8.0.4,<9"],
-    packages=["cwltest", "cwltest.tests"],
-    package_dir={"cwltest.tests": "tests"},
-    package_data={"cwltest": ["py.typed"], "tests": ["test-data/*"]},
-    include_package_data=True,
-    install_requires=open(
-        os.path.join(pathlib.Path(__file__).parent, "requirements.txt")
-    )
-    .read()
-    .splitlines(),
-    test_suite="tests",
-    tests_require=open(
-        os.path.join(pathlib.Path(__file__).parent, "test-requirements.txt")
-    )
-    .read()
-    .splitlines(),
-    extras_require={"pytest-plugin": ["pytest"]},
-    entry_points={
-        "console_scripts": [
-            "cwltest=cwltest.main:main",
-        ],
-        "pytest11": [
-            "cwl = cwltest.plugin [pytest-plugin]",
-        ],
-    },
-    zip_safe=True,
-    classifiers=[
-        "Environment :: Console",
-        "License :: OSI Approved :: Apache Software License",
-        "Operating System :: POSIX",
-        "Operating System :: MacOS :: MacOS X",
-        "Development Status :: 5 - Production/Stable",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Typing :: Typed",
-    ],
-)
diff --git a/tox.ini b/tox.ini
index a41f0f0..3130f29 100644
--- a/tox.ini
+++ b/tox.ini
@@ -8,6 +8,7 @@ envlist =
   py312-pydocstyle
 
 skip_missing_interpreters = True
+isolated_build = True
 
 [pytest]
 addopts = -p pytester -n auto
@@ -46,13 +47,12 @@ deps =
   py3{8,9,10,11,12}-bandit: bandit
   py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
 
-setenv =
+set_env =
   py3{8,3,10,11,12}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
-
 commands =
   py3{8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
   py3{8,9,10,11,12}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}

From 7286f592f7edbb10bbb90304aec88b60986ba11d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 8 Dec 2023 17:08:06 +0100
Subject: [PATCH 099/165] convert setup.cfg to pyproject.toml

Thank you https://pypi.org/project/ini2toml/ !
---
 pyproject.toml | 66 ++++++++++++++++++++++++++++++++++++++++++++++++--
 setup.cfg      | 54 -----------------------------------------
 2 files changed, 64 insertions(+), 56 deletions(-)
 delete mode 100644 setup.cfg

diff --git a/pyproject.toml b/pyproject.toml
index 81d4f6e..ddc54be 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,71 @@
 [build-system]
 requires = [
-    "setuptools>=45",
-    "setuptools_scm[toml]>=8.0.4,<9",
+    "setuptools>=61.2",
+    "setuptools_scm>=8.0.4,<9",
 ]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "cwltest"
+authors = [{name = "Common workflow language working group", email = "common-workflow-language@googlegroups.com"}]
+license = {text = "Apache 2.0"}
+description = "Common Workflow Language testing framework"
+classifiers = [
+    "Environment :: Console",
+    "Framework :: Pytest",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS :: MacOS X",
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Typing :: Typed",
+]
+requires-python = ">=3.8,<3.13"
+dynamic = ["version", "dependencies"]
+
+[project.readme]
+file = "README.rst"
+content-type = "text/x-rst"
+
+[project.urls]
+Homepage = "https://github.com/common-workflow-language/cwltest"
+Download = "https://github.com/common-workflow-language/cwltest"
+
+[project.entry-points.pytest11]
+cwl = "cwltest.plugin"
+
+[project.optional-dependencies]
+pytest-plugin = ["pytest"]
+
+[project.scripts]
+cwltest = "cwltest.main:main"
+
+[tool.aliases]
+test = "pytest"
+
+[tool.setuptools]
+package-dir = {"cwltest.tests" = "tests"}
+packages = ["cwltest", "cwltest.tests"]
+zip-safe = true
+include-package-data = true
+
+[tool.setuptools.package-data]
+cwltest = ["py.typed"]
+tests = ["test-data/*"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+
+[tool.isort]
+multi_line_output = "3"
+include_trailing_comma = "True"
+force_grid_wrap = "0"
+use_parentheses = "True"
+line_length = "88"
+
 [tool.setuptools_scm]
 write_to = "cwltest/_version.py"
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index d61885f..0000000
--- a/setup.cfg
+++ /dev/null
@@ -1,54 +0,0 @@
-[aliases]
-test = pytest
-
-[metadata]
-name = cwltest
-author = Common workflow language working group
-author_email = common-workflow-language@googlegroups.com
-license = Apache 2.0
-description = Common Workflow Language testing framework
-url = https://github.com/common-workflow-language/cwltest
-download_url = https://github.com/common-workflow-language/cwltest
-long_description = file: README.rst
-long_description_content_type = text/x-rst
-classifiers =
-    Environment :: Console
-    License :: OSI Approved :: Apache Software License
-    Operating System :: POSIX
-    Operating System :: MacOS :: MacOS X
-    Development Status :: 5 - Production/Stable
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    Programming Language :: Python :: 3.12
-    Typing :: Typed
-
-[options]
-package_dir =
-    cwltest.tests = tests
-packages = cwltest, cwltest.tests
-zip_safe = True
-setup_requires = setuptools_scm>=8.0.4,<9
-install_requires = file: requirements.txt
-include_package_data = True
-python_requires = >=3.8,<3.13
-test_suite = tests
-
-[tool:isort]
-multi_line_output = 3
-include_trailing_comma = True
-force_grid_wrap = 0
-use_parentheses = True
-line_length = 88
-
-[options.entry_points]
-console_scripts = cwltest=cwltest.main:main
-pytest11 = cwl = cwltest.plugin [pytest-plugin]
-
-[options.extras_require]
-pytest-plugin = pytest
-
-[options.package_data]
-cwltest = py.typed
-tests = test-data/*

From 4eed3441175cf2930a23ede86887eaab002735a7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 13 Dec 2023 00:37:29 +0000
Subject: [PATCH 100/165] Update black requirement from ~=23.11 to ~=23.12

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.11.0...23.12.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 14263d6..be07d6a 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.11
+black ~= 23.12
 pylint
 pep257
 pydocstyle

From 8d5df9b140c5b8fa98c7b362403ce269bcd01717 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 14 Dec 2023 00:56:15 +0000
Subject: [PATCH 101/165] Bump github/codeql-action from 2 to 3

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/codeql-analysis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index e759476..47cc649 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -32,9 +32,9 @@ jobs:
       
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: python
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

From 8cf6bf770202b0a4377f59298ebb213ef4033271 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 22 Dec 2023 00:43:33 +0000
Subject: [PATCH 102/165] Bump mypy from 1.7.1 to 1.8.0

Bumps [mypy](https://github.com/python/mypy) from 1.7.1 to 1.8.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.7.1...v1.8.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 988f5d4..a9650a3 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.7.1
+mypy==1.8.0
 types-setuptools
 types-requests
 types-PyYAML

From 5ed25ece7d8a816ab507b62edbc7cfc903c3c952 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 18 Jan 2024 00:35:11 +0000
Subject: [PATCH 103/165] Bump actions/cache from 3 to 4

Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index d52fa4f..691a145 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -50,7 +50,7 @@ jobs:
 
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: .mypy_cache/${{ env.py-semver }}
           key: mypy-${{ env.py-semver }}

From 31712c8d34e9bb5a24b2cdef1585eb98dad498a0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Jan 2024 00:03:45 +0000
Subject: [PATCH 104/165] Update black requirement from ~=23.12 to ~=24.1

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.12.0...24.1.1)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index be07d6a..ef6b5ae 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 23.12
+black ~= 24.1
 pylint
 pep257
 pydocstyle

From dfacef5c0fa70ae67e055628eef6f7e796eaba70 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 29 Jan 2024 10:24:28 +0000
Subject: [PATCH 105/165] Update pytest requirement from <8,>=7 to >=7,<9

Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.0.0...8.0.0)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt      | 2 +-
 test-requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index b6c5a46..16577e2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
-pytest >= 7, < 8
+pytest >= 7, < 9
 defusedxml
 importlib_resources>=1.4;python_version<'3.9'
diff --git a/test-requirements.txt b/test-requirements.txt
index 6f0a196..c186dac 100644
--- a/test-requirements.txt
+++ b/test-requirements.txt
@@ -1,5 +1,5 @@
 cwlref-runner
 cwltool
-pytest >= 7, < 8
+pytest >= 7, < 9
 pytest-cov
 pytest-xdist

From 370f4778982ad55b5583a3adbdf6acfbce081793 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 29 Jan 2024 15:51:35 +0100
Subject: [PATCH 106/165] adjust types for Pytest 8.x; retaining compatability
 with Pytest 7.x

---
 cwltest/plugin.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 40da5f5..1a5e5b1 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -33,6 +33,7 @@
     from _pytest.config import PytestPluginManager
     from _pytest.config.argparsing import Parser as PytestParser
     from _pytest.nodes import Node
+    from pluggy import HookCaller
 
 
 class TestRunner(Protocol):
@@ -58,7 +59,7 @@ def _get_comma_separated_option(config: "Config", name: str) -> List[str]:
 def _run_test_hook_or_plain(
     test: Dict[str, str],
     config: utils.CWLTestConfig,
-    hook: TestRunner,
+    hook: "HookCaller",
 ) -> utils.TestResult:
     """Run tests using a provided pytest_cwl_execute_test hook or the --cwl-runner."""
     processfile, jobfile = utils.prepare_test_paths(test, config.basedir)

From 7493f2ea6c96199fa7fd5674f6792ddb11ce79ec Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 13 Feb 2024 00:26:32 +0000
Subject: [PATCH 107/165] Update black requirement from ~=24.1 to ~=24.2

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.1.0...24.2.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index ef6b5ae..fc86991 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 24.1
+black ~= 24.2
 pylint
 pep257
 pydocstyle

From 4f6e030d532b06753da04cbb8c4fba441307224d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 4 Mar 2024 12:20:36 +0100
Subject: [PATCH 108/165] remove deprecated LEGACY_PATH support.

Pytest 8.1.0 removed support for that.

No need to change our supported Pytest range, the modern pathlib.Path
support has been there since Pytest 7.0
---
 Makefile              | 2 +-
 cwltest/argparser.py  | 1 +
 cwltest/plugin.py     | 6 +++---
 docs/pytest.rst       | 4 ++--
 tests/test_prepare.py | 1 +
 tests/util.py         | 1 +
 6 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index c5771b5..3207ee5 100644
--- a/Makefile
+++ b/Makefile
@@ -29,7 +29,7 @@ PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py)
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.4.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.5.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 
 ## all                    : default task (install in dev mode)
diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index 2f7c7d9..888a491 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -1,4 +1,5 @@
 """Command line argument parsing for cwltest."""
+
 import argparse
 import sys
 from importlib.metadata import PackageNotFoundError, version
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 1a5e5b1..75453a8 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -1,4 +1,5 @@
 """Discovers CWL test files and converts them to pytest.Items."""
+
 import argparse
 import json
 import os
@@ -27,7 +28,6 @@
 
 if TYPE_CHECKING:
     from _pytest._code.code import ExceptionInfo, _TracebackStyle
-    from _pytest.compat import LEGACY_PATH
     from _pytest.config import Config
     from _pytest.config import Config as PytestConfig
     from _pytest.config import PytestPluginManager
@@ -198,7 +198,7 @@ def repr_failure(
 
     def reportinfo(self) -> Tuple[Union["os.PathLike[str]", str], Optional[int], str]:
         """Status report."""
-        return self.fspath, 0, "cwl test: %s" % self.name
+        return self.path, 0, "cwl test: %s" % self.name
 
 
 class CWLYamlFile(pytest.File):
@@ -342,7 +342,7 @@ def _doc_options() -> argparse.ArgumentParser:
 
 
 def pytest_collect_file(
-    file_path: Path, path: "LEGACY_PATH", parent: pytest.Collector
+    file_path: Path, parent: pytest.Collector
 ) -> Optional[pytest.Collector]:
     """Is this file for us."""
     if (
diff --git a/docs/pytest.rst b/docs/pytest.rst
index 195d392..b8d0ad9 100644
--- a/docs/pytest.rst
+++ b/docs/pytest.rst
@@ -2,8 +2,8 @@
 Pytest plugin
 *************
 
-``cwltest`` can also be used as a Pytest plugin. The CWL test filename must
-end with ``.cwltest.yml`` or ``.cwltest.yaml``.
+``cwltest`` can also be used as a Pytest 7.x or 8.x plugin. The CWL test
+filename must end with ``.cwltest.yml`` or ``.cwltest.yaml``.
 
 In this case, the simple command::
 
diff --git a/tests/test_prepare.py b/tests/test_prepare.py
index 9c3c3c1..8112ef6 100644
--- a/tests/test_prepare.py
+++ b/tests/test_prepare.py
@@ -1,4 +1,5 @@
 """Test prepare_test_command()"""
+
 import os
 
 from cwltest import utils
diff --git a/tests/util.py b/tests/util.py
index 20cd99a..3c5cff3 100644
--- a/tests/util.py
+++ b/tests/util.py
@@ -1,4 +1,5 @@
 """Test functions."""
+
 import atexit
 import os
 import subprocess  # nosec

From f43b98db755e14656be9e19e214e5b2bed5a765d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Mar 2024 00:40:28 +0000
Subject: [PATCH 109/165] Bump mypy from 1.8.0 to 1.9.0

Bumps [mypy](https://github.com/python/mypy) from 1.8.0 to 1.9.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.8.0...1.9.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index a9650a3..9eaba5e 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.8.0
+mypy==1.9.0
 types-setuptools
 types-requests
 types-PyYAML

From 3823ee83ed269337abcee291abe46f0ce7582266 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 15 Apr 2024 00:56:06 +0000
Subject: [PATCH 110/165] Update black requirement from ~=24.2 to ~=24.4

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.2.0...24.4.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index fc86991..4280a59 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 24.2
+black ~= 24.4
 pylint
 pep257
 pydocstyle

From e36af9ec018701bf0cfb4b91c8cace48dbe9d14d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 25 Apr 2024 00:53:24 +0000
Subject: [PATCH 111/165] Bump mypy from 1.9.0 to 1.10.0

Bumps [mypy](https://github.com/python/mypy) from 1.9.0 to 1.10.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/1.9.0...v1.10.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 9eaba5e..fbaccfc 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.9.0
+mypy==1.10.0
 types-setuptools
 types-requests
 types-PyYAML

From 01a82353195e8e7ccd88f616ef5629b3369f17c6 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Apr 2024 13:45:43 +0300
Subject: [PATCH 112/165] mark this editing of a mutable while looping as okay

---
 cwltest/main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cwltest/main.py b/cwltest/main.py
index f93a279..321a9b1 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -132,7 +132,7 @@ def main() -> int:
     for t in tests:
         if t.get("label"):
             logger.warning("The `label` field is deprecated. Use `id` field instead.")
-            t["short_name"] = t["label"]
+            t["short_name"] = t["label"]  # noqa: B909
         elif t.get("id"):
             if isinstance(t.get("id"), str):
                 t["short_name"] = utils.shortname(t["id"])

From 2eb15377fc5829761e1efb0d6cc66f163ba144aa Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 25 Apr 2024 13:49:01 +0300
Subject: [PATCH 113/165] mypy: simplify configuration

---
 mypy.ini | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

diff --git a/mypy.ini b/mypy.ini
index 6a442f8..11917ac 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -1,24 +1,10 @@
 [mypy]
+strict = True
 show_error_context = true
 show_column_numbers = true
 show_error_codes = true
 pretty = true
-
-# --strict options as of mypy 0.910
-warn_unused_configs = True
-disallow_any_generics = True
-disallow_subclassing_any = True
-disallow_untyped_calls = True
-disallow_untyped_defs = True
-disallow_incomplete_defs = True
-check_untyped_defs = True
-disallow_untyped_decorators = True
-no_implicit_optional = True
-warn_redundant_casts = True
-warn_unused_ignores = True
-warn_return_any = True
-implicit_reexport = False
-strict_equality = True
+warn_unreachable = True
 
 [mypy-ruamel.*]
 ignore_errors = True

From 7266ad44c871524c5ac9e4b0934b5014d001f5d4 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sat, 13 Apr 2024 09:04:37 +0000
Subject: [PATCH 114/165] Handling invalid output object from engines

---
 cwltest/utils.py                  | 17 +++++++++++++++++
 tests/test-data/dummy-executor.sh |  3 +++
 tests/test-data/empty.yml         |  1 +
 tests/test-data/nothing.yml       | 10 ++++++++++
 tests/test-data/true.cwl          |  5 +++++
 tests/test_invalid_outputs.py     | 17 +++++++++++++++++
 tests/util.py                     |  9 ++++++---
 7 files changed, 59 insertions(+), 3 deletions(-)
 create mode 100755 tests/test-data/dummy-executor.sh
 create mode 100644 tests/test-data/empty.yml
 create mode 100644 tests/test-data/nothing.yml
 create mode 100644 tests/test-data/true.cwl
 create mode 100644 tests/test_invalid_outputs.py

diff --git a/cwltest/utils.py b/cwltest/utils.py
index d4c0570..012e286 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -422,6 +422,23 @@ def run_test_plain(
             " ".join([shlex.quote(tc) for tc in test_command]),
         )
         raise
+    except json.JSONDecodeError:
+        logger.error(
+            """Test %s failed: %s""",
+            number,
+            " ".join([shlex.quote(tc) for tc in test_command]),
+        )
+        logger.error(test.get("doc", "").replace("\n", " ").strip())
+        invalid_json_msg = "Output is not a valid JSON document: '%s'" % outstr
+        logger.error(invalid_json_msg)
+        return TestResult(
+            1,
+            outstr,
+            outerr,
+            duration,
+            config.classname,
+            invalid_json_msg,
+        )
     except subprocess.TimeoutExpired:
         logger.error(
             """Test %s timed out: %s""",
diff --git a/tests/test-data/dummy-executor.sh b/tests/test-data/dummy-executor.sh
new file mode 100755
index 0000000..ca3a674
--- /dev/null
+++ b/tests/test-data/dummy-executor.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+echo "it is not JSON format!"
diff --git a/tests/test-data/empty.yml b/tests/test-data/empty.yml
new file mode 100644
index 0000000..0967ef4
--- /dev/null
+++ b/tests/test-data/empty.yml
@@ -0,0 +1 @@
+{}
diff --git a/tests/test-data/nothing.yml b/tests/test-data/nothing.yml
new file mode 100644
index 0000000..1e860a7
--- /dev/null
+++ b/tests/test-data/nothing.yml
@@ -0,0 +1,10 @@
+- job: empty.yml
+  tool: true.cwl
+  output: {}
+  id: do_nothing
+  doc: Example of doing nothing
+- job: empty.yml
+  tool: true.cwl
+  output: {}
+  id: do_nothing2
+  doc: Example of doing nothing more
diff --git a/tests/test-data/true.cwl b/tests/test-data/true.cwl
new file mode 100644
index 0000000..f8e5e7a
--- /dev/null
+++ b/tests/test-data/true.cwl
@@ -0,0 +1,5 @@
+class: CommandLineTool
+cwlVersion: v1.0
+inputs: {}
+outputs: {}
+baseCommand: ["true"]
diff --git a/tests/test_invalid_outputs.py b/tests/test_invalid_outputs.py
new file mode 100644
index 0000000..d57182d
--- /dev/null
+++ b/tests/test_invalid_outputs.py
@@ -0,0 +1,17 @@
+from pathlib import Path
+
+import schema_salad.ref_resolver
+
+from .util import get_data, run_with_mock_cwl_runner
+
+
+def test_invalid_outputs(tmp_path: Path) -> None:
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(get_data("tests/test-data/nothing.yml")),
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(
+        args, get_data("tests/test-data/dummy-executor.sh")
+    )
+    assert error_code == 1
+    assert "0 tests passed, 2 failures, 0 unsupported features" in stderr
diff --git a/tests/util.py b/tests/util.py
index 3c5cff3..9394612 100644
--- a/tests/util.py
+++ b/tests/util.py
@@ -5,7 +5,7 @@
 import subprocess  # nosec
 from contextlib import ExitStack
 from pathlib import Path
-from typing import List, Tuple
+from typing import List, Optional, Tuple
 
 from cwltest.utils import as_file, files
 
@@ -28,9 +28,12 @@ def get_data(filename: str) -> str:
     return str(filepath.resolve())
 
 
-def run_with_mock_cwl_runner(args: List[str]) -> Tuple[int, str, str]:
+def run_with_mock_cwl_runner(
+    args: List[str], cwl_runner: Optional[str] = None
+) -> Tuple[int, str, str]:
     """Bind a mock cwlref-runner implementation to cwltest."""
-    cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
+    if cwl_runner is None:
+        cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
     process = subprocess.Popen(  # nosec
         ["cwltest", "--tool", cwl_runner] + args,
         stdout=subprocess.PIPE,

From 2b1ac8081006af630a701a0cf1f16828616ef569 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Fri, 17 May 2024 13:02:15 +0200
Subject: [PATCH 115/165] Generate markdown reports to badgedir for each tag

---
 .flake8                                       |   2 +
 cwltest/argparser.py                          |   3 +
 cwltest/main.py                               |  18 +-
 cwltest/plugin.py                             |  50 ++++-
 cwltest/utils.py                              | 188 ++++++++++++++++--
 tests/test-data/badgedir.yaml                 |  38 ++++
 .../conformance_test_v1.2.cwltest.yaml        |   8 +-
 tests/test-data/mock_cwl_runner.py            |   2 +-
 .../test-data/v1.0/null-expression2-tool.cwl  |  14 ++
 tests/test_badgedir.py                        |  98 +++++++++
 tests/test_plugin.py                          |   3 +-
 11 files changed, 394 insertions(+), 30 deletions(-)
 create mode 100644 tests/test-data/badgedir.yaml
 create mode 100644 tests/test-data/v1.0/null-expression2-tool.cwl
 create mode 100644 tests/test_badgedir.py

diff --git a/.flake8 b/.flake8
index ed7277f..60ef4d0 100644
--- a/.flake8
+++ b/.flake8
@@ -5,3 +5,5 @@ select = B,C,E,F,W,T4
 extend-ignore = E501,B905
 # when Python 3.10 is the minimum version, re-enable check B905 for zip + strict
 extend-select = B9
+per-file-ignores=
+    ./tests/test_badgedir.py:B950
diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index 888a491..1d2458c 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -18,6 +18,9 @@ def arg_parser() -> argparse.ArgumentParser:
     parser.add_argument(
         "--basedir", type=str, help="Basedir to use for tests", default="."
     )
+    parser.add_argument(
+        "--baseuri", type=str, help="Base URI to use links in the report", default=None
+    )
     parser.add_argument("-l", action="https://github.com/store_true", help="List tests then exit")
     parser.add_argument(
         "-n", type=str, default=None, help="Run specific tests, format is 1,3-6,9"
diff --git a/cwltest/main.py b/cwltest/main.py
index 321a9b1..4909c89 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -13,7 +13,7 @@
 import schema_salad.ref_resolver
 import schema_salad.schema
 from cwltest.argparser import arg_parser
-from cwltest.utils import CWLTestConfig, TestResult
+from cwltest.utils import CWLTestConfig, CWLTestReport, TestResult
 from schema_salad.exceptions import ValidationException
 
 from cwltest import logger, utils
@@ -58,7 +58,11 @@ def _run_test(
     sys.stderr.flush()
     config = CWLTestConfig(
         basedir=args.basedir,
+        test_baseuri=args.baseuri,
+        test_basedir=args.test_basedir,
         classname=args.classname,
+        entry=args.test,
+        entry_line=test["line"],
         tool=args.tool,
         args=args.args,
         testargs=args.testargs,
@@ -96,6 +100,12 @@ def main() -> int:
         arg_parser().print_help()
         return 1
 
+    args.test_basedir = os.path.dirname(utils.absuri(args.test)) + "/"
+    if args.baseuri is None:
+        args.baseuri = "file://" + args.test_basedir
+    if not args.baseuri.endswith("/"):
+        args.baseuri = args.baseuri + "/"
+
     try:
         tests, metadata = utils.load_and_validate_tests(args.test)
     except ValidationException:
@@ -106,8 +116,8 @@ def main() -> int:
     suite_name, _ = os.path.splitext(os.path.basename(args.test))
     report: Optional[junit_xml.TestSuite] = junit_xml.TestSuite(suite_name, [])
 
-    ntotal = defaultdict(int)  # type: Dict[str, int]
-    npassed = defaultdict(int)  # type: Dict[str, int]
+    ntotal: Dict[str, int] = defaultdict(int)
+    npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
 
     if args.only_tools:
         alltests = tests
@@ -233,7 +243,7 @@ def main() -> int:
             junit_xml.to_xml_report_file(xml, [cast(junit_xml.TestSuite, report)])
 
     if args.badgedir:
-        utils.generate_badges(args.badgedir, ntotal, npassed)
+        utils.generate_badges(args.badgedir, ntotal, npassed, nfailures, nunsupported)
 
     if failures == 0 and unsupported == 0:
         logger.info("All tests passed")
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 75453a8..baa4cae 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -20,6 +20,7 @@
     Union,
     cast,
 )
+from urllib.parse import urljoin
 
 import pytest
 from cwltest.compare import CompareFail, compare
@@ -64,6 +65,13 @@ def _run_test_hook_or_plain(
     """Run tests using a provided pytest_cwl_execute_test hook or the --cwl-runner."""
     processfile, jobfile = utils.prepare_test_paths(test, config.basedir)
     start_time = time.time()
+    reltool = os.path.relpath(test["tool"], start=config.test_basedir)
+    tooluri = urljoin(config.test_baseuri, reltool)
+    if "job" in test:
+        reljob = os.path.relpath(test["job"], start=config.test_basedir)
+        joburi = urljoin(config.test_baseuri, reljob)
+    else:
+        joburi = None
     outerr = ""
     hook_out = hook(config=config, processfile=processfile, jobfile=jobfile)
     if not hook_out:
@@ -74,7 +82,14 @@ def _run_test_hook_or_plain(
     if returncode == UNSUPPORTED_FEATURE:
         if REQUIRED not in test.get("tags", ["required"]):
             return utils.TestResult(
-                UNSUPPORTED_FEATURE, outstr, "", duration, config.classname
+                UNSUPPORTED_FEATURE,
+                outstr,
+                "",
+                duration,
+                config.classname,
+                config.entry,
+                tooluri,
+                joburi,
             )
     elif returncode != 0:
         if not bool(test.get("should_fail", False)):
@@ -82,9 +97,26 @@ def _run_test_hook_or_plain(
             logger.warning(test.get("doc"))
             message = "Returned non-zero but it should be zero"
             return utils.TestResult(
-                1, outstr, outerr, duration, config.classname, message
+                1,
+                outstr,
+                outerr,
+                duration,
+                config.classname,
+                config.entry,
+                tooluri,
+                joburi,
+                message,
             )
-        return utils.TestResult(0, outstr, outerr, duration, config.classname)
+        return utils.TestResult(
+            0,
+            outstr,
+            outerr,
+            duration,
+            config.classname,
+            config.entry,
+            tooluri,
+            joburi,
+        )
     if bool(test.get("should_fail", False)):
         return utils.TestResult(
             1,
@@ -92,6 +124,9 @@ def _run_test_hook_or_plain(
             outerr,
             duration,
             config.classname,
+            config.entry,
+            tooluri,
+            joburi,
             "Test should failed, but it did not.",
         )
 
@@ -111,6 +146,9 @@ def _run_test_hook_or_plain(
         outerr,
         duration,
         config.classname,
+        config.entry,
+        tooluri,
+        joburi,
         fail_message,
     )
 
@@ -137,6 +175,10 @@ def runtest(self) -> None:
         cwl_args = self.config.getoption("cwl_args")
         config = utils.CWLTestConfig(
             basedir=self.config.getoption("cwl_basedir"),
+            test_baseuri=self.config.getoption("cwl_basedir"),
+            test_basedir=self.config.getoption("cwl_basedir"),
+            entry="tests.yaml",
+            entry_line="0",
             outdir=str(
                 self.config._tmp_path_factory.mktemp(  # type: ignore[attr-defined]
                     self.spec.get("label", "unlabled_test")
@@ -382,7 +424,7 @@ def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
         _,
     ) = utils.parse_results(results, tests)
     if cwl_badgedir := session.config.getoption("cwl_badgedir"):
-        utils.generate_badges(cwl_badgedir, ntotal, npassed)
+        utils.generate_badges(cwl_badgedir, ntotal, npassed, nfailures, nunsupported)
 
 
 def pytest_addhooks(pluginmanager: "PytestPluginManager") -> None:
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 012e286..c9ef724 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -20,6 +20,7 @@
     Union,
     cast,
 )
+from urllib.parse import urljoin
 
 import junit_xml
 import ruamel.yaml.scanner
@@ -46,7 +47,11 @@ class CWLTestConfig:
 
     def __init__(
         self,
+        entry: str,
+        entry_line: str,
         basedir: Optional[str] = None,
+        test_baseuri: Optional[str] = None,
+        test_basedir: Optional[str] = None,
         outdir: Optional[str] = None,
         classname: Optional[str] = None,
         tool: Optional[str] = None,
@@ -58,8 +63,13 @@ def __init__(
     ) -> None:
         """Initialize test configuration."""
         self.basedir: str = basedir or os.getcwd()
+        self.test_baseuri: str = test_baseuri or "file://" + self.basedir
+        self.test_basedir: str = test_basedir or self.basedir
         self.outdir: Optional[str] = outdir
         self.classname: str = classname or ""
+        self.entry = urljoin(
+            self.test_baseuri, os.path.basename(entry) + f"#L{entry_line}"
+        )
         self.tool: str = tool or "cwl-runner"
         self.args: List[str] = args or []
         self.testargs: List[str] = testargs or []
@@ -68,6 +78,20 @@ def __init__(
         self.runner_quiet: bool = runner_quiet or True
 
 
+class CWLTestReport:
+    """Encapsulate relevant test result data for a markdown report."""
+
+    def __init__(
+        self, id: str, category: List[str], entry: str, tool: str, job: Optional[str]
+    ) -> None:
+        """Initialize a CWLTestReport object."""
+        self.id = id
+        self.category = category
+        self.entry = entry
+        self.tool = tool
+        self.job = job
+
+
 class TestResult:
     """Encapsulate relevant test result data."""
 
@@ -78,6 +102,9 @@ def __init__(
         error_output: str,
         duration: float,
         classname: str,
+        entry: str,
+        tool: str,
+        job: Optional[str],
         message: str = "",
     ) -> None:
         """Initialize a TestResult object."""
@@ -87,6 +114,9 @@ def __init__(
         self.duration = duration
         self.message = message
         self.classname = classname
+        self.entry = entry
+        self.tool = tool
+        self.job = job
 
     def create_test_case(self, test: Dict[str, Any]) -> junit_xml.TestCase:
         """Create a jUnit XML test case from this test result."""
@@ -108,6 +138,25 @@ def create_test_case(self, test: Dict[str, Any]) -> junit_xml.TestCase:
             case.failure_message = self.message
         return case
 
+    def create_report_entry(self, test: Dict[str, Any]) -> CWLTestReport:
+        return CWLTestReport(
+            test.get("id", "no-id"),
+            test.get("tags", ["required"]),
+            self.entry,
+            self.tool,
+            self.job,
+        )
+
+
+def _clean_ruamel_list(obj: List[Any]) -> Any:
+    """Entrypoint to transform roundtrip loaded ruamel.yaml to plain objects."""
+    new_list = []
+    for entry in obj:
+        e: Any = _clean_ruamel(entry)
+        e["line"] = str(entry.lc.line)
+        new_list.append(e)
+    return new_list
+
 
 def _clean_ruamel(obj: Any) -> Any:
     """Transform roundtrip loaded ruamel.yaml to plain objects."""
@@ -132,13 +181,17 @@ def _clean_ruamel(obj: Any) -> Any:
 
 
 def generate_badges(
-    badgedir: str, ntotal: Dict[str, int], npassed: Dict[str, int]
+    badgedir: str,
+    ntotal: Dict[str, int],
+    npassed: Dict[str, List[CWLTestReport]],
+    nfailures: Dict[str, List[CWLTestReport]],
+    nunsupported: Dict[str, List[CWLTestReport]],
 ) -> None:
     """Generate badges with conformance levels."""
     os.mkdir(badgedir)
     for t, v in ntotal.items():
-        percent = int((npassed[t] / float(v)) * 100)
-        if npassed[t] == v:
+        percent = int((len(npassed[t]) / float(v)) * 100)
+        if len(npassed[t]) == v:
             color = "green"
         elif t == "required":
             color = "red"
@@ -156,6 +209,42 @@ def generate_badges(
                 )
             )
 
+        with open(f"{badgedir}/{t}.md", "w") as out:
+            print(f"# `{t}` tests", file=out)
+
+            print("## List of passed tests", file=out)
+            for e in npassed[t]:
+                base = f"[{shortname(e.id)}]({e.entry})"
+                tool = f"[tool]({e.tool})"
+                if e.job:
+                    arr = [tool, f"[job]({e.job})"]
+                else:
+                    arr = [tool]
+                args = ", ".join(arr)
+                print(f"- {base} ({args})", file=out)
+
+            print("## List of failed tests", file=out)
+            for e in nfailures[t]:
+                base = f"[{shortname(e.id)}]({e.entry})"
+                tool = f"[tool]({e.tool})"
+                if e.job:
+                    arr = [tool, f"[job]({e.job})"]
+                else:
+                    arr = [tool]
+                args = ", ".join(arr)
+                print(f"- {base} ({args})", file=out)
+
+            print("## List of unsupported tests", file=out)
+            for e in nunsupported[t]:
+                base = f"[{shortname(e.id)}]({e.entry})"
+                tool = f"[tool]({e.tool})"
+                if e.job:
+                    arr = [tool, f"[job]({e.job})"]
+                else:
+                    arr = [tool]
+                args = ", ".join(arr)
+                print(f"- {base} ({args})", file=out)
+
 
 def get_test_number_by_key(
     tests: List[Dict[str, str]], key: str, value: str
@@ -194,7 +283,7 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
     tests, metadata = schema_salad.schema.load_and_validate(
         document_loader, avsc_names, path, True
     )
-    tests = cast(List[Dict[str, Any]], _clean_ruamel(tests))
+    tests = cast(List[Dict[str, Any]], _clean_ruamel_list(tests))
 
     return tests, metadata
 
@@ -209,10 +298,10 @@ def parse_results(
     int,  # passed
     int,  # failures
     int,  # unsupported
-    Dict[str, int],
-    Dict[str, int],
-    Dict[str, int],
-    Dict[str, int],
+    Dict[str, int],  # total for each tag
+    Dict[str, List[CWLTestReport]],  # passed for each tag
+    Dict[str, List[CWLTestReport]],  # failures for each tag
+    Dict[str, List[CWLTestReport]],  # unsupported for each tag
     Optional[junit_xml.TestSuite],
 ]:
     """
@@ -226,12 +315,13 @@ def parse_results(
     failures = 0
     unsupported = 0
     ntotal: Dict[str, int] = defaultdict(int)
-    nfailures: Dict[str, int] = defaultdict(int)
-    nunsupported: Dict[str, int] = defaultdict(int)
-    npassed: Dict[str, int] = defaultdict(int)
+    nfailures: Dict[str, List[CWLTestReport]] = defaultdict(list)
+    nunsupported: Dict[str, List[CWLTestReport]] = defaultdict(list)
+    npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
 
     for i, test_result in enumerate(results):
         test_case = test_result.create_test_case(tests[i])
+        test_report = test_result.create_report_entry(tests[i])
         test_case.url = (
             f"cwltest:{suite_name}#{i + 1}"
             if suite_name is not None
@@ -247,21 +337,21 @@ def parse_results(
         if return_code == 0:
             passed += 1
             for t in tags:
-                npassed[t] += 1
+                npassed[t].append(test_report)
         elif return_code != 0 and return_code != UNSUPPORTED_FEATURE:
             failures += 1
             for t in tags:
-                nfailures[t] += 1
+                nfailures[t].append(test_report)
             test_case.add_failure_info(output=test_result.message)
         elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
             failures += 1
             for t in tags:
-                nfailures[t] += 1
+                nfailures[t].append(test_report)
             test_case.add_failure_info(output=test_result.message)
         elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
             unsupported += 1
             for t in tags:
-                nunsupported[t] += 1
+                nunsupported[t].append(test_report)
             test_case.add_skipped_info("Unsupported")
         else:
             raise Exception(
@@ -352,6 +442,15 @@ def run_test_plain(
     test_command: List[str] = []
     duration = 0.0
     number = "?"
+
+    reltool = os.path.relpath(test["tool"], start=config.test_basedir)
+    tooluri = urljoin(config.test_baseuri, reltool)
+    if "job" in test:
+        reljob = os.path.relpath(test["job"], start=config.test_basedir)
+        joburi = urljoin(config.test_baseuri, reljob)
+    else:
+        joburi = None
+
     if test_number is not None:
         number = str(test_number)
     process: Optional[subprocess.Popen[str]] = None
@@ -385,10 +484,26 @@ def run_test_plain(
             "tags", ["required"]
         ):
             return TestResult(
-                UNSUPPORTED_FEATURE, outstr, outerr, duration, config.classname
+                UNSUPPORTED_FEATURE,
+                outstr,
+                outerr,
+                duration,
+                config.classname,
+                config.entry,
+                tooluri,
+                joburi,
             )
         if test.get("should_fail", False):
-            return TestResult(0, outstr, outerr, duration, config.classname)
+            return TestResult(
+                0,
+                outstr,
+                outerr,
+                duration,
+                config.classname,
+                config.entry,
+                tooluri,
+                joburi,
+            )
         if test_number:
             logger.error(
                 """Test %i failed: %s""",
@@ -405,7 +520,17 @@ def run_test_plain(
             logger.error("Does not support required feature")
         else:
             logger.error("Returned non-zero")
-        return TestResult(1, outstr, outerr, duration, config.classname, str(err))
+        return TestResult(
+            1,
+            outstr,
+            outerr,
+            duration,
+            config.classname,
+            config.entry,
+            tooluri,
+            joburi,
+            str(err),
+        )
     except (ruamel.yaml.scanner.ScannerError, TypeError) as err:
         logger.error(
             """Test %s failed: %s""",
@@ -437,6 +562,9 @@ def run_test_plain(
             outerr,
             duration,
             config.classname,
+            config.entry,
+            tooluri,
+            joburi,
             invalid_json_msg,
         )
     except subprocess.TimeoutExpired:
@@ -457,6 +585,9 @@ def run_test_plain(
             outerr,
             float(cast(int, config.timeout)),
             config.classname,
+            config.entry,
+            tooluri,
+            joburi,
             "Test timed out",
         )
     finally:
@@ -480,7 +611,16 @@ def run_test_plain(
         )
         logger.warning(test.get("doc", "").replace("\n", " ").strip())
         logger.warning("Returned zero but it should be non-zero")
-        return TestResult(1, outstr, outerr, duration, config.classname)
+        return TestResult(
+            1,
+            outstr,
+            outerr,
+            duration,
+            config.classname,
+            config.entry,
+            tooluri,
+            joburi,
+        )
 
     try:
         compare(test.get("output"), out)
@@ -503,6 +643,9 @@ def run_test_plain(
         outerr,
         duration,
         config.classname,
+        config.entry,
+        tooluri,
+        joburi,
         fail_message,
     )
 
@@ -514,3 +657,10 @@ def shortname(name: str) -> str:
     It is a workaround of https://github.com/common-workflow-language/schema_salad/issues/511.
     """
     return [n for n in re.split("[/#]", name) if len(n)][-1]
+
+
+def absuri(path: str) -> str:
+    """Return an absolute URI."""
+    if "://" in path:
+        return path
+    return "file://" + os.path.abspath(path)
diff --git a/tests/test-data/badgedir.yaml b/tests/test-data/badgedir.yaml
new file mode 100644
index 0000000..80bd1bd
--- /dev/null
+++ b/tests/test-data/badgedir.yaml
@@ -0,0 +1,38 @@
+- output: {}
+  job: empty.yml
+  tool: return-0.cwl
+  id: success_w_job
+  doc: Successful test with a job file
+  tags: [ command_line_tool ]
+
+- output: {}
+  tool: return-0.cwl
+  id: success_wo_job
+  doc: Successful test without a job file
+  tags: [ command_line_tool ]
+
+- output: {}
+  job: empty.yml
+  tool: return-1.cwl
+  id: failure_w_job
+  doc: Failed test with a job file
+  tags: [ command_line_tool ]
+
+- output: {}
+  tool: return-1.cwl
+  id: failure_wo_job
+  doc: Failed test without a job file
+  tags: [ command_line_tool ]
+
+- output: {}
+  job: empty.yml
+  tool: return-unsupported.cwl
+  id: unsupported_w_job
+  doc: Unsupported test with a job file
+  tags: [ command_line_tool ]
+
+- output: {}
+  tool: return-unsupported.cwl
+  id: unsupported_wo_job
+  doc: Unsupported test without a job file
+  tags: [ command_line_tool ]
diff --git a/tests/test-data/conformance_test_v1.2.cwltest.yaml b/tests/test-data/conformance_test_v1.2.cwltest.yaml
index 0b78da9..3f7a605 100644
--- a/tests/test-data/conformance_test_v1.2.cwltest.yaml
+++ b/tests/test-data/conformance_test_v1.2.cwltest.yaml
@@ -12,4 +12,10 @@
   tool: v1.0/cat1-testcli.cwl
   id: cl_optional_bindings_provided
   doc: Test command line with optional input (provided)
-  tags: [ command_line_tool ]
\ No newline at end of file
+  tags: [ command_line_tool ]
+
+- tool: v1.0/null-expression2-tool.cwl
+  should_fail: true
+  id: expression_any_nodefaultany
+  doc: Test Any without defaults cannot be unspecified.
+  tags: [ required, inline_javascript, expression_tool ]
diff --git a/tests/test-data/mock_cwl_runner.py b/tests/test-data/mock_cwl_runner.py
index d807203..98d668e 100755
--- a/tests/test-data/mock_cwl_runner.py
+++ b/tests/test-data/mock_cwl_runner.py
@@ -15,7 +15,7 @@
 def main() -> int:
     parser = argparse.ArgumentParser()
     parser.add_argument("processfile")
-    parser.add_argument("jobfile")
+    parser.add_argument("jobfile", nargs='?', default=None)
     parser.add_argument("--version", action="https://github.com/version", version="%(prog)s 1.0")
     parser.add_argument("--outdir")
     parser.add_argument("--quiet", action="https://github.com/store_true")
diff --git a/tests/test-data/v1.0/null-expression2-tool.cwl b/tests/test-data/v1.0/null-expression2-tool.cwl
new file mode 100644
index 0000000..2b09ec0
--- /dev/null
+++ b/tests/test-data/v1.0/null-expression2-tool.cwl
@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+
+class: ExpressionTool
+requirements:
+  - class: InlineJavascriptRequirement
+cwlVersion: v1.2
+
+inputs:
+  i1: Any
+
+outputs:
+  output: int
+
+expression: "$({'output': (inputs.i1 == 'the-default' ? 1 : 2)})"
\ No newline at end of file
diff --git a/tests/test_badgedir.py b/tests/test_badgedir.py
new file mode 100644
index 0000000..cf2f3ac
--- /dev/null
+++ b/tests/test_badgedir.py
@@ -0,0 +1,98 @@
+import os
+import json
+from pathlib import Path
+from textwrap import dedent
+
+import schema_salad.ref_resolver
+
+from .util import get_data, run_with_mock_cwl_runner
+
+
+def test_badgedir(tmp_path: Path) -> None:
+    badgedir = tmp_path / "badgedir"
+
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/conformance_test_v1.2.cwltest.yaml")
+        ),
+        "--badgedir",
+        str(badgedir),
+    ]
+    cwd = os.getcwd()
+    try:
+        os.chdir(get_data("tests/test-data/"))
+        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    finally:
+        os.chdir(cwd)
+
+    assert error_code == 1
+    required_json = badgedir / "required.json"
+    assert required_json.exists()
+    with open(required_json) as file:
+        obj = json.load(file)
+        assert obj.get("subject", "") == "required"
+        assert obj.get("status", "") == "0%"
+        assert obj.get("color", "") == "red"
+
+    required_md = badgedir / "required.md"
+    assert required_md.exists()
+    with open(required_md) as file:
+        s = file.read()
+        assert "file://" in s
+        assert "tests/test-data/conformance_test_v1.2.cwltest.yaml" in s
+        assert "v1.0/cat-job.json" in s
+        assert "v1.0/cat1-testcli.cwl" in s
+
+    clt = badgedir / "command_line_tool.json"
+    assert clt.exists()
+    with open(clt) as file:
+        obj = json.load(file)
+        assert obj.get("subject", "") == "command_line_tool"
+        assert obj.get("status", "") == "0%"
+        assert obj.get("color", "") == "yellow"
+    assert (badgedir / "command_line_tool.md").exists()
+
+
+def test_badgedir_report_with_baseuri(tmp_path: Path) -> None:
+    badgedir = tmp_path / "badgedir"
+
+    baseuri = "https://example.com/specified/uri"
+
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(get_data("tests/test-data/badgedir.yaml")),
+        "--badgedir",
+        str(badgedir),
+        "--baseuri",
+        baseuri,
+    ]
+    cwd = os.getcwd()
+    try:
+        os.chdir(get_data("tests/test-data/"))
+        error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    finally:
+        os.chdir(cwd)
+
+    clt_md = badgedir / "command_line_tool.md"
+    assert clt_md.exists()
+    with open(clt_md) as file:
+        contents = file.read()
+        assert contents == markdown_report_with(baseuri)
+
+
+def markdown_report_with(baseuri: str) -> str:
+    return dedent(
+        f"""
+        # `command_line_tool` tests
+        ## List of passed tests
+        - [success_w_job]({baseuri}/badgedir.yaml#L0) ([tool]({baseuri}/return-0.cwl), [job]({baseuri}/empty.yml))
+        - [success_wo_job]({baseuri}/badgedir.yaml#L7) ([tool]({baseuri}/return-0.cwl))
+        ## List of failed tests
+        - [failure_w_job]({baseuri}/badgedir.yaml#L13) ([tool]({baseuri}/return-1.cwl), [job]({baseuri}/empty.yml))
+        - [failure_wo_job]({baseuri}/badgedir.yaml#L20) ([tool]({baseuri}/return-1.cwl))
+        ## List of unsupported tests
+        - [unsupported_w_job]({baseuri}/badgedir.yaml#L26) ([tool]({baseuri}/return-unsupported.cwl), [job]({baseuri}/empty.yml))
+        - [unsupported_wo_job]({baseuri}/badgedir.yaml#L33) ([tool]({baseuri}/return-unsupported.cwl))
+        """
+    )[1:]
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
index 4951c3f..4bc4a69 100644
--- a/tests/test_plugin.py
+++ b/tests/test_plugin.py
@@ -13,6 +13,7 @@ def _load_v1_0_dir(path: Path) -> None:
     inner_dir = os.path.join(path.parent, "v1.0")
     os.mkdir(inner_dir)
     shutil.copy(get_data("tests/test-data/v1.0/cat1-testcli.cwl"), inner_dir)
+    shutil.copy(get_data("tests/test-data/v1.0/null-expression2-tool.cwl"), inner_dir)
     shutil.copy(get_data("tests/test-data/v1.0/cat-job.json"), inner_dir)
     shutil.copy(get_data("tests/test-data/v1.0/cat-n-job.json"), inner_dir)
     shutil.copy(get_data("tests/test-data/v1.0/hello.txt"), inner_dir)
@@ -104,7 +105,7 @@ def test_no_label(pytester: "Pytester") -> None:
     result = pytester.runpytest(
         "-k", "conformance_test_v1.2.cwltest.yaml", "--cwl-tags", "required"
     )
-    result.assert_outcomes(passed=1, skipped=1)
+    result.assert_outcomes(passed=2, skipped=1)
 
 
 def test_cwltool_hook(pytester: "Pytester") -> None:

From dd269f36d182786322b668a80b61c736887325f9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 25 Jun 2024 00:38:59 +0000
Subject: [PATCH 116/165] Bump mypy from 1.10.0 to 1.10.1

Bumps [mypy](https://github.com/python/mypy) from 1.10.0 to 1.10.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.10.0...v1.10.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index fbaccfc..43adedd 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.10.0
+mypy==1.10.1
 types-setuptools
 types-requests
 types-PyYAML

From c3a268f044004eed32ac0ab5f574d6d6a3e96cff Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Wed, 26 Jun 2024 11:10:25 +0900
Subject: [PATCH 117/165] Replace `{distdir}` with `dist`

---
 tox.ini | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index 3130f29..f036283 100644
--- a/tox.ini
+++ b/tox.ini
@@ -83,8 +83,8 @@ skip_install = true
 [testenv:py312-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
-  python -m build --outdir {distdir}
-  twine check {distdir}/*
+  python -m build --outdir dist
+  twine check dist/*
 deps =
     twine
     build

From 8b81c1f020c03168e61cc89f4906b39bd0068f9d Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Thu, 27 Jun 2024 17:05:10 +0900
Subject: [PATCH 118/165] Fix .gitignore

---
 .gitignore | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.gitignore b/.gitignore
index 613149a..dbcde96 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,12 @@ build
 dist
 
 cwltest/_version.py
+
+# Generated by tox
+coverage.xml
+.coverage
+.coverage.*
+pydocstyle_report.txt
+
+# Generated by `make release-test`
+testenv*

From 06b640ef3ead80271f428b56e0f9d656a41897ee Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Tue, 9 Jul 2024 03:58:01 +0000
Subject: [PATCH 119/165] Remove redundant code

---
 cwltest/utils.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/cwltest/utils.py b/cwltest/utils.py
index c9ef724..d2fa57e 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -343,11 +343,6 @@ def parse_results(
             for t in tags:
                 nfailures[t].append(test_report)
             test_case.add_failure_info(output=test_result.message)
-        elif return_code == UNSUPPORTED_FEATURE and category == REQUIRED:
-            failures += 1
-            for t in tags:
-                nfailures[t].append(test_report)
-            test_case.add_failure_info(output=test_result.message)
         elif category != REQUIRED and return_code == UNSUPPORTED_FEATURE:
             unsupported += 1
             for t in tags:

From 12a0f7c849933d0f22a12bd51502bb4988ab12e5 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Tue, 9 Jul 2024 10:34:42 +0000
Subject: [PATCH 120/165] Always use lightweight tags for releases

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 3207ee5..097ccc6 100644
--- a/Makefile
+++ b/Makefile
@@ -183,7 +183,7 @@ release:
 		python -m build testenv2/src/${PACKAGE} && \
 		pip install twine && \
 		twine upload testenv2/src/${PACKAGE}/dist/* && \
-		git tag ${VERSION} && git push --tags
+		git tag --no-sign ${VERSION} && git push --tags
 
 flake8: FORCE
 	flake8 $(PYSOURCES)

From 72087015b84d949758f96aac2f4cc223d9bfc07f Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sun, 14 Jul 2024 05:48:27 +0000
Subject: [PATCH 121/165] Fix badgedir.yaml to reproduce #216

---
 tests/test-data/badgedir.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test-data/badgedir.yaml b/tests/test-data/badgedir.yaml
index 80bd1bd..ea6e551 100644
--- a/tests/test-data/badgedir.yaml
+++ b/tests/test-data/badgedir.yaml
@@ -32,6 +32,7 @@
   tags: [ command_line_tool ]
 
 - output: {}
+  job: null
   tool: return-unsupported.cwl
   id: unsupported_wo_job
   doc: Unsupported test without a job file

From 713f6e214f3adb63edbe589aa2d6abf969d0e943 Mon Sep 17 00:00:00 2001
From: Tomoya Tanjo <ttanjo@gmail.com>
Date: Sun, 14 Jul 2024 05:49:17 +0000
Subject: [PATCH 122/165] Fix #216 by considering the case of `job` field with
 null value

---
 cwltest/plugin.py | 2 +-
 cwltest/utils.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index baa4cae..57a8ab4 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -67,7 +67,7 @@ def _run_test_hook_or_plain(
     start_time = time.time()
     reltool = os.path.relpath(test["tool"], start=config.test_basedir)
     tooluri = urljoin(config.test_baseuri, reltool)
-    if "job" in test:
+    if test.get("job", None):
         reljob = os.path.relpath(test["job"], start=config.test_basedir)
         joburi = urljoin(config.test_baseuri, reljob)
     else:
diff --git a/cwltest/utils.py b/cwltest/utils.py
index d2fa57e..3a6a15b 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -440,7 +440,7 @@ def run_test_plain(
 
     reltool = os.path.relpath(test["tool"], start=config.test_basedir)
     tooluri = urljoin(config.test_baseuri, reltool)
-    if "job" in test:
+    if test.get("job", None):
         reljob = os.path.relpath(test["job"], start=config.test_basedir)
         joburi = urljoin(config.test_baseuri, reljob)
     else:

From bc6445651af013be193e0407746db6f171ef6ddc Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 31 Jul 2024 00:08:16 +0000
Subject: [PATCH 123/165] Bump mypy from 1.10.1 to 1.11.1

Bumps [mypy](https://github.com/python/mypy) from 1.10.1 to 1.11.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.10.1...v1.11.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 43adedd..2002bdc 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.10.1
+mypy==1.11.1
 types-setuptools
 types-requests
 types-PyYAML

From 8db140eb542bd8cd1ba62539120ff7c4b0da9b8c Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Wed, 31 Jul 2024 15:31:52 +0200
Subject: [PATCH 124/165] pytest 8.3 changed an internal detail

---
 cwltest/plugin.py     | 4 ++--
 mypy-requirements.txt | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 57a8ab4..a27ee92 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -28,7 +28,7 @@
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
 
 if TYPE_CHECKING:
-    from _pytest._code.code import ExceptionInfo, _TracebackStyle
+    from _pytest._code.code import ExceptionInfo, TracebackStyle
     from _pytest.config import Config
     from _pytest.config import Config as PytestConfig
     from _pytest.config import PytestPluginManager
@@ -207,7 +207,7 @@ def runtest(self) -> None:
     def repr_failure(
         self,
         excinfo: "ExceptionInfo[BaseException]",
-        style: Optional["_TracebackStyle"] = None,
+        style: Optional["TracebackStyle"] = None,
     ) -> str:
         """
         Document failure reason.
diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 2002bdc..0976a9f 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,5 @@
 mypy==1.11.1
+pytest >= 8.3, < 9
 types-setuptools
 types-requests
 types-PyYAML

From 3282914fc58d635a048a70416fa32b29f45ed17c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Aug 2024 00:43:33 +0000
Subject: [PATCH 125/165] Update black requirement from ~=24.4 to ~=24.8

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.4.0...24.8.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 4280a59..32b201d 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 24.4
+black ~= 24.8
 pylint
 pep257
 pydocstyle

From 291f0d66b83357257cb99aac167de887698efc7f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 26 Aug 2024 00:16:08 +0000
Subject: [PATCH 126/165] Bump mypy from 1.11.1 to 1.11.2

Bumps [mypy](https://github.com/python/mypy) from 1.11.1 to 1.11.2.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.11.1...v1.11.2)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 0976a9f..bf3c7c3 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.11.1
+mypy==1.11.2
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 59c4cc450b6f4ecc94b4d9ba275749280dde9eb1 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 6 Sep 2024 14:59:16 +0100
Subject: [PATCH 127/165] Fix B910 errors from flake8-bugbear

---
 cwltest/main.py  | 4 ++--
 cwltest/utils.py | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/cwltest/main.py b/cwltest/main.py
index 4909c89..a731531 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -4,7 +4,7 @@
 import argparse
 import os
 import sys
-from collections import defaultdict
+from collections import Counter, defaultdict
 from concurrent.futures import ThreadPoolExecutor
 from typing import Dict, List, Optional, Set, cast
 
@@ -116,7 +116,7 @@ def main() -> int:
     suite_name, _ = os.path.splitext(os.path.basename(args.test))
     report: Optional[junit_xml.TestSuite] = junit_xml.TestSuite(suite_name, [])
 
-    ntotal: Dict[str, int] = defaultdict(int)
+    ntotal: Dict[str, int] = Counter()
     npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
 
     if args.only_tools:
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 3a6a15b..b9cd745 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -7,7 +7,7 @@
 import sys
 import tempfile
 import time
-from collections import defaultdict
+from collections import Counter, defaultdict
 from typing import (
     Any,
     Dict,
@@ -314,7 +314,7 @@ def parse_results(
     passed = 0
     failures = 0
     unsupported = 0
-    ntotal: Dict[str, int] = defaultdict(int)
+    ntotal: Dict[str, int] = Counter()
     nfailures: Dict[str, List[CWLTestReport]] = defaultdict(list)
     nunsupported: Dict[str, List[CWLTestReport]] = defaultdict(list)
     npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)

From 90008b837ee4b325efe12a30dce40e926ed69e65 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 6 Sep 2024 13:51:38 +0100
Subject: [PATCH 128/165] Add support for Python 3.13

Fix https://github.com/common-workflow-language/cwltest/issues/223 .
---
 .github/workflows/ci-tests.yml |  4 ++-
 README.rst                     |  2 +-
 pyproject.toml                 |  3 +-
 tox.ini                        | 57 +++++++++++++++++-----------------
 4 files changed, 35 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 691a145..152b8fe 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -18,10 +18,11 @@ jobs:
     runs-on: ubuntu-20.04  # 22.04 doesn't support Python 3.6
 
     strategy:
+      fail-fast: false
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12]
+        py-ver-minor: [8, 9, 10, 11, 12, 13]
         step: [lint, unit, mypy, bandit]
 
     env:
@@ -37,6 +38,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ env.py-semver }}
+          allow-prereleases: true
           cache: pip
           cache-dependency-path: |
             requirements.txt
diff --git a/README.rst b/README.rst
index c4c50dd..d1cc50e 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.8, 3.9, 3.10, 3.11, and 3.12.
+This is written and tested for Python 3.8, 3.9, 3.10, 3.11, 3.12, and 3.13.
 
 .. contents:: Table of Contents
    :local:
diff --git a/pyproject.toml b/pyproject.toml
index ddc54be..8daf19f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,9 +22,10 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Typing :: Typed",
 ]
-requires-python = ">=3.8,<3.13"
+requires-python = ">=3.8,<3.14"
 dynamic = ["version", "dependencies"]
 
 [project.readme]
diff --git a/tox.ini b/tox.ini
index f036283..93aadfa 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,9 +1,9 @@
 [tox]
 envlist =
-  py3{8,9,10,11,12}-lint,
-  py3{8,9,10,11,12}-unit,
-  py3{8,9,10,11,12}-bandit,
-  py3{8,9,10,11,12}-mypy,
+  py3{8,9,10,11,12,13}-lint,
+  py3{8,9,10,11,12,13}-unit,
+  py3{8,9,10,11,12,13}-bandit,
+  py3{8,9,10,11,12,13}-mypy,
   py312-lintreadme,
   py312-pydocstyle
 
@@ -22,16 +22,17 @@ python =
   3.10: py310
   3.11: py311
   3.12: py312
+  3.13: py313
 
 [testenv]
 skipsdist =
-  py3{8,9,10,11,12}-!{unit,mypy,lintreadme} = True
+  py3{8,9,10,11,12,13}-!{unit,mypy,lintreadme} = True
 
 description =
-  py3{8,9,10,11,12}-unit: Run the unit tests
-  py3{8,9,10,11,12}-lint: Lint the Python code
-  py3{8,9,10,11,12}-bandit: Search for common security issues
-  py3{8,9,10,11,12}-mypy: Check for type safety
+  py3{8,9,10,11,12,13}-unit: Run the unit tests
+  py3{8,9,10,11,12,13}-lint: Lint the Python code
+  py3{8,9,10,11,12,13}-bandit: Search for common security issues
+  py3{8,9,10,11,12,13}-mypy: Check for type safety
   py312-pydocstyle: docstring style checker
   py312-lintreadme: Lint the README.rst->.md conversion
 
@@ -40,36 +41,36 @@ passenv =
   GITHUB_*
 
 deps =
-  py3{8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
-  py3{8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
-  py3{8,9,10,11,12}-lint: flake8-bugbear
-  py3{8,9,10,11,12}-lint: black~=23.1
-  py3{8,9,10,11,12}-bandit: bandit
-  py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
+  py3{8,9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
+  py3{8,9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
+  py3{8,9,10,11,12,13}-lint: flake8-bugbear
+  py3{8,9,10,11,12,13}-lint: black~=23.1
+  py3{8,9,10,11,12,13}-bandit: bandit
+  py3{8,9,10,11,12,13}-mypy: -rmypy-requirements.txt
 
 set_env =
-  py3{8,3,10,11,12}-unit: LC_ALL = C.UTF-8
+  py3{8,3,10,11,12,13}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
 commands =
-  py3{8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
-  py3{8,9,10,11,12}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
-  py3{8,9,10,11,12}-unit: coverage xml
-  py3{8,9,10,11,12}-bandit: bandit --recursive cwltest
-  py3{8,9,10,11,12}-lint: make flake8
-  py3{8,9,10,11,12}-lint: make format-check
-  py3{8,9,10,11,12}-mypy: make mypy
+  py3{8,9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
+  py3{8,9,10,11,12,13}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py3{8,9,10,11,12,13}-unit: coverage xml
+  py3{8,9,10,11,12,13}-bandit: bandit --recursive cwltest
+  py3{8,9,10,11,12,13}-lint: make flake8
+  py3{8,9,10,11,12,13}-lint: make format-check
+  py3{8,9,10,11,12,13}-mypy: make mypy
 
 allowlist_externals =
-  py3{8,9,10,11,12}-lint: flake8
-  py3{8,9,10,11,12}-lint: black
-  py3{8,9,10,11,12}-{mypy,shellcheck,lint,unit}: make
+  py3{8,9,10,11,12,13}-lint: flake8
+  py3{8,9,10,11,12,13}-lint: black
+  py3{8,9,10,11,12,13}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py3{8,9,10,11,12}-lint: true
-  py3{8,9,10,11,12}-bandit: true
+  py3{8,9,10,11,12,13}-lint: true
+  py3{8,9,10,11,12,13}-bandit: true
 
 
 [testenv:py312-pydocstyle]

From f7ce9445a91cc405b8bec21cca10550a5e08ef74 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 00:03:39 +0000
Subject: [PATCH 129/165] Update black requirement from ~=24.8 to ~=24.10

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.8.0...24.10.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 32b201d..0316d33 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 24.8
+black ~= 24.10
 pylint
 pep257
 pydocstyle

From 4889565a4f0fdd16a36457a336558f1436529f88 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 8 Oct 2024 03:31:00 +0000
Subject: [PATCH 130/165] Bump sphinx-rtd-theme from 2.0.0 to 3.0.0

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 2.0.0 to 3.0.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/2.0.0...3.0.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 1cdb96e..fdfa727 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==2.0.0
+sphinx-rtd-theme==3.0.0
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 9e2c3952d5c8f678c22583c96e82021c87fa0719 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 10 Oct 2024 00:43:58 +0000
Subject: [PATCH 131/165] Bump sphinx-rtd-theme from 3.0.0 to 3.0.1

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 3.0.0 to 3.0.1.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/3.0.0...3.0.1)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index fdfa727..545b2ae 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==3.0.0
+sphinx-rtd-theme==3.0.1
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From 9afd074c36e4f99d0e461f8539ecc2daef8f3a78 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 15 Oct 2024 00:42:02 +0000
Subject: [PATCH 132/165] Bump mypy from 1.11.2 to 1.12.0

Bumps [mypy](https://github.com/python/mypy) from 1.11.2 to 1.12.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.11.2...v1.12.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index bf3c7c3..94e56a2 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.11.2
+mypy==1.12.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 70f115fe5eafdb149e61ed74ecdf3724ca28d81b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Oct 2024 00:53:36 +0000
Subject: [PATCH 133/165] Bump mypy from 1.12.0 to 1.12.1

Bumps [mypy](https://github.com/python/mypy) from 1.12.0 to 1.12.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.12.0...v1.12.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 94e56a2..b75562f 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.12.0
+mypy==1.12.1
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 3ece638a7d6c280c202d6cbc71f6ccfc1f1bd1e1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 23 Oct 2024 00:57:51 +0000
Subject: [PATCH 134/165] Bump mypy from 1.12.1 to 1.13.0

Bumps [mypy](https://github.com/python/mypy) from 1.12.1 to 1.13.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.12.1...v1.13.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index b75562f..1f01ab5 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.12.1
+mypy==1.13.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 18bafe2b3f9c58a1915e22f5a02bcba5dc4ed2dd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 14 Nov 2024 00:12:45 +0000
Subject: [PATCH 135/165] Bump sphinx-rtd-theme from 3.0.1 to 3.0.2

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 3.0.1 to 3.0.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/3.0.1...3.0.2)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 545b2ae..8c1e1f4 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 sphinx >= 2.2
-sphinx-rtd-theme==3.0.1
+sphinx-rtd-theme==3.0.2
 sphinx-autoapi
 sphinx-autodoc-typehints
 typed_ast;python_version<'3.8'

From feeb0da1475d5cdce9f2dba167d35475f220e5c1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 00:40:40 +0000
Subject: [PATCH 136/165] Bump codecov/codecov-action from 3 to 5

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 152b8fe..1907d13 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -62,7 +62,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ matrix.step == 'unit' }}
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}

From fc92b4863ac4720d5d0bf2e4036591f200fa2ff0 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Fri, 22 Nov 2024 08:33:19 -0500
Subject: [PATCH 137/165] support plugins for alternative FsAccess  (#233)

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 README.rst             | 54 ++++++++++++++++++++++++++++++++++++++++++
 cwltest/compare.py     | 30 +++++++++++++----------
 cwltest/main.py        |  9 ++++++-
 cwltest/stdfsaccess.py | 48 +++++++++++++++++++++++++++++++++++++
 cwltest/utils.py       | 38 +++++++++++++++++++++++++++++
 5 files changed, 166 insertions(+), 13 deletions(-)
 create mode 100644 cwltest/stdfsaccess.py

diff --git a/README.rst b/README.rst
index d1cc50e..f5f646a 100644
--- a/README.rst
+++ b/README.rst
@@ -91,3 +91,57 @@ Once you upload JSON file to a server, you make a badge by using a link like htt
 Here is an example of markdown to add a badge::
 
   ![test result](https://flat.badgen.net/https/path/to/generated/json?icon=commonwl)
+
+*************************
+Custom file access module
+*************************
+
+If your CWL implementation does not write output files to a local file
+system location but instead to some other remote storage system, you
+can provide an alternate implementation of the *StdFsAccess* object
+that is able to access your storage system.
+
+Step 1:
+
+Implement your own class with the same public interface of the
+*StdFsAccess* object in *cwltest/stdfsaccess.py* (as of this writing,
+the methods are *open*, *size*, *isfile* and *isdir*).  These methods
+should expect to be called with URIs from the *location* field of the
+outputs of test cases.
+
+Define a function that, when called, returns a new instance of your object.
+
+Step 2:
+
+Create a Python package containing your class (or add it to an
+existing one).
+
+In the package metadata, add an entry point that declares the module
+(in this example, *my_cwl_runner.fsaccess*) containing the function
+(in this example, *get_fsaccess*) that *cwltest* will invoke to get an
+object implementing the *StdFsAccess* interface.
+
+In *setup.py* this looks like:
+
+.. code:: python
+
+  setup(
+    ...
+    entry_points={"cwltest.fsaccess": ["fsaccess=my_cwl_runner.fsaccess:get_fsaccess"]}},
+    ...
+  )
+
+In *pyproject.toml* it looks like:
+
+.. code::
+
+  [project.entry-points.'cwltest.fsaccess']
+  fsaccess = 'my_cwl_runner.fsaccess:get_fsaccess'
+
+
+Step 3:
+
+Install your package in the same Python environemnt as the
+installation of *cwltest*. When invoked, *cwltest* will query Python
+package metadata for a package with the *cwltest.fsaccess* entry point
+and call it to get back a custom filesystem access object.
diff --git a/cwltest/compare.py b/cwltest/compare.py
index 18452ed..0e3008b 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -2,9 +2,10 @@
 
 import hashlib
 import json
-import os.path
-import urllib.parse
 from typing import Any, Callable, Dict, Optional, Set
+import cwltest.stdfsaccess
+
+fs_access = cwltest.stdfsaccess.StdFsAccess("")
 
 
 class CompareFail(Exception):
@@ -130,13 +131,14 @@ def _compare_location(
         actual_comp = "path"
     else:
         actual_comp = "location"
-    path = urllib.parse.urlparse(actual[actual_comp]).path
+
     if actual.get("class") == "Directory":
         actual[actual_comp] = actual[actual_comp].rstrip("/")
-        exist_fun: Callable[[str], bool] = os.path.isdir
+        exist_fun: Callable[[str], bool] = fs_access.isdir
     else:
-        exist_fun = os.path.isfile
-    if not exist_fun(path) and not skip_details:
+        exist_fun = fs_access.isfile
+
+    if not exist_fun(actual[actual_comp]) and not skip_details:
         raise CompareFail.format(
             expected,
             actual,
@@ -160,15 +162,17 @@ def _compare_location(
 
 def _compare_checksum(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     if "path" in actual:
-        path = urllib.parse.urlparse(actual["path"]).path
+        path = actual["path"]
     else:
-        path = urllib.parse.urlparse(actual["location"]).path
+        path = actual["location"]
     checksum = hashlib.sha1()  # nosec
-    with open(path, "rb") as f:
+
+    with fs_access.open(path, "rb") as f:
         contents = f.read(1024 * 1024)
         while contents != b"":
             checksum.update(contents)
             contents = f.read(1024 * 1024)
+
     actual_checksum_on_disk = f"sha1${checksum.hexdigest()}"
     if "checksum" in actual:
         actual_checksum_declared = actual["checksum"]
@@ -193,10 +197,12 @@ def _compare_checksum(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
 
 def _compare_size(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
     if "path" in actual:
-        path = urllib.parse.urlparse(actual["path"]).path
+        path = actual["path"]
     else:
-        path = urllib.parse.urlparse(actual["location"]).path
-    actual_size_on_disk = os.path.getsize(path)
+        path = actual["location"]
+
+    actual_size_on_disk = fs_access.size(path)
+
     if "size" in actual:
         actual_size_declared = actual["size"]
         if actual_size_on_disk != actual_size_declared:
diff --git a/cwltest/main.py b/cwltest/main.py
index a731531..d8a7218 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -13,7 +13,12 @@
 import schema_salad.ref_resolver
 import schema_salad.schema
 from cwltest.argparser import arg_parser
-from cwltest.utils import CWLTestConfig, CWLTestReport, TestResult
+from cwltest.utils import (
+    CWLTestConfig,
+    CWLTestReport,
+    TestResult,
+    load_optional_fsaccess_plugin,
+)
 from schema_salad.exceptions import ValidationException
 
 from cwltest import logger, utils
@@ -116,6 +121,8 @@ def main() -> int:
     suite_name, _ = os.path.splitext(os.path.basename(args.test))
     report: Optional[junit_xml.TestSuite] = junit_xml.TestSuite(suite_name, [])
 
+    load_optional_fsaccess_plugin()
+
     ntotal: Dict[str, int] = Counter()
     npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
 
diff --git a/cwltest/stdfsaccess.py b/cwltest/stdfsaccess.py
new file mode 100644
index 0000000..b59375e
--- /dev/null
+++ b/cwltest/stdfsaccess.py
@@ -0,0 +1,48 @@
+"""Abstracted IO access."""
+
+import os
+import urllib
+from typing import IO, Any
+
+from schema_salad.ref_resolver import uri_file_path
+
+
+def abspath(src: str, basedir: str) -> str:
+    """Determine local filesystem absolute path given a basedir, handling both plain paths and URIs."""
+    if src.startswith("file://"):
+        abpath = uri_file_path(src)
+    elif urllib.parse.urlsplit(src).scheme in ["http", "https"]:
+        return src
+    else:
+        if basedir.startswith("file://"):
+            abpath = src if os.path.isabs(src) else basedir + "/" + src
+        else:
+            abpath = src if os.path.isabs(src) else os.path.join(basedir, src)
+    return abpath
+
+
+class StdFsAccess:
+    """Local filesystem implementation."""
+
+    def __init__(self, basedir: str) -> None:
+        """Perform operations with respect to a base directory."""
+        self.basedir = basedir
+
+    def _abs(self, p: str) -> str:
+        return abspath(p, self.basedir)
+
+    def open(self, fn: str, mode: str) -> IO[Any]:
+        """Open a file from a file: URI."""
+        return open(self._abs(fn), mode)
+
+    def size(self, fn: str) -> int:
+        """Get the size of the file resource pointed to by a URI."""
+        return os.stat(self._abs(fn)).st_size
+
+    def isfile(self, fn: str) -> bool:
+        """Determine if a resource pointed to by a URI represents a file."""
+        return os.path.isfile(self._abs(fn))
+
+    def isdir(self, fn: str) -> bool:
+        """Determine if a resource pointed to by a URI represents a directory."""
+        return os.path.isdir(self._abs(fn))
diff --git a/cwltest/utils.py b/cwltest/utils.py
index b9cd745..a638042 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -27,6 +27,8 @@
 import schema_salad.avro
 import schema_salad.ref_resolver
 import schema_salad.schema
+import cwltest.compare
+import cwltest.stdfsaccess
 from cwltest.compare import CompareFail, compare
 from rdflib import Graph
 from ruamel.yaml.scalarstring import ScalarString
@@ -37,6 +39,10 @@
 else:
     from importlib_resources import as_file, files
 
+# available since Python 3.8 (minimum version supports as of this
+# writing) so we don't need to fuss with backports
+from importlib.metadata import entry_points, EntryPoint
+
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, templock
 
 __all__ = ["files", "as_file"]
@@ -659,3 +665,35 @@ def absuri(path: str) -> str:
     if "://" in path:
         return path
     return "file://" + os.path.abspath(path)
+
+
+def load_optional_fsaccess_plugin() -> None:
+    """
+    Load optional fsaccess plugin.
+
+    Looks for a package with cwltest.fsaccess entry point and if so,
+    use that to get a filesystem access object that will be used for
+    checking test output.
+    """
+    fsaccess_eps: List[EntryPoint]
+
+    try:
+        # The interface to importlib.metadata.entry_points() changed
+        # several times between Python 3.8 and 3.13; the code below
+        # actually works fine on all of them but there's no single
+        # mypy annotation that works across of them.  Explicitly cast
+        # it to a consistent type to make mypy shut up.
+        fsaccess_eps = cast(List[EntryPoint], entry_points()["cwltest.fsaccess"])  # type: ignore [redundant-cast, unused-ignore]
+    except KeyError:
+        return
+
+    if len(fsaccess_eps) == 0:
+        return
+
+    if len(fsaccess_eps) > 1:
+        logger.warn(
+            "More than one cwltest.fsaccess entry point found, selected %s",
+            fsaccess_eps[0],
+        )
+
+    cwltest.compare.fs_access = fsaccess_eps[0].load()()

From b54c3ba42df1f9eeca317d857f7971d4555823a2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Sun, 22 Dec 2024 16:42:16 -0800
Subject: [PATCH 138/165] Bump mypy from 1.13.0 to 1.14.0 (#234)

Bumps [mypy](https://github.com/python/mypy) from 1.13.0 to 1.14.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.13.0...v1.14.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 1f01ab5..ad380f0 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.13.0
+mypy==1.14.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 8b5cdbc9d96b44f0eebafc4efdda0355ff3eed12 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 2 Jan 2025 22:51:16 +0100
Subject: [PATCH 139/165] Bump mypy from 1.14.0 to 1.14.1 (#235)

Bumps [mypy](https://github.com/python/mypy) from 1.14.0 to 1.14.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.14.0...v1.14.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index ad380f0..5f2bb8c 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.14.0
+mypy==1.14.1
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 68781bc883903a79d8ab1d15502eae6c41fdfbc2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 30 Jan 2025 14:53:38 +0100
Subject: [PATCH 140/165] Update black requirement from ~=24.10 to ~=25.1
 (#236)

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/24.10.0...25.1.0)

---
updated-dependencies:
- dependency-name: black
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 0316d33..c5c27be 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 24.10
+black ~= 25.1
 pylint
 pep257
 pydocstyle

From 5df6c58a3139f2cec35db01493134806820d4cde Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 6 Feb 2025 00:13:12 +0000
Subject: [PATCH 141/165] Bump mypy from 1.14.1 to 1.15.0

Bumps [mypy](https://github.com/python/mypy) from 1.14.1 to 1.15.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.14.1...v1.15.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 5f2bb8c..1327dd1 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.14.1
+mypy==1.15.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 55025bc3bb7930c00a29bad150fb28f8f59f37c6 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 6 Feb 2025 12:56:20 +0100
Subject: [PATCH 142/165] drop mypy from the Python 3.8 configuration

---
 .github/workflows/ci-tests.yml | 3 +++
 tox.ini                        | 8 ++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 1907d13..88dc10e 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -24,6 +24,9 @@ jobs:
         py-ver-major: [3]
         py-ver-minor: [8, 9, 10, 11, 12, 13]
         step: [lint, unit, mypy, bandit]
+        exclude:
+          - step: mypy
+            py-ver-minor: 8
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
diff --git a/tox.ini b/tox.ini
index 93aadfa..0d54cfb 100644
--- a/tox.ini
+++ b/tox.ini
@@ -3,7 +3,7 @@ envlist =
   py3{8,9,10,11,12,13}-lint,
   py3{8,9,10,11,12,13}-unit,
   py3{8,9,10,11,12,13}-bandit,
-  py3{8,9,10,11,12,13}-mypy,
+  py3{9,10,11,12,13}-mypy,
   py312-lintreadme,
   py312-pydocstyle
 
@@ -32,7 +32,7 @@ description =
   py3{8,9,10,11,12,13}-unit: Run the unit tests
   py3{8,9,10,11,12,13}-lint: Lint the Python code
   py3{8,9,10,11,12,13}-bandit: Search for common security issues
-  py3{8,9,10,11,12,13}-mypy: Check for type safety
+  py3{9,10,11,12,13}-mypy: Check for type safety
   py312-pydocstyle: docstring style checker
   py312-lintreadme: Lint the README.rst->.md conversion
 
@@ -46,7 +46,7 @@ deps =
   py3{8,9,10,11,12,13}-lint: flake8-bugbear
   py3{8,9,10,11,12,13}-lint: black~=23.1
   py3{8,9,10,11,12,13}-bandit: bandit
-  py3{8,9,10,11,12,13}-mypy: -rmypy-requirements.txt
+  py3{9,10,11,12,13}-mypy: -rmypy-requirements.txt
 
 set_env =
   py3{8,3,10,11,12,13}-unit: LC_ALL = C.UTF-8
@@ -61,7 +61,7 @@ commands =
   py3{8,9,10,11,12,13}-bandit: bandit --recursive cwltest
   py3{8,9,10,11,12,13}-lint: make flake8
   py3{8,9,10,11,12,13}-lint: make format-check
-  py3{8,9,10,11,12,13}-mypy: make mypy
+  py3{9,10,11,12,13}-mypy: make mypy
 
 allowlist_externals =
   py3{8,9,10,11,12,13}-lint: flake8

From e8a70ca5aa07141939970bd1dea9b05a6b880bc6 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Wed, 12 Feb 2025 13:58:49 +0000
Subject: [PATCH 143/165] Replace ubuntu-20.04 runner (#238)

https://github.blog/changelog/2025-01-15-github-actions-ubuntu-20-runner-image-brownout-dates-and-other-breaking-changes/
---
 .github/workflows/ci-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 88dc10e..dcc41e0 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -15,7 +15,7 @@ jobs:
   tox:
     name: CI tests via Tox
 
-    runs-on: ubuntu-20.04  # 22.04 doesn't support Python 3.6
+    runs-on: ubuntu-latest
 
     strategy:
       fail-fast: false

From e4b0d02baf9e43006f6a16ed8ed7b100e42a417e Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Mar 2025 14:19:48 +0100
Subject: [PATCH 144/165] Badges: compute a fake 'all' tag, containing all
 tests

---
 cwltest/argparser.py   | 3 ++-
 cwltest/plugin.py      | 3 ++-
 cwltest/utils.py       | 5 ++++-
 tests/test_badgedir.py | 9 +++++++++
 4 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/cwltest/argparser.py b/cwltest/argparser.py
index 1d2458c..b5698cf 100644
--- a/cwltest/argparser.py
+++ b/cwltest/argparser.py
@@ -107,7 +107,8 @@ def arg_parser() -> argparse.ArgumentParser:
     parser.add_argument(
         "--badgedir",
         type=str,
-        help="Create JSON badges and store them in this directory.",
+        help="Create JSON badges, one for each tag (plus a computed 'all' tag) "
+        " and store them in this directory.",
     )
 
     try:
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index a27ee92..4d89412 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -325,7 +325,8 @@ def collect(self) -> Iterator[CWLItem]:
         "--cwl-badgedir",
         {
             "type": str,
-            "help": "Create badge JSON files and store them in this directory.",
+            "help": "Create badge JSON files, one for each tag (plus a computed "
+            "'all' tag), and store them in this directory.",
         },
     ),
     (
diff --git a/cwltest/utils.py b/cwltest/utils.py
index a638042..9c8ed25 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -313,6 +313,9 @@ def parse_results(
     """
     Parse the results and return statistics and an optional report.
 
+    An additional tag named "all" will be computed, containing all the test
+    results.
+
     Returns the total number of tests, dictionary of test counts
     (total, passed, failed, unsupported) by tag, and a jUnit XML report.
     """
@@ -334,7 +337,7 @@ def parse_results(
             else "cwltest:#{i + 1}"
         )
         total += 1
-        tags = tests[i].get("tags", [])
+        tags = tests[i].get("tags", []) + ["all"]
         for t in tags:
             ntotal[t] += 1
 
diff --git a/tests/test_badgedir.py b/tests/test_badgedir.py
index cf2f3ac..fa421df 100644
--- a/tests/test_badgedir.py
+++ b/tests/test_badgedir.py
@@ -53,6 +53,15 @@ def test_badgedir(tmp_path: Path) -> None:
         assert obj.get("color", "") == "yellow"
     assert (badgedir / "command_line_tool.md").exists()
 
+    all_tests = badgedir / "all.json"
+    assert all_tests.exists()
+    with open(all_tests) as file:
+        obj = json.load(file)
+        assert obj.get("subject", "") == "all"
+        assert obj.get("status", "") == "0%"
+        assert obj.get("color", "") == "yellow"
+    assert (badgedir / "all.md").exists()
+
 
 def test_badgedir_report_with_baseuri(tmp_path: Path) -> None:
     badgedir = tmp_path / "badgedir"

From a8113b19dbee334a856680305516751c618c9274 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Mar 2025 14:20:09 +0100
Subject: [PATCH 145/165] Drop support for Python 3.8

miscellaneous formatting & pyupgrade
---
 .github/workflows/ci-tests.yml |   5 +-
 Makefile                       |   2 +-
 README.rst                     |   2 +-
 cwltest/compare.py             |  19 ++---
 cwltest/hooks.py               |   4 +-
 cwltest/main.py                |  20 +++---
 cwltest/plugin.py              |  45 +++++-------
 cwltest/utils.py               | 126 ++++++++++++++-------------------
 docs/requirements.txt          |   1 -
 pyproject.toml                 |   3 +-
 requirements.txt               |   1 -
 tests/test_badgedir.py         |   2 +-
 tests/test_compare.py          |   9 +--
 tests/util.py                  |   9 ++-
 tox.ini                        |  49 +++++++------
 15 files changed, 131 insertions(+), 166 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index dcc41e0..7875d79 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -22,11 +22,8 @@ jobs:
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13]
         step: [lint, unit, mypy, bandit]
-        exclude:
-          - step: mypy
-            py-ver-minor: 8
 
     env:
       py-semver: ${{ format('{0}.{1}', matrix.py-ver-major, matrix.py-ver-minor) }}
diff --git a/Makefile b/Makefile
index 097ccc6..9abf584 100644
--- a/Makefile
+++ b/Makefile
@@ -168,7 +168,7 @@ mypy: $(PYSOURCES)
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 pyupgrade: $(filter-out schema_salad/metaschema.py,$(PYSOURCES))
-	pyupgrade --exit-zero-even-if-changed --py38-plus $^
+	pyupgrade --exit-zero-even-if-changed --py39-plus $^
 	auto-walrus $^
 
 release-test: FORCE
diff --git a/README.rst b/README.rst
index f5f646a..7c17c99 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.8, 3.9, 3.10, 3.11, 3.12, and 3.13.
+This is written and tested for Python 3.9, 3.10, 3.11, 3.12, and 3.13.
 
 .. contents:: Table of Contents
    :local:
diff --git a/cwltest/compare.py b/cwltest/compare.py
index 0e3008b..9af3561 100644
--- a/cwltest/compare.py
+++ b/cwltest/compare.py
@@ -2,7 +2,8 @@
 
 import hashlib
 import json
-from typing import Any, Callable, Dict, Optional, Set
+from typing import Any, Callable, Optional
+
 import cwltest.stdfsaccess
 
 fs_access = cwltest.stdfsaccess.StdFsAccess("")
@@ -26,7 +27,7 @@ def format(
 
 
 def _check_keys(
-    keys: Set[str], expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+    keys: set[str], expected: dict[str, Any], actual: dict[str, Any], skip_details: bool
 ) -> None:
     for k in keys:
         try:
@@ -37,7 +38,7 @@ def _check_keys(
             ) from e
 
 
-def _compare_contents(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+def _compare_contents(expected: dict[str, Any], actual: dict[str, Any]) -> None:
     with open(actual["path"]) as f:
         actual_contents = f.read()
     if (expected_contents := expected["contents"]) != actual_contents:
@@ -52,7 +53,7 @@ def _compare_contents(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
 
 
 def _compare_dict(
-    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+    expected: dict[str, Any], actual: dict[str, Any], skip_details: bool
 ) -> None:
     for c in expected:
         try:
@@ -68,7 +69,7 @@ def _compare_dict(
 
 
 def _compare_directory(
-    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+    expected: dict[str, Any], actual: dict[str, Any], skip_details: bool
 ) -> None:
     if actual.get("class") != "Directory":
         raise CompareFail.format(
@@ -97,7 +98,7 @@ def _compare_directory(
 
 
 def _compare_file(
-    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+    expected: dict[str, Any], actual: dict[str, Any], skip_details: bool
 ) -> None:
     _compare_location(expected, actual, skip_details)
     if "contents" in expected:
@@ -117,7 +118,7 @@ def _compare_file(
 
 
 def _compare_location(
-    expected: Dict[str, Any], actual: Dict[str, Any], skip_details: bool
+    expected: dict[str, Any], actual: dict[str, Any], skip_details: bool
 ) -> None:
     if "path" in expected:
         expected_comp = "path"
@@ -160,7 +161,7 @@ def _compare_location(
         )
 
 
-def _compare_checksum(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+def _compare_checksum(expected: dict[str, Any], actual: dict[str, Any]) -> None:
     if "path" in actual:
         path = actual["path"]
     else:
@@ -195,7 +196,7 @@ def _compare_checksum(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
             )
 
 
-def _compare_size(expected: Dict[str, Any], actual: Dict[str, Any]) -> None:
+def _compare_size(expected: dict[str, Any], actual: dict[str, Any]) -> None:
     if "path" in actual:
         path = actual["path"]
     else:
diff --git a/cwltest/hooks.py b/cwltest/hooks.py
index 9b3faae..9b792e8 100644
--- a/cwltest/hooks.py
+++ b/cwltest/hooks.py
@@ -1,13 +1,13 @@
 """Hooks for pytest-cwl users."""
 
-from typing import Any, Dict, Optional, Tuple
+from typing import Any, Optional
 
 from cwltest import utils
 
 
 def pytest_cwl_execute_test(  # type: ignore[empty-body]
     config: utils.CWLTestConfig, processfile: str, jobfile: Optional[str]
-) -> Tuple[int, Optional[Dict[str, Any]]]:
+) -> tuple[int, Optional[dict[str, Any]]]:
     """
     Execute CWL test using a Python function instead of a command line runner.
 
diff --git a/cwltest/main.py b/cwltest/main.py
index d8a7218..92fe672 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -6,12 +6,15 @@
 import sys
 from collections import Counter, defaultdict
 from concurrent.futures import ThreadPoolExecutor
-from typing import Dict, List, Optional, Set, cast
+from typing import Optional, cast
 
 import junit_xml
 import schema_salad.avro
 import schema_salad.ref_resolver
 import schema_salad.schema
+from schema_salad.exceptions import ValidationException
+
+from cwltest import logger, utils
 from cwltest.argparser import arg_parser
 from cwltest.utils import (
     CWLTestConfig,
@@ -19,9 +22,6 @@
     TestResult,
     load_optional_fsaccess_plugin,
 )
-from schema_salad.exceptions import ValidationException
-
-from cwltest import logger, utils
 
 if sys.stderr.isatty():
     PREFIX = "\r"
@@ -33,7 +33,7 @@
 
 def _run_test(
     args: argparse.Namespace,
-    test: Dict[str, str],
+    test: dict[str, str],
     test_number: int,
     total_tests: int,
 ) -> TestResult:
@@ -78,8 +78,8 @@ def _run_test(
     return utils.run_test_plain(config, test, test_number)
 
 
-def _expand_number_range(nr: str) -> List[int]:
-    result: List[int] = []
+def _expand_number_range(nr: str) -> list[int]:
+    result: list[int] = []
     for s in nr.split(","):
         sp = s.split("-")
         if len(sp) == 2:
@@ -123,8 +123,8 @@ def main() -> int:
 
     load_optional_fsaccess_plugin()
 
-    ntotal: Dict[str, int] = Counter()
-    npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
+    ntotal: dict[str, int] = Counter()
+    npassed: dict[str, list[CWLTestReport]] = defaultdict(list)
 
     if args.only_tools:
         alltests = tests
@@ -161,7 +161,7 @@ def main() -> int:
             logger.warning("The `id` field is missing.")
 
     if args.show_tags:
-        alltags: Set[str] = set()
+        alltags: set[str] = set()
         for t in tests:
             ts = t.get("tags", [])
             alltags |= set(ts)
diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 4d89412..c780504 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -5,27 +5,16 @@
 import os
 import time
 import traceback
+from collections.abc import Iterator
 from io import StringIO
 from pathlib import Path
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Dict,
-    Iterator,
-    List,
-    Optional,
-    Protocol,
-    Set,
-    Tuple,
-    Union,
-    cast,
-)
+from typing import TYPE_CHECKING, Any, Optional, Protocol, Union, cast
 from urllib.parse import urljoin
 
 import pytest
-from cwltest.compare import CompareFail, compare
 
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, utils
+from cwltest.compare import CompareFail, compare
 
 if TYPE_CHECKING:
     from _pytest._code.code import ExceptionInfo, TracebackStyle
@@ -42,12 +31,12 @@ class TestRunner(Protocol):
 
     def __call__(
         self, config: utils.CWLTestConfig, processfile: str, jobfile: Optional[str]
-    ) -> List[Optional[Dict[str, Any]]]:
+    ) -> list[Optional[dict[str, Any]]]:
         """Type signature for pytest_cwl_execute_test hook results."""
         ...
 
 
-def _get_comma_separated_option(config: "Config", name: str) -> List[str]:
+def _get_comma_separated_option(config: "Config", name: str) -> list[str]:
     options = config.getoption(name)
     if options is None:
         return []
@@ -58,7 +47,7 @@ def _get_comma_separated_option(config: "Config", name: str) -> List[str]:
 
 
 def _run_test_hook_or_plain(
-    test: Dict[str, str],
+    test: dict[str, str],
     config: utils.CWLTestConfig,
     hook: "HookCaller",
 ) -> utils.TestResult:
@@ -76,7 +65,7 @@ def _run_test_hook_or_plain(
     hook_out = hook(config=config, processfile=processfile, jobfile=jobfile)
     if not hook_out:
         return utils.run_test_plain(config, test)
-    returncode, out = cast(Tuple[int, Optional[Dict[str, Any]]], hook_out[0])
+    returncode, out = cast(tuple[int, Optional[dict[str, Any]]], hook_out[0])
     duration = time.time() - start_time
     outstr = json.dumps(out) if out is not None else "{}"
     if returncode == UNSUPPORTED_FEATURE:
@@ -164,7 +153,7 @@ def __init__(
         self,
         name: str,
         parent: Optional["Node"],
-        spec: Dict[str, Any],
+        spec: dict[str, Any],
     ) -> None:
         """Initialize this CWLItem."""
         super().__init__(name, parent)
@@ -198,7 +187,7 @@ def runtest(self) -> None:
             hook,
         )
         cwl_results = self.config.cwl_results  # type: ignore[attr-defined]
-        cast(List[Tuple[Dict[str, Any], utils.TestResult]], cwl_results).append(
+        cast(list[tuple[dict[str, Any], utils.TestResult]], cwl_results).append(
             (self.spec, result)
         )
         if result.return_code != 0:
@@ -238,7 +227,7 @@ def repr_failure(
                 )
             )
 
-    def reportinfo(self) -> Tuple[Union["os.PathLike[str]", str], Optional[int], str]:
+    def reportinfo(self) -> tuple[Union["os.PathLike[str]", str], Optional[int], str]:
         """Status report."""
         return self.path, 0, "cwl test: %s" % self.name
 
@@ -258,10 +247,10 @@ def _add_global_properties(self) -> None:
 
     def collect(self) -> Iterator[CWLItem]:
         """Load the cwltest file and yield parsed entries."""
-        include: Set[str] = set(_get_comma_separated_option(self.config, "cwl_include"))
-        exclude: Set[str] = set(_get_comma_separated_option(self.config, "cwl_exclude"))
-        tags: Set[str] = set(_get_comma_separated_option(self.config, "cwl_tags"))
-        exclude_tags: Set[str] = set(
+        include: set[str] = set(_get_comma_separated_option(self.config, "cwl_include"))
+        exclude: set[str] = set(_get_comma_separated_option(self.config, "cwl_exclude"))
+        tags: set[str] = set(_get_comma_separated_option(self.config, "cwl_tags"))
+        exclude_tags: set[str] = set(
             _get_comma_separated_option(self.config, "cwl_exclude_tags")
         )
         tests, _ = utils.load_and_validate_tests(str(self.path))
@@ -302,7 +291,7 @@ def collect(self) -> Iterator[CWLItem]:
             yield item
 
 
-__OPTIONS: List[Tuple[str, Dict[str, Any]]] = [
+__OPTIONS: list[tuple[str, dict[str, Any]]] = [
     (
         "--cwl-runner",
         {
@@ -400,14 +389,14 @@ def pytest_collect_file(
 
 def pytest_configure(config: "PytestConfig") -> None:
     """Store the raw tests and the test results."""
-    cwl_results: List[Tuple[Dict[str, Any], utils.TestResult]] = []
+    cwl_results: list[tuple[dict[str, Any], utils.TestResult]] = []
     config.cwl_results = cwl_results  # type: ignore[attr-defined]
 
 
 def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
     """Generate badges."""
     cwl_results = cast(
-        List[Tuple[Dict[str, Any], utils.TestResult]],
+        list[tuple[dict[str, Any], utils.TestResult]],
         getattr(session.config, "cwl_results", None),
     )
     if not cwl_results:
diff --git a/cwltest/utils.py b/cwltest/utils.py
index 9c8ed25..33aee52 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -8,18 +8,10 @@
 import tempfile
 import time
 from collections import Counter, defaultdict
-from typing import (
-    Any,
-    Dict,
-    Iterable,
-    List,
-    MutableMapping,
-    MutableSequence,
-    Optional,
-    Tuple,
-    Union,
-    cast,
-)
+from collections.abc import Iterable, MutableMapping, MutableSequence
+from importlib.metadata import EntryPoint, entry_points
+from importlib.resources import files
+from typing import Any, Optional, Union, cast
 from urllib.parse import urljoin
 
 import junit_xml
@@ -27,25 +19,14 @@
 import schema_salad.avro
 import schema_salad.ref_resolver
 import schema_salad.schema
-import cwltest.compare
-import cwltest.stdfsaccess
-from cwltest.compare import CompareFail, compare
 from rdflib import Graph
 from ruamel.yaml.scalarstring import ScalarString
 from schema_salad.exceptions import ValidationException
 
-if sys.version_info >= (3, 9):
-    from importlib.resources import as_file, files
-else:
-    from importlib_resources import as_file, files
-
-# available since Python 3.8 (minimum version supports as of this
-# writing) so we don't need to fuss with backports
-from importlib.metadata import entry_points, EntryPoint
-
+import cwltest.compare
+import cwltest.stdfsaccess
 from cwltest import REQUIRED, UNSUPPORTED_FEATURE, logger, templock
-
-__all__ = ["files", "as_file"]
+from cwltest.compare import CompareFail, compare
 
 
 class CWLTestConfig:
@@ -61,8 +42,8 @@ def __init__(
         outdir: Optional[str] = None,
         classname: Optional[str] = None,
         tool: Optional[str] = None,
-        args: Optional[List[str]] = None,
-        testargs: Optional[List[str]] = None,
+        args: Optional[list[str]] = None,
+        testargs: Optional[list[str]] = None,
         timeout: Optional[int] = None,
         verbose: Optional[bool] = None,
         runner_quiet: Optional[bool] = None,
@@ -77,8 +58,8 @@ def __init__(
             self.test_baseuri, os.path.basename(entry) + f"#L{entry_line}"
         )
         self.tool: str = tool or "cwl-runner"
-        self.args: List[str] = args or []
-        self.testargs: List[str] = testargs or []
+        self.args: list[str] = args or []
+        self.testargs: list[str] = testargs or []
         self.timeout: Optional[int] = timeout
         self.verbose: bool = verbose or False
         self.runner_quiet: bool = runner_quiet or True
@@ -88,7 +69,7 @@ class CWLTestReport:
     """Encapsulate relevant test result data for a markdown report."""
 
     def __init__(
-        self, id: str, category: List[str], entry: str, tool: str, job: Optional[str]
+        self, id: str, category: list[str], entry: str, tool: str, job: Optional[str]
     ) -> None:
         """Initialize a CWLTestReport object."""
         self.id = id
@@ -124,7 +105,7 @@ def __init__(
         self.tool = tool
         self.job = job
 
-    def create_test_case(self, test: Dict[str, Any]) -> junit_xml.TestCase:
+    def create_test_case(self, test: dict[str, Any]) -> junit_xml.TestCase:
         """Create a jUnit XML test case from this test result."""
         doc = test.get("doc", "N/A").strip()
         if test.get("tags"):
@@ -144,7 +125,8 @@ def create_test_case(self, test: Dict[str, Any]) -> junit_xml.TestCase:
             case.failure_message = self.message
         return case
 
-    def create_report_entry(self, test: Dict[str, Any]) -> CWLTestReport:
+    def create_report_entry(self, test: dict[str, Any]) -> CWLTestReport:
+        """Package test result into a CWLTestReport."""
         return CWLTestReport(
             test.get("id", "no-id"),
             test.get("tags", ["required"]),
@@ -154,7 +136,7 @@ def create_report_entry(self, test: Dict[str, Any]) -> CWLTestReport:
         )
 
 
-def _clean_ruamel_list(obj: List[Any]) -> Any:
+def _clean_ruamel_list(obj: list[Any]) -> Any:
     """Entrypoint to transform roundtrip loaded ruamel.yaml to plain objects."""
     new_list = []
     for entry in obj:
@@ -188,10 +170,10 @@ def _clean_ruamel(obj: Any) -> Any:
 
 def generate_badges(
     badgedir: str,
-    ntotal: Dict[str, int],
-    npassed: Dict[str, List[CWLTestReport]],
-    nfailures: Dict[str, List[CWLTestReport]],
-    nunsupported: Dict[str, List[CWLTestReport]],
+    ntotal: dict[str, int],
+    npassed: dict[str, list[CWLTestReport]],
+    nfailures: dict[str, list[CWLTestReport]],
+    nunsupported: dict[str, list[CWLTestReport]],
 ) -> None:
     """Generate badges with conformance levels."""
     os.mkdir(badgedir)
@@ -253,7 +235,7 @@ def generate_badges(
 
 
 def get_test_number_by_key(
-    tests: List[Dict[str, str]], key: str, value: str
+    tests: list[dict[str, str]], key: str, value: str
 ) -> Optional[int]:
     """Retrieve the test index from its name."""
     for i, test in enumerate(tests):
@@ -262,7 +244,7 @@ def get_test_number_by_key(
     return None
 
 
-def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
+def load_and_validate_tests(path: str) -> tuple[Any, dict[str, Any]]:
     """
     Load and validate the given test file against the cwltest schema.
 
@@ -270,7 +252,7 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
     """
     schema_resource = files("cwltest").joinpath("cwltest-schema.yml")
     with schema_resource.open("r", encoding="utf-8") as fp:
-        cache: Optional[Dict[str, Union[str, Graph, bool]]] = {
+        cache: Optional[dict[str, Union[str, Graph, bool]]] = {
             "https://w3id.org/cwl/cwltest/cwltest-schema.yml": fp.read()
         }
     (
@@ -289,25 +271,25 @@ def load_and_validate_tests(path: str) -> Tuple[Any, Dict[str, Any]]:
     tests, metadata = schema_salad.schema.load_and_validate(
         document_loader, avsc_names, path, True
     )
-    tests = cast(List[Dict[str, Any]], _clean_ruamel_list(tests))
+    tests = cast(list[dict[str, Any]], _clean_ruamel_list(tests))
 
     return tests, metadata
 
 
 def parse_results(
     results: Iterable[TestResult],
-    tests: List[Dict[str, Any]],
+    tests: list[dict[str, Any]],
     suite_name: Optional[str] = None,
     report: Optional[junit_xml.TestSuite] = None,
-) -> Tuple[
+) -> tuple[
     int,  # total
     int,  # passed
     int,  # failures
     int,  # unsupported
-    Dict[str, int],  # total for each tag
-    Dict[str, List[CWLTestReport]],  # passed for each tag
-    Dict[str, List[CWLTestReport]],  # failures for each tag
-    Dict[str, List[CWLTestReport]],  # unsupported for each tag
+    dict[str, int],  # total for each tag
+    dict[str, list[CWLTestReport]],  # passed for each tag
+    dict[str, list[CWLTestReport]],  # failures for each tag
+    dict[str, list[CWLTestReport]],  # unsupported for each tag
     Optional[junit_xml.TestSuite],
 ]:
     """
@@ -323,10 +305,10 @@ def parse_results(
     passed = 0
     failures = 0
     unsupported = 0
-    ntotal: Dict[str, int] = Counter()
-    nfailures: Dict[str, List[CWLTestReport]] = defaultdict(list)
-    nunsupported: Dict[str, List[CWLTestReport]] = defaultdict(list)
-    npassed: Dict[str, List[CWLTestReport]] = defaultdict(list)
+    ntotal: dict[str, int] = Counter()
+    nfailures: dict[str, list[CWLTestReport]] = defaultdict(list)
+    nunsupported: dict[str, list[CWLTestReport]] = defaultdict(list)
+    npassed: dict[str, list[CWLTestReport]] = defaultdict(list)
 
     for i, test_result in enumerate(results):
         test_case = test_result.create_test_case(tests[i])
@@ -379,12 +361,12 @@ def parse_results(
 
 def prepare_test_command(
     tool: str,
-    args: List[str],
-    testargs: Optional[List[str]],
-    test: Dict[str, Any],
+    args: list[str],
+    testargs: Optional[list[str]],
+    test: dict[str, Any],
     cwd: str,
     quiet: Optional[bool] = True,
-) -> List[str]:
+) -> list[str]:
     """Turn the test into a command line."""
     test_command = [tool]
     test_command.extend(args)
@@ -419,9 +401,9 @@ def prepare_test_command(
 
 
 def prepare_test_paths(
-    test: Dict[str, str],
+    test: dict[str, str],
     cwd: str,
-) -> Tuple[str, Optional[str]]:
+) -> tuple[str, Optional[str]]:
     """Determine the test path and the tool path."""
     cwd = schema_salad.ref_resolver.file_uri(cwd)
     processfile = test["tool"]
@@ -437,13 +419,13 @@ def prepare_test_paths(
 
 def run_test_plain(
     config: CWLTestConfig,
-    test: Dict[str, str],
+    test: dict[str, str],
     test_number: Optional[int] = None,
 ) -> TestResult:
     """Plain test runner."""
-    out: Dict[str, Any] = {}
+    out: dict[str, Any] = {}
     outstr = outerr = ""
-    test_command: List[str] = []
+    test_command: list[str] = []
     duration = 0.0
     number = "?"
 
@@ -512,12 +494,12 @@ def run_test_plain(
             logger.error(
                 """Test %i failed: %s""",
                 test_number,
-                " ".join([shlex.quote(tc) for tc in test_command]),
+                shlex.join(test_command),
             )
         else:
             logger.error(
                 """Test failed: %s""",
-                " ".join([shlex.quote(tc) for tc in test_command]),
+                shlex.join(test_command),
             )
         logger.error(test.get("doc", "").replace("\n", " ").strip())
         if err.returncode == UNSUPPORTED_FEATURE:
@@ -539,7 +521,7 @@ def run_test_plain(
         logger.error(
             """Test %s failed: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         logger.error(outstr)
         logger.error("Parse error %s", str(err))
@@ -548,14 +530,14 @@ def run_test_plain(
         logger.error(
             """Test %s interrupted: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         raise
     except json.JSONDecodeError:
         logger.error(
             """Test %s failed: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         logger.error(test.get("doc", "").replace("\n", " ").strip())
         invalid_json_msg = "Output is not a valid JSON document: '%s'" % outstr
@@ -575,7 +557,7 @@ def run_test_plain(
         logger.error(
             """Test %s timed out: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         logger.error(test.get("doc", "").replace("\n", " ").strip())
         # Kill and re-communicate to get the logs and reap the child, as
@@ -611,7 +593,7 @@ def run_test_plain(
         logger.warning(
             """Test %s failed: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         logger.warning(test.get("doc", "").replace("\n", " ").strip())
         logger.warning("Returned zero but it should be non-zero")
@@ -632,7 +614,7 @@ def run_test_plain(
         logger.warning(
             """Test %s failed: %s""",
             number,
-            " ".join([shlex.quote(tc) for tc in test_command]),
+            shlex.join(test_command),
         )
         logger.warning(test.get("doc", "").replace("\n", " ").strip())
         logger.warning("Compare failure %s", ex)
@@ -678,15 +660,15 @@ def load_optional_fsaccess_plugin() -> None:
     use that to get a filesystem access object that will be used for
     checking test output.
     """
-    fsaccess_eps: List[EntryPoint]
+    fsaccess_eps: list[EntryPoint]
 
     try:
         # The interface to importlib.metadata.entry_points() changed
-        # several times between Python 3.8 and 3.13; the code below
+        # several times between Python 3.9 and 3.13; the code below
         # actually works fine on all of them but there's no single
         # mypy annotation that works across of them.  Explicitly cast
         # it to a consistent type to make mypy shut up.
-        fsaccess_eps = cast(List[EntryPoint], entry_points()["cwltest.fsaccess"])  # type: ignore [redundant-cast, unused-ignore]
+        fsaccess_eps = cast(list[EntryPoint], entry_points()["cwltest.fsaccess"])  # type: ignore [redundant-cast, unused-ignore]
     except KeyError:
         return
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 8c1e1f4..e9d8921 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,5 +2,4 @@ sphinx >= 2.2
 sphinx-rtd-theme==3.0.2
 sphinx-autoapi
 sphinx-autodoc-typehints
-typed_ast;python_version<'3.8'
 sphinxcontrib-autoprogram
diff --git a/pyproject.toml b/pyproject.toml
index 8daf19f..6d2afc3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,6 @@ classifiers = [
     "Operating System :: POSIX",
     "Operating System :: MacOS :: MacOS X",
     "Development Status :: 5 - Production/Stable",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -25,7 +24,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Typing :: Typed",
 ]
-requires-python = ">=3.8,<3.14"
+requires-python = ">=3.9,<3.14"
 dynamic = ["version", "dependencies"]
 
 [project.readme]
diff --git a/requirements.txt b/requirements.txt
index 16577e2..832cc52 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,4 +2,3 @@ schema-salad >= 5.0.20200220195218, < 9
 junit-xml >= 1.8
 pytest >= 7, < 9
 defusedxml
-importlib_resources>=1.4;python_version<'3.9'
diff --git a/tests/test_badgedir.py b/tests/test_badgedir.py
index fa421df..e1516d6 100644
--- a/tests/test_badgedir.py
+++ b/tests/test_badgedir.py
@@ -1,5 +1,5 @@
-import os
 import json
+import os
 from pathlib import Path
 from textwrap import dedent
 
diff --git a/tests/test_compare.py b/tests/test_compare.py
index b26c074..8149d92 100644
--- a/tests/test_compare.py
+++ b/tests/test_compare.py
@@ -1,8 +1,9 @@
 import os
 from pathlib import Path
-from typing import Any, Dict
+from typing import Any
 
 import pytest
+
 from cwltest.compare import CompareFail, _compare_directory, _compare_file, compare
 
 from .util import get_data
@@ -10,7 +11,7 @@
 
 def test_compare_any_success() -> None:
     expected = "Any"
-    actual: Dict[str, Any] = {}
+    actual: dict[str, Any] = {}
     compare(expected, actual)
 
 
@@ -385,7 +386,7 @@ def test_compare_file_failure_none() -> None:
         "class": "File",
         "checksum": "sha1$7448d8798a4380162d4b56f9b452e2f6f9e24e7b",
     }
-    actual: Dict[str, Any] = {}
+    actual: dict[str, Any] = {}
     with pytest.raises(CompareFail):
         compare(expected, actual)
 
@@ -554,7 +555,7 @@ def test_compare_list_failure_type() -> None:
             "10",
         ]
     }
-    actual: Dict[str, Any] = {"args": {}}
+    actual: dict[str, Any] = {"args": {}}
     with pytest.raises(CompareFail):
         compare(expected, actual)
 
diff --git a/tests/util.py b/tests/util.py
index 9394612..937b777 100644
--- a/tests/util.py
+++ b/tests/util.py
@@ -4,10 +4,9 @@
 import os
 import subprocess  # nosec
 from contextlib import ExitStack
+from importlib.resources import as_file, files
 from pathlib import Path
-from typing import List, Optional, Tuple
-
-from cwltest.utils import as_file, files
+from typing import Optional
 
 
 def get_data(filename: str) -> str:
@@ -29,8 +28,8 @@ def get_data(filename: str) -> str:
 
 
 def run_with_mock_cwl_runner(
-    args: List[str], cwl_runner: Optional[str] = None
-) -> Tuple[int, str, str]:
+    args: list[str], cwl_runner: Optional[str] = None
+) -> tuple[int, str, str]:
     """Bind a mock cwlref-runner implementation to cwltest."""
     if cwl_runner is None:
         cwl_runner = get_data("tests/test-data/mock_cwl_runner.py")
diff --git a/tox.ini b/tox.ini
index 0d54cfb..e2860c0 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,8 +1,8 @@
 [tox]
 envlist =
-  py3{8,9,10,11,12,13}-lint,
-  py3{8,9,10,11,12,13}-unit,
-  py3{8,9,10,11,12,13}-bandit,
+  py3{9,10,11,12,13}-lint,
+  py3{9,10,11,12,13}-unit,
+  py3{9,10,11,12,13}-bandit,
   py3{9,10,11,12,13}-mypy,
   py312-lintreadme,
   py312-pydocstyle
@@ -17,7 +17,6 @@ testpaths = tests
 
 [gh-actions]
 python =
-  3.8: py38
   3.9: py39
   3.10: py310
   3.11: py311
@@ -26,12 +25,12 @@ python =
 
 [testenv]
 skipsdist =
-  py3{8,9,10,11,12,13}-!{unit,mypy,lintreadme} = True
+  py3{9,10,11,12,13}-!{unit,mypy,lintreadme} = True
 
 description =
-  py3{8,9,10,11,12,13}-unit: Run the unit tests
-  py3{8,9,10,11,12,13}-lint: Lint the Python code
-  py3{8,9,10,11,12,13}-bandit: Search for common security issues
+  py3{9,10,11,12,13}-unit: Run the unit tests
+  py3{9,10,11,12,13}-lint: Lint the Python code
+  py3{9,10,11,12,13}-bandit: Search for common security issues
   py3{9,10,11,12,13}-mypy: Check for type safety
   py312-pydocstyle: docstring style checker
   py312-lintreadme: Lint the README.rst->.md conversion
@@ -41,36 +40,36 @@ passenv =
   GITHUB_*
 
 deps =
-  py3{8,9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
-  py3{8,9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
-  py3{8,9,10,11,12,13}-lint: flake8-bugbear
-  py3{8,9,10,11,12,13}-lint: black~=23.1
-  py3{8,9,10,11,12,13}-bandit: bandit
+  py3{9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
+  py3{9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
+  py3{9,10,11,12,13}-lint: flake8-bugbear
+  py3{9,10,11,12,13}-lint: black~=23.1
+  py3{9,10,11,12,13}-bandit: bandit
   py3{9,10,11,12,13}-mypy: -rmypy-requirements.txt
 
 set_env =
-  py3{8,3,10,11,12,13}-unit: LC_ALL = C.UTF-8
+  py3{9,10,11,12,13}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
 commands =
-  py3{8,9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
-  py3{8,9,10,11,12,13}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
-  py3{8,9,10,11,12,13}-unit: coverage xml
-  py3{8,9,10,11,12,13}-bandit: bandit --recursive cwltest
-  py3{8,9,10,11,12,13}-lint: make flake8
-  py3{8,9,10,11,12,13}-lint: make format-check
+  py3{9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
+  py3{9,10,11,12,13}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py3{9,10,11,12,13}-unit: coverage xml
+  py3{9,10,11,12,13}-bandit: bandit --recursive cwltest
+  py3{9,10,11,12,13}-lint: make flake8
+  py3{9,10,11,12,13}-lint: make format-check
   py3{9,10,11,12,13}-mypy: make mypy
 
 allowlist_externals =
-  py3{8,9,10,11,12,13}-lint: flake8
-  py3{8,9,10,11,12,13}-lint: black
-  py3{8,9,10,11,12,13}-{mypy,shellcheck,lint,unit}: make
+  py3{9,10,11,12,13}-lint: flake8
+  py3{9,10,11,12,13}-lint: black
+  py3{9,10,11,12,13}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py3{8,9,10,11,12,13}-lint: true
-  py3{8,9,10,11,12,13}-bandit: true
+  py3{9,10,11,12,13}-lint: true
+  py3{9,10,11,12,13}-bandit: true
 
 
 [testenv:py312-pydocstyle]

From 7e919f62efa71c4ed7d76829c69b5e76871befbc Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Mar 2025 14:58:07 +0100
Subject: [PATCH 146/165] Improve test coverage

---
 tests/test_numeric_id.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 tests/test_numeric_id.py

diff --git a/tests/test_numeric_id.py b/tests/test_numeric_id.py
new file mode 100644
index 0000000..64a2128
--- /dev/null
+++ b/tests/test_numeric_id.py
@@ -0,0 +1,15 @@
+from os import linesep as n
+
+from .util import get_data, run_with_mock_cwl_runner
+
+
+def test_include_by_number() -> None:
+    args = [
+        "--test",
+        get_data("tests/test-data/exclude-tags.yml"),
+        "-n1",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert f"[1/3] opt-error1: Test with label{n}" in stderr
+    assert "opt-error2" not in stderr
+    assert "opt-error3" not in stderr

From d565670410e42576313c62d0bb1b511e00dac9ee Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Mar 2025 15:06:03 +0100
Subject: [PATCH 147/165] --show-tags: sort the output & add a test

---
 cwltest/main.py          |  2 +-
 tests/test_categories.py | 20 ++++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/cwltest/main.py b/cwltest/main.py
index 92fe672..c38efd2 100644
--- a/cwltest/main.py
+++ b/cwltest/main.py
@@ -165,7 +165,7 @@ def main() -> int:
         for t in tests:
             ts = t.get("tags", [])
             alltags |= set(ts)
-        for tag in alltags:
+        for tag in sorted(alltags):
             print(tag)
         return 0
 
diff --git a/tests/test_categories.py b/tests/test_categories.py
index ceb2f3b..bc948f9 100644
--- a/tests/test_categories.py
+++ b/tests/test_categories.py
@@ -93,3 +93,23 @@ def test_category_in_junit_xml(tmp_path: Path) -> None:
         Element, cast(Element, root.find("testsuite")).find("testcase")
     ).attrib["class"]
     assert category == "js, init_work_dir"
+
+
+def test_list_all_tags() -> None:
+    args = [
+        "--test",
+        schema_salad.ref_resolver.file_uri(
+            get_data("tests/test-data/conformance_test_v1.2.cwltest.yaml")
+        ),
+        "--show-tags",
+    ]
+    error_code, stdout, stderr = run_with_mock_cwl_runner(args)
+    assert error_code == 0, stderr
+    assert (
+        stdout
+        == """command_line_tool
+expression_tool
+inline_javascript
+required
+"""
+    )

From 24da941a3551e5bed7ceee455c316a9d1d0869c9 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Feb 2025 14:59:38 +0100
Subject: [PATCH 148/165] simplify some imports

---
 cwltest/plugin.py    | 16 ++++++----------
 tests/test_plugin.py | 22 ++++++++++------------
 2 files changed, 16 insertions(+), 22 deletions(-)

diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index c780504..006b11a 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -17,11 +17,7 @@
 from cwltest.compare import CompareFail, compare
 
 if TYPE_CHECKING:
-    from _pytest._code.code import ExceptionInfo, TracebackStyle
-    from _pytest.config import Config
-    from _pytest.config import Config as PytestConfig
-    from _pytest.config import PytestPluginManager
-    from _pytest.config.argparsing import Parser as PytestParser
+    from _pytest._code.code import TracebackStyle
     from _pytest.nodes import Node
     from pluggy import HookCaller
 
@@ -36,7 +32,7 @@ def __call__(
         ...
 
 
-def _get_comma_separated_option(config: "Config", name: str) -> list[str]:
+def _get_comma_separated_option(config: pytest.Config, name: str) -> list[str]:
     options = config.getoption(name)
     if options is None:
         return []
@@ -195,7 +191,7 @@ def runtest(self) -> None:
 
     def repr_failure(
         self,
-        excinfo: "ExceptionInfo[BaseException]",
+        excinfo: pytest.ExceptionInfo[BaseException],
         style: Optional["TracebackStyle"] = None,
     ) -> str:
         """
@@ -359,7 +355,7 @@ def collect(self) -> Iterator[CWLItem]:
 ]
 
 
-def pytest_addoption(parser: "PytestParser") -> None:
+def pytest_addoption(parser: pytest.Parser) -> None:
     """Add our options to the pytest command line."""
     for entry in __OPTIONS:
         parser.addoption(entry[0], **entry[1])
@@ -387,7 +383,7 @@ def pytest_collect_file(
     return None
 
 
-def pytest_configure(config: "PytestConfig") -> None:
+def pytest_configure(config: pytest.Config) -> None:
     """Store the raw tests and the test results."""
     cwl_results: list[tuple[dict[str, Any], utils.TestResult]] = []
     config.cwl_results = cwl_results  # type: ignore[attr-defined]
@@ -417,7 +413,7 @@ def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
         utils.generate_badges(cwl_badgedir, ntotal, npassed, nfailures, nunsupported)
 
 
-def pytest_addhooks(pluginmanager: "PytestPluginManager") -> None:
+def pytest_addhooks(pluginmanager: pytest.PytestPluginManager) -> None:
     """Register our cwl hooks."""
     from cwltest import hooks
 
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
index 4bc4a69..5820831 100644
--- a/tests/test_plugin.py
+++ b/tests/test_plugin.py
@@ -1,12 +1,10 @@
 import os
 import shutil
 from pathlib import Path
-from typing import TYPE_CHECKING
 
-from .util import get_data
+import pytest
 
-if TYPE_CHECKING:
-    from _pytest.pytester import Pytester
+from .util import get_data
 
 
 def _load_v1_0_dir(path: Path) -> None:
@@ -20,7 +18,7 @@ def _load_v1_0_dir(path: Path) -> None:
     shutil.copy(get_data("tests/test-data/v1.0/args.py"), inner_dir)
 
 
-def test_include(pytester: "Pytester") -> None:
+def test_include(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using cwltool as cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -36,7 +34,7 @@ def test_include(pytester: "Pytester") -> None:
     result.assert_outcomes(passed=1, skipped=1)
 
 
-def test_exclude(pytester: "Pytester") -> None:
+def test_exclude(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using cwltool as cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -52,7 +50,7 @@ def test_exclude(pytester: "Pytester") -> None:
     result.assert_outcomes(passed=0, skipped=2)
 
 
-def test_tags(pytester: "Pytester") -> None:
+def test_tags(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using cwltool as cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -65,7 +63,7 @@ def test_tags(pytester: "Pytester") -> None:
     result.assert_outcomes(passed=1, skipped=1)
 
 
-def test_exclude_tags(pytester: "Pytester") -> None:
+def test_exclude_tags(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using cwltool as cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -81,7 +79,7 @@ def test_exclude_tags(pytester: "Pytester") -> None:
     result.assert_outcomes(skipped=2)
 
 
-def test_badgedir(pytester: "Pytester") -> None:
+def test_badgedir(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin creates the badges directory."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -95,7 +93,7 @@ def test_badgedir(pytester: "Pytester") -> None:
     assert os.path.exists("cwl-badges")
 
 
-def test_no_label(pytester: "Pytester") -> None:
+def test_no_label(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin correctly extracts test names from the id field when label is missing."""
     path = pytester.copy_example("conformance_test_v1.2.cwltest.yaml")
     shutil.copy(
@@ -108,7 +106,7 @@ def test_no_label(pytester: "Pytester") -> None:
     result.assert_outcomes(passed=2, skipped=1)
 
 
-def test_cwltool_hook(pytester: "Pytester") -> None:
+def test_cwltool_hook(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using cwltool as cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     shutil.copy(
@@ -119,7 +117,7 @@ def test_cwltool_hook(pytester: "Pytester") -> None:
     result.assert_outcomes(passed=2)
 
 
-def test_no_hook(pytester: "Pytester") -> None:
+def test_no_hook(pytester: pytest.Pytester) -> None:
     """Test the pytest plugin using the default cwl-runner."""
     path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
     _load_v1_0_dir(path)

From 1117ba59a99f2752c59bdd1526bb3ef98cadb33b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Feb 2025 15:00:06 +0100
Subject: [PATCH 149/165] fix badge generation for test with int IDs.

---
 cwltest/utils.py     | 14 +++++++++-----
 tests/test_plugin.py | 11 ++++++++---
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/cwltest/utils.py b/cwltest/utils.py
index 33aee52..a14ae7a 100644
--- a/cwltest/utils.py
+++ b/cwltest/utils.py
@@ -69,7 +69,12 @@ class CWLTestReport:
     """Encapsulate relevant test result data for a markdown report."""
 
     def __init__(
-        self, id: str, category: list[str], entry: str, tool: str, job: Optional[str]
+        self,
+        id: Union[int, str],
+        category: list[str],
+        entry: str,
+        tool: str,
+        job: Optional[str],
     ) -> None:
         """Initialize a CWLTestReport object."""
         self.id = id
@@ -199,10 +204,9 @@ def generate_badges(
 
         with open(f"{badgedir}/{t}.md", "w") as out:
             print(f"# `{t}` tests", file=out)
-
             print("## List of passed tests", file=out)
             for e in npassed[t]:
-                base = f"[{shortname(e.id)}]({e.entry})"
+                base = f"[{shortname(str(e.id))}]({e.entry})"
                 tool = f"[tool]({e.tool})"
                 if e.job:
                     arr = [tool, f"[job]({e.job})"]
@@ -213,7 +217,7 @@ def generate_badges(
 
             print("## List of failed tests", file=out)
             for e in nfailures[t]:
-                base = f"[{shortname(e.id)}]({e.entry})"
+                base = f"[{shortname(str(e.id))}]({e.entry})"
                 tool = f"[tool]({e.tool})"
                 if e.job:
                     arr = [tool, f"[job]({e.job})"]
@@ -224,7 +228,7 @@ def generate_badges(
 
             print("## List of unsupported tests", file=out)
             for e in nunsupported[t]:
-                base = f"[{shortname(e.id)}]({e.entry})"
+                base = f"[{shortname(str(e.id))}]({e.entry})"
                 tool = f"[tool]({e.tool})"
                 if e.job:
                     arr = [tool, f"[job]({e.job})"]
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
index 5820831..12c72ab 100644
--- a/tests/test_plugin.py
+++ b/tests/test_plugin.py
@@ -86,11 +86,16 @@ def test_badgedir(pytester: pytest.Pytester) -> None:
         get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
     )
     _load_v1_0_dir(path)
-    assert not os.path.exists("cwl-badges")
+    badge_path = path.parent / "cwl-badges"
+    assert not badge_path.exists()
     pytester.runpytest(
-        "-k", "conformance_test_v1.0.cwltest.yml", "--cwl-badgedir", "cwl-badges"
+        "-k", "conformance_test_v1.0.cwltest.yml", "--cwl-badgedir", str(badge_path)
     )
-    assert os.path.exists("cwl-badges")
+    assert badge_path.exists()
+    assert (badge_path / "command_line_tool.json").exists()
+    assert (badge_path / "command_line_tool.md").exists()
+    assert (badge_path / "required.json").exists()
+    assert (badge_path / "required.md").exists()
 
 
 def test_no_label(pytester: pytest.Pytester) -> None:

From 7fc69d6c80598844af21449206f56e8324f8f33c Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Sat, 1 Mar 2025 16:15:52 +0100
Subject: [PATCH 150/165] support xdist via pickling the per-worker results

---
 cwltest/plugin.py    | 59 ++++++++++++++++++++++++++++++++++++++------
 tests/test_plugin.py | 28 ++++++++++++++++++++-
 2 files changed, 79 insertions(+), 8 deletions(-)

diff --git a/cwltest/plugin.py b/cwltest/plugin.py
index 006b11a..5dabf9e 100644
--- a/cwltest/plugin.py
+++ b/cwltest/plugin.py
@@ -3,6 +3,7 @@
 import argparse
 import json
 import os
+import pickle  # nosec
 import time
 import traceback
 from collections.abc import Iterator
@@ -389,15 +390,59 @@ def pytest_configure(config: pytest.Config) -> None:
     config.cwl_results = cwl_results  # type: ignore[attr-defined]
 
 
-def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
+def _zip_results(
+    cwl_results: list[tuple[dict[str, Any], utils.TestResult]],
+) -> tuple[list[dict[str, Any]], list[utils.TestResult]]:
+    tests, results = (list(item) for item in zip(*cwl_results))
+    return tests, results
+
+
+def pytest_sessionfinish(session: pytest.Session) -> None:
     """Generate badges."""
+    cwl_badgedir = session.config.getoption("cwl_badgedir")
+    if not cwl_badgedir:
+        return
+
     cwl_results = cast(
         list[tuple[dict[str, Any], utils.TestResult]],
-        getattr(session.config, "cwl_results", None),
+        session.config.cwl_results,  # type: ignore[attr-defined]
     )
-    if not cwl_results:
-        return
-    tests, results = (list(item) for item in zip(*cwl_results))
+
+    if session.config.pluginmanager.has_plugin("xdist"):
+        import xdist  # type: ignore[import-untyped]
+
+        directory = cast(
+            pytest.TempPathFactory,
+            session.config._tmp_path_factory,  # type: ignore[attr-defined]
+        ).getbasetemp()
+        if xdist.is_xdist_worker(session):
+            if not cwl_results:
+                return
+            pickle_filename = f"cwltest_{xdist.get_xdist_worker_id(session)}.pickle"
+            with (directory.parent / pickle_filename).open("wb") as handle:
+                pickle.dump(
+                    _zip_results(cwl_results), handle, protocol=pickle.HIGHEST_PROTOCOL
+                )
+            return
+
+        if xdist.is_xdist_controller(session):
+            tests: list[dict[str, Any]] = []
+            results: list[utils.TestResult] = []
+            for pickle_filepath in directory.glob("cwltest_*"):
+                with pickle_filepath.open("rb") as handle:
+                    new_tests, new_results = pickle.load(handle)  # nosec
+                tests.extend(new_tests)
+                results.extend(new_results)
+        else:
+            if not cwl_results:
+                return
+            tests, results = _zip_results(cwl_results)
+
+    else:
+        if not cwl_results:
+            return
+        tests, results = _zip_results(cwl_results)
+
     (
         total,
         passed,
@@ -409,8 +454,8 @@ def pytest_sessionfinish(session: pytest.Session, exitstatus: int) -> None:
         nunsupported,
         _,
     ) = utils.parse_results(results, tests)
-    if cwl_badgedir := session.config.getoption("cwl_badgedir"):
-        utils.generate_badges(cwl_badgedir, ntotal, npassed, nfailures, nunsupported)
+
+    utils.generate_badges(cwl_badgedir, ntotal, npassed, nfailures, nunsupported)
 
 
 def pytest_addhooks(pluginmanager: pytest.PytestPluginManager) -> None:
diff --git a/tests/test_plugin.py b/tests/test_plugin.py
index 12c72ab..d0e3d0c 100644
--- a/tests/test_plugin.py
+++ b/tests/test_plugin.py
@@ -88,9 +88,35 @@ def test_badgedir(pytester: pytest.Pytester) -> None:
     _load_v1_0_dir(path)
     badge_path = path.parent / "cwl-badges"
     assert not badge_path.exists()
-    pytester.runpytest(
+    result = pytester.runpytest_inprocess(
         "-k", "conformance_test_v1.0.cwltest.yml", "--cwl-badgedir", str(badge_path)
     )
+    result.assert_outcomes(passed=2)
+    assert badge_path.exists()
+    assert (badge_path / "command_line_tool.json").exists()
+    assert (badge_path / "command_line_tool.md").exists()
+    assert (badge_path / "required.json").exists()
+    assert (badge_path / "required.md").exists()
+
+
+def test_badgedir_xdist(pytester: pytest.Pytester) -> None:
+    """Test the pytest plugin creates the badges directory even with xdist."""
+    path = pytester.copy_example("conformance_test_v1.0.cwltest.yml")
+    shutil.copy(
+        get_data("tests/test-data/cwltool-conftest.py"), path.parent / "conftest.py"
+    )
+    _load_v1_0_dir(path)
+    badge_path = path.parent / "cwl-badges"
+    assert not badge_path.exists()
+    result = pytester.runpytest_inprocess(
+        "-n",
+        "2",
+        "-k",
+        "conformance_test_v1.0.cwltest.yml",
+        "--cwl-badgedir",
+        str(badge_path),
+    )
+    result.assert_outcomes(passed=2)
     assert badge_path.exists()
     assert (badge_path / "command_line_tool.json").exists()
     assert (badge_path / "command_line_tool.md").exists()

From 2949b84bc50a0c5eb382f9db57e65d30d62f6a1c Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 14 Mar 2025 16:25:37 +0100
Subject: [PATCH 151/165] bump version to 2.6 due to dropped support for Python
 3.8; and fixed badge generation

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 9abf584..6bcc2a5 100644
--- a/Makefile
+++ b/Makefile
@@ -29,7 +29,7 @@ PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py)
 DEVPKGS=-rdev-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
 	   python-flake8 python-mock shellcheck
-VERSION=2.5.$(shell TZ=UTC git log --first-parent --max-count=1 \
+VERSION=2.6.$(shell TZ=UTC git log --first-parent --max-count=1 \
 	--format=format:%cd --date=format-local:%Y%m%d%H%M%S)
 
 ## all                    : default task (install in dev mode)

From a1c3ee13d9196ddf9cde7307ad39838b4a383f04 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 30 May 2025 00:02:44 +0000
Subject: [PATCH 152/165] Bump mypy from 1.15.0 to 1.16.0

Bumps [mypy](https://github.com/python/mypy) from 1.15.0 to 1.16.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.15.0...v1.16.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.16.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 1327dd1..f42c273 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.15.0
+mypy==1.16.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 5c72297ceacdaf0d54e757ca1e201238ac0e1e4c Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 30 May 2025 12:14:48 +0100
Subject: [PATCH 153/165] Fix new type annotation errors from mypy 1.16.0

---
 tests/test_categories.py  | 10 ++++------
 tests/test_short_names.py | 10 ++++------
 tests/test_timeout.py     | 22 +++++++---------------
 3 files changed, 15 insertions(+), 27 deletions(-)

diff --git a/tests/test_categories.py b/tests/test_categories.py
index bc948f9..ba08407 100644
--- a/tests/test_categories.py
+++ b/tests/test_categories.py
@@ -3,8 +3,6 @@
 from os import linesep as n
 from os import sep as p
 from pathlib import Path
-from typing import cast
-from xml.etree.ElementTree import Element
 
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
@@ -88,10 +86,10 @@ def test_category_in_junit_xml(tmp_path: Path) -> None:
     ]
     run_with_mock_cwl_runner(args)
     tree = ET.parse(junit_xml_report)
-    root = tree.getroot()
-    category = cast(
-        Element, cast(Element, root.find("testsuite")).find("testcase")
-    ).attrib["class"]
+    assert (root := tree.getroot()) is not None
+    assert (testsuite_el := root.find("testsuite")) is not None
+    assert (testcase_el := testsuite_el.find("testcase")) is not None
+    category = testcase_el.attrib["class"]
     assert category == "js, init_work_dir"
 
 
diff --git a/tests/test_short_names.py b/tests/test_short_names.py
index da87b6c..fbd2f19 100644
--- a/tests/test_short_names.py
+++ b/tests/test_short_names.py
@@ -1,7 +1,5 @@
 from os import linesep as n
 from pathlib import Path
-from typing import cast
-from xml.etree.ElementTree import Element
 
 import defusedxml.ElementTree as ET
 
@@ -49,8 +47,8 @@ def test_short_name_in_junit_xml(tmp_path: Path) -> None:
     ]
     run_with_mock_cwl_runner(args)
     tree = ET.parse(junit_xml_report)
-    root = tree.getroot()
-    category = cast(
-        Element, cast(Element, root.find("testsuite")).find("testcase")
-    ).attrib["file"]
+    assert (root := tree.getroot()) is not None
+    assert (testsuite_el := root.find("testsuite")) is not None
+    assert (testcase_el := testsuite_el.find("testcase")) is not None
+    category = testcase_el.attrib["file"]
     assert category == "opt-error"
diff --git a/tests/test_timeout.py b/tests/test_timeout.py
index bc01636..ad85219 100644
--- a/tests/test_timeout.py
+++ b/tests/test_timeout.py
@@ -1,7 +1,5 @@
 import os
 from pathlib import Path
-from typing import cast
-from xml.etree.ElementTree import Element
 
 import defusedxml.ElementTree as ET
 import schema_salad.ref_resolver
@@ -31,20 +29,14 @@ def test_timeout_stderr_stdout(tmp_path: Path) -> None:
     assert "Test 1 timed out" in stderr
     tree = ET.parse(junit_xml_report)
     try:
-        root = tree.getroot()
-        timeout_text = cast(
-            Element,
-            cast(Element, cast(Element, root.find("testsuite")).find("testcase")).find(
-                "failure"
-            ),
-        ).text
-        timeout_stderr = cast(
-            Element,
-            cast(Element, cast(Element, root.find("testsuite")).find("testcase")).find(
-                "system-err"
-            ),
-        ).text
+        assert (root := tree.getroot()) is not None
+        assert (testsuite_el := root.find("testsuite")) is not None
+        assert (testcase_el := testsuite_el.find("testcase")) is not None
+        assert (failure_el := testcase_el.find("failure")) is not None
+        timeout_text = failure_el.text
         assert timeout_text is not None and "Test timed out" in timeout_text
+        assert (system_err_el := testcase_el.find("system-err")) is not None
+        timeout_stderr = system_err_el.text
         assert timeout_stderr is not None and "timeout stderr" in timeout_stderr
     except AttributeError as e:
         print(junit_xml_report.read_text())

From 54a9033f442d525f48d6fb8906f9c4d873a98842 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 17 Jun 2025 02:00:37 +0000
Subject: [PATCH 154/165] Bump mypy from 1.16.0 to 1.16.1

Bumps [mypy](https://github.com/python/mypy) from 1.16.0 to 1.16.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.16.0...v1.16.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.16.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f42c273..df3e2e8 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.16.0
+mypy==1.16.1
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From bbde3154a29a57322224075056f5e8c9f5e33a6e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 15 Jul 2025 03:39:41 +0000
Subject: [PATCH 155/165] Bump mypy from 1.16.1 to 1.17.0

Bumps [mypy](https://github.com/python/mypy) from 1.16.1 to 1.17.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.16.1...v1.17.0)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.17.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index df3e2e8..f2a4e19 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.16.1
+mypy==1.17.0
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 3f345a4de7788144d76fe0803258529af80dd7c3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 1 Aug 2025 00:17:09 +0000
Subject: [PATCH 156/165] Bump mypy from 1.17.0 to 1.17.1

Bumps [mypy](https://github.com/python/mypy) from 1.17.0 to 1.17.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.17.0...v1.17.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.17.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index f2a4e19..ddb4b10 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.17.0
+mypy==1.17.1
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 8798950a1938f1eb9bab679efed993a9fb73107d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Aug 2025 10:21:51 +0000
Subject: [PATCH 157/165] Update setuptools-scm requirement from <9,>=8.0.4 to
 >=8.0.4,<10

Updates the requirements on [setuptools-scm](https://github.com/pypa/setuptools-scm) to permit the latest version.
- [Release notes](https://github.com/pypa/setuptools-scm/releases)
- [Changelog](https://github.com/pypa/setuptools-scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools-scm/compare/v8.0.4...v9.1.1)

---
updated-dependencies:
- dependency-name: setuptools-scm
  dependency-version: 9.1.1
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6d2afc3..0cf0bd5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 requires = [
     "setuptools>=61.2",
-    "setuptools_scm>=8.0.4,<9",
+    "setuptools_scm>=8.0.4,<10",
 ]
 build-backend = "setuptools.build_meta"
 

From e12e3657bc6849fea6faf54f06164f1ef118c52d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Aug 2025 09:35:23 +0000
Subject: [PATCH 158/165] Bump actions/checkout from 4 to 5

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml        | 6 +++---
 .github/workflows/codeql-analysis.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 7875d79..7972b7f 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -30,7 +30,7 @@ jobs:
       TOXENV: ${{ format('py{0}{1}-{2}', matrix.py-ver-major, matrix.py-ver-minor, matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -81,7 +81,7 @@ jobs:
       TOXENV: ${{ format('py312-{0}', matrix.step) }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -113,7 +113,7 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Set up Python
         uses: actions/setup-python@v5
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 47cc649..e1a42c8 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -19,7 +19,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         # We must fetch at least the immediate parents so that if this is
         # a pull request then we can checkout the head.

From 6028c3c794d8936ab63f5888637528bef54af9b5 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 18 Aug 2025 01:43:17 +0100
Subject: [PATCH 159/165] Support Python 3.14.x

---
 .github/workflows/ci-tests.yml | 15 ++++----
 pyproject.toml                 |  3 +-
 tox.ini                        | 65 +++++++++++++++++-----------------
 3 files changed, 44 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 7972b7f..b2b3a91 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -22,7 +22,7 @@ jobs:
       matrix:
         # The README.rst file mentions the versions tested, please update it as well
         py-ver-major: [3]
-        py-ver-minor: [9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13, 14]
         step: [lint, unit, mypy, bandit]
 
     env:
@@ -50,6 +50,9 @@ jobs:
           pip install -U pip setuptools wheel
           pip install "tox>4,<5" "tox-gh-actions>3"
 
+      - name: install dev libraries
+        run: sudo apt-get install -y libxml2-dev libxslt-dev
+
       - name: MyPy cache
         if: ${{ matrix.step == 'mypy' }}
         uses: actions/cache@v4
@@ -70,15 +73,15 @@ jobs:
   tox-style:
     name: CI linters via Tox
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
         step: [lintreadme, pydocstyle]
 
     env:
-      py-semver: "3.12"
-      TOXENV: ${{ format('py312-{0}', matrix.step) }}
+      py-semver: "3.13"
+      TOXENV: ${{ format('py313-{0}', matrix.step) }}
 
     steps:
       - uses: actions/checkout@v5
@@ -110,7 +113,7 @@ jobs:
   release_test:
     name: cwltest release test
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v5
@@ -118,7 +121,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache: pip
           cache-dependency-path: |
             requirements.txt
diff --git a/pyproject.toml b/pyproject.toml
index 0cf0bd5..da2775f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,9 +22,10 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Typing :: Typed",
 ]
-requires-python = ">=3.9,<3.14"
+requires-python = ">=3.9,<3.15"
 dynamic = ["version", "dependencies"]
 
 [project.readme]
diff --git a/tox.ini b/tox.ini
index e2860c0..5bb9fae 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,9 +1,9 @@
 [tox]
 envlist =
-  py3{9,10,11,12,13}-lint,
-  py3{9,10,11,12,13}-unit,
-  py3{9,10,11,12,13}-bandit,
-  py3{9,10,11,12,13}-mypy,
+  py3{9,10,11,12,13,14}-lint,
+  py3{9,10,11,12,13,14}-unit,
+  py3{9,10,11,12,13,14}-bandit,
+  py3{9,10,11,12,13,14}-mypy,
   py312-lintreadme,
   py312-pydocstyle
 
@@ -22,57 +22,58 @@ python =
   3.11: py311
   3.12: py312
   3.13: py313
+  3.14: py314
 
 [testenv]
 skipsdist =
-  py3{9,10,11,12,13}-!{unit,mypy,lintreadme} = True
+  py3{9,10,11,12,13,14}-!{unit,mypy,lintreadme} = True
 
 description =
-  py3{9,10,11,12,13}-unit: Run the unit tests
-  py3{9,10,11,12,13}-lint: Lint the Python code
-  py3{9,10,11,12,13}-bandit: Search for common security issues
-  py3{9,10,11,12,13}-mypy: Check for type safety
-  py312-pydocstyle: docstring style checker
-  py312-lintreadme: Lint the README.rst->.md conversion
+  py3{9,10,11,12,13,14}-unit: Run the unit tests
+  py3{9,10,11,12,13,14}-lint: Lint the Python code
+  py3{9,10,11,12,13,14}-bandit: Search for common security issues
+  py3{9,10,11,12,13,14}-mypy: Check for type safety
+  py313-pydocstyle: docstring style checker
+  py313-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 
 deps =
-  py3{9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
-  py3{9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
-  py3{9,10,11,12,13}-lint: flake8-bugbear
-  py3{9,10,11,12,13}-lint: black~=23.1
-  py3{9,10,11,12,13}-bandit: bandit
-  py3{9,10,11,12,13}-mypy: -rmypy-requirements.txt
+  py3{9,10,11,12,13,14}-{unit,mypy}: -rrequirements.txt
+  py3{9,10,11,12,13,14}-{unit,mypy}: -rtest-requirements.txt
+  py3{9,10,11,12,13,14}-lint: flake8-bugbear
+  py3{9,10,11,12,13,14}-lint: black~=23.1
+  py3{9,10,11,12,13,14}-bandit: bandit
+  py3{9,10,11,12,13,14}-mypy: -rmypy-requirements.txt
 
 set_env =
-  py3{9,10,11,12,13}-unit: LC_ALL = C.UTF-8
+  py3{9,10,11,12,13,14}-unit: LC_ALL = C.UTF-8
   COV_CORE_SOURCE=cwltest
   COV_CORE_CONFIG={toxinidir}/.coveragerc
   COV_CORE_DATAFILE={toxinidir}/.coverage.eager
 
 commands =
-  py3{9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
-  py3{9,10,11,12,13}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
-  py3{9,10,11,12,13}-unit: coverage xml
-  py3{9,10,11,12,13}-bandit: bandit --recursive cwltest
-  py3{9,10,11,12,13}-lint: make flake8
-  py3{9,10,11,12,13}-lint: make format-check
-  py3{9,10,11,12,13}-mypy: make mypy
+  py3{9,10,11,12,13,14}-unit: python -m pip install -U pip setuptools wheel
+  py3{9,10,11,12,13,14}-unit: python -m pytest --cov --cov-config={toxinidir}/.coveragerc --cov-append {posargs}
+  py3{9,10,11,12,13,14}-unit: coverage xml
+  py3{9,10,11,12,13,14}-bandit: bandit --recursive cwltest
+  py3{9,10,11,12,13,14}-lint: make flake8
+  py3{9,10,11,12,13,14}-lint: make format-check
+  py3{9,10,11,12,13,14}-mypy: make mypy
 
 allowlist_externals =
-  py3{9,10,11,12,13}-lint: flake8
-  py3{9,10,11,12,13}-lint: black
-  py3{9,10,11,12,13}-{mypy,shellcheck,lint,unit}: make
+  py3{9,10,11,12,13,14}-lint: flake8
+  py3{9,10,11,12,13,14}-lint: black
+  py3{9,10,11,12,13,14}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py3{9,10,11,12,13}-lint: true
-  py3{9,10,11,12,13}-bandit: true
+  py3{9,10,11,12,13,14}-lint: true
+  py3{9,10,11,12,13,14}-bandit: true
 
 
-[testenv:py312-pydocstyle]
+[testenv:py313-pydocstyle]
 allowlist_externals = make
 commands = make diff_pydocstyle_report
 deps =
@@ -80,7 +81,7 @@ deps =
     diff-cover
 skip_install = true
 
-[testenv:py312-lintreadme]
+[testenv:py313-lintreadme]
 description = Lint the README.rst->.md conversion
 commands =
   python -m build --outdir dist

From 88e9e0787feeb482e3a799ec1a73a5f18695f52a Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 18 Aug 2025 02:08:57 +0100
Subject: [PATCH 160/165] README: note Python 3.14 support

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 7c17c99..9a5a295 100644
--- a/README.rst
+++ b/README.rst
@@ -32,7 +32,7 @@ This is a testing tool for checking the output of Tools and Workflows described
 with the Common Workflow Language.  Among other uses, it is used to run the CWL
 conformance tests.
 
-This is written and tested for Python 3.9, 3.10, 3.11, 3.12, and 3.13.
+This is written and tested for Python 3.9, 3.10, 3.11, 3.12, 3.13, and 3.14
 
 .. contents:: Table of Contents
    :local:

From ea243c20b4361f97bce80ccd1635751879c573d3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 5 Sep 2025 00:05:35 +0000
Subject: [PATCH 161/165] Bump actions/setup-python from 5 to 6

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci-tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index b2b3a91..bbda8ef 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -35,7 +35,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.py-semver }}
           allow-prereleases: true
@@ -89,7 +89,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -119,7 +119,7 @@ jobs:
       - uses: actions/checkout@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.13"
           cache: pip

From 9d0631371cd4be4227302eac53874d0513e489cd Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 12 Sep 2025 00:02:09 +0000
Subject: [PATCH 162/165] Bump mypy from 1.17.1 to 1.18.1

Bumps [mypy](https://github.com/python/mypy) from 1.17.1 to 1.18.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.17.1...v1.18.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.18.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index ddb4b10..8619669 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.17.1
+mypy==1.18.1
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 8cb1be0edf7ecffab5886708f606da207652b3ec Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Sep 2025 00:01:53 +0000
Subject: [PATCH 163/165] Bump mypy from 1.18.1 to 1.18.2

Bumps [mypy](https://github.com/python/mypy) from 1.18.1 to 1.18.2.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.18.1...v1.18.2)

---
updated-dependencies:
- dependency-name: mypy
  dependency-version: 1.18.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 mypy-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mypy-requirements.txt b/mypy-requirements.txt
index 8619669..f2e4771 100644
--- a/mypy-requirements.txt
+++ b/mypy-requirements.txt
@@ -1,4 +1,4 @@
-mypy==1.18.1
+mypy==1.18.2
 pytest >= 8.3, < 9
 types-setuptools
 types-requests

From 062da72c21fcc644d669e827cf014580fa747b2b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 22 Sep 2025 00:01:58 +0000
Subject: [PATCH 164/165] Update black requirement from ~=25.1 to ~=25.9

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/25.1.0...25.9.0)

---
updated-dependencies:
- dependency-name: black
  dependency-version: 25.9.0
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index c5c27be..2373021 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,5 +1,5 @@
 diff_cover
-black ~= 25.1
+black ~= 25.9
 pylint
 pep257
 pydocstyle

From 22cd6f6a7a4ae49d9c8b801d539e0690a44bdeba Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 8 Oct 2025 00:06:33 +0000
Subject: [PATCH 165/165] Bump github/codeql-action from 3 to 4

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3 to 4.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v3...v4)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-version: '4'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/codeql-analysis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index e1a42c8..6ba449c 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -32,9 +32,9 @@ jobs:
       
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v4
       with:
         languages: python
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v4