Update latest main

.circleci/config.yml

@@ -0,0 +1,101 @@
+version: 2.1
+
+parameters:
+  REF:
+    type: string
+    default: ''
+    description: Optional tag to build
+
+jobs:
+  arm-wheels:
+    parameters:
+      build:
+        type: string
+      image:
+        type: string
+
+    machine:
+      image: ubuntu-2404:current
+    resource_class: arm.large  # 4 vCPUs
+
+    environment:
+      CIBW_ARCHS: "aarch64"
+      CIBW_MANYLINUX_AARCH64_IMAGE: "<< parameters.image >>"
+      CIBW_MUSLLINUX_AARCH64_IMAGE: "<< parameters.image >>"
+      CIBW_BUILD: "<< parameters.build >>"
+
+    steps:
+      - checkout
+      - when:
+          condition: << pipeline.parameters.REF >>
+          steps:
+          - run:
+              name: Checkout branch/tag << pipeline.parameters.REF >>
+              command: |
+                echo "Switching to branch/tag << pipeline.parameters.REF >> if it exists"
+                git checkout << pipeline.parameters.REF >> || true
+                git pull origin << pipeline.parameters.REF >> || true
+      - run:
+          name: install cibuildwheel and other build reqs
+          command: |
+            python3 -m pip install --upgrade pip setuptools setuptools_scm[toml]
+            python3 -m pip install -rcibw-requirements.txt
+
+      - run:
+          name: pip freeze
+          command: |
+            python3 -m pip freeze
+
+      - run:
+          name: list wheels
+          command: |
+            python3 -m cibuildwheel . --print-build-identifiers
+
+      - run:
+          name: cibuildwheel
+          command: |
+            python3 -m cibuildwheel .
+
+      - store_test_results:
+          path: test-results/
+
+      - store_artifacts:
+          path: wheelhouse/
+
+      # - when:
+      #     condition:
+      #       or:
+      #         - matches:
+      #             pattern: ".+"
+      #             value: "<< pipeline.git.tag >>"
+      #         - << pipeline.parameters.REF >>
+      #     steps:
+      #       - run:
+      #           environment:
+      #             TWINE_NONINTERACTIVE: "1"
+      #           command: |
+      #             python3 -m pip install twine
+      #             python3 -m twine upload --verbose --skip-existing wheelhouse/*
+
+workflows:
+  wheels: # This is the name of the workflow, feel free to change it to better match your workflow.
+    # Inside the workflow, you define the jobs you want to run.
+    jobs:
+      - arm-wheels:
+          name: arm-wheels-manylinux_2_28
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+          build: "*manylinux*"
+          image: quay.io/pypa/manylinux_2_28_aarch64
+      - arm-wheels:
+          name: arm-wheels-musllinux_1_2
+          filters:
+            branches:
+              only: main
+            tags:
+              only: /.*/
+          build: "*musllinux*"
+          image: quay.io/pypa/musllinux_1_2_aarch64

.github/workflows/ci-tests.yml

@@ -32,30 +32,30 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12, 13]
+        py-ver-minor: [9, 10, 11, 12, 13, 14]
         step: [lint, unit, bandit, 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@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Give the test runner user a name to make provenance happy.
         if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
         run: sudo usermod -c 'CI Runner' "$(whoami)"
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.py-semver }}
           allow-prereleases: true
@@ -64,6 +64,9 @@ jobs:
             requirements.txt
             tox.ini
 
+      - name: install dev libraries
+        run: sudo apt-get install -y libxml2-dev libxslt-dev
+
       - name: Upgrade setuptools and install tox
         run: |
           pip install -U pip setuptools wheel
@@ -81,31 +84,31 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: ${{ matrix.step == 'unit' }}
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   tox-style:
     name: Linters
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
         step: [lintreadme, shellcheck, 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@v4
+      - uses: actions/checkout@v5
         with:
           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
@@ -126,22 +129,22 @@ jobs:
     name: No leftovers
     runs-on: ubuntu-22.04
     env:
-      py-semver: "3.12"
+      py-semver: "3.13"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Give the test runner user a name to make provenance happy.
         run: sudo usermod -c 'CI Runner' "$(whoami)"
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ env.py-semver }}
           cache: pip
@@ -157,14 +160,15 @@ jobs:
           chmod a-w .
 
       - name: run tests
-        run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test
+        run: APPTAINER_TMPDIR=${RUNNER_TEMP} make test PYTEST_EXTRA=-vvv
 
 
   conformance_tests:
     name: CWL conformance
     runs-on: ubuntu-22.04
 
     strategy:
+      fail-fast: false
       matrix:
         cwl-version: [v1.0, v1.1, v1.2]
         container: [docker, singularity, podman]
@@ -177,13 +181,13 @@ jobs:
             extras: "--relax-path-checks"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         if: ${{ matrix.container == 'singularity' }}
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Singularity cache
         if: ${{ matrix.container == 'singularity' }}
@@ -197,9 +201,9 @@ jobs:
         run: sudo rm -f /usr/bin/docker ; sudo apt-get install -y podman
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
 
       - name: "Test CWL ${{ matrix.cwl-version }} conformance"
@@ -216,7 +220,7 @@ jobs:
           path: |
             **/cwltool_conf*.xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:
@@ -226,17 +230,17 @@ jobs:
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - name: Set up Singularity
+      - name: Set up Singularity and environment-modules
         run: |
-          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
-          sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
+          wget --no-verbose https://github.com/sylabs/singularity/releases/download/v4.2.1/singularity-ce_4.2.1-focal_amd64.deb
+          sudo apt-get install -y ./singularity-ce_4.2.1-focal_amd64.deb environment-modules
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
           cache-dependency-path: |
             requirements.txt
@@ -258,7 +262,7 @@ jobs:
   build_test_container:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: record cwltool version
@@ -268,17 +272,17 @@ jobs:
 
   macos:
     name: Test on macos-latest
-    runs-on: macos-13  # not latest, that is now an Apple Silicon M1, for which seqtk is not yet built on bioconda
+    runs-on: macos-latest
     env:
-      TOXENV: py312-unit
+      TOXENV: py313-unit
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: 3.12
+          python-version: 3.13
           cache: pip
           cache-dependency-path: |
             requirements.txt
@@ -301,7 +305,7 @@ jobs:
       - name: Test with tox
         run: tox
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
         env:

.github/workflows/codeql-analysis.yml

@@ -23,13 +23,13 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     # 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

.github/workflows/quay-publish.yml

@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Get image tags