[GR-64995] Update few patches

PullRequest: graalpython/3796

Author: msimacek

graalpython/lib-graalpython/patches/lxml-4.9.1.patch renamed to graalpython/lib-graalpython/patches/lxml-4.9.patch

@@ -0,0 +1,22 @@
+diff --git a/pyproject.toml b/pyproject.toml
+new file mode 100644
+index 0000000..2a76435
+--- /dev/null
++++ b/pyproject.toml
+@@ -0,0 +1,3 @@
++[build-system]
++requires = ["setuptools >= 40.6.0", "wheel", "Cython==3.0.11"]
++build-backend = "setuptools.build_meta:__legacy__"
+diff --git a/setupinfo.py b/setupinfo.py
+index 5feb13b..6ea719a 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -539,7 +539,7 @@ OPTION_WITH_UNICODE_STRINGS = has_option('with-unicode-strings')
+ OPTION_WITHOUT_ASSERT = has_option('without-assert')
+ OPTION_WITHOUT_THREADING = has_option('without-threading')
+ OPTION_WITHOUT_CYTHON = has_option('without-cython')
+-OPTION_WITH_CYTHON = has_option('with-cython')
++OPTION_WITH_CYTHON = True # GraalVM change
+ OPTION_WITH_CYTHON_GDB = has_option('cython-gdb')
+ OPTION_WITH_REFNANNY = has_option('with-refnanny')
+ OPTION_WITH_COVERAGE = has_option('with-coverage')

graalpython/lib-graalpython/patches/lxml-5.0.patch

@@ -0,0 +1,24 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 85c9214..90c6da8 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -1,5 +1,6 @@
+ [build-system]
+ requires = ["Cython>=3.0.7", "setuptools", "wheel"]
++build-backend = "setuptools.build_meta:__legacy__"
+ 
+ [tool.cibuildwheel]
+ build-verbosity = 2
+diff --git a/setupinfo.py b/setupinfo.py
+index d111128..5ad5a23 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -536,7 +536,7 @@ OPTION_WITH_UNICODE_STRINGS = has_option('with-unicode-strings')
+ OPTION_WITHOUT_ASSERT = has_option('without-assert')
+ OPTION_WITHOUT_THREADING = has_option('without-threading')
+ OPTION_WITHOUT_CYTHON = has_option('without-cython')
+-OPTION_WITH_CYTHON = has_option('with-cython')
++OPTION_WITH_CYTHON = True
+ OPTION_WITH_CYTHON_GDB = has_option('cython-gdb')
+ OPTION_WITH_REFNANNY = has_option('with-refnanny')
+ OPTION_WITH_COVERAGE = has_option('with-coverage')

graalpython/lib-graalpython/patches/lxml-5.1.0.patch

@@ -0,0 +1,24 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index e7f6bb6..230f261 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -1,5 +1,6 @@
+ [build-system]
+ requires = ["Cython>=3.0.9", "setuptools", "wheel"]
++build-backend = "setuptools.build_meta:__legacy__"
+ 
+ [tool.cibuildwheel]
+ build-verbosity = 2
+diff --git a/setupinfo.py b/setupinfo.py
+index 43e283f..d415905 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -564,7 +564,7 @@ OPTION_WITH_UNICODE_STRINGS = has_option('with-unicode-strings')
+ OPTION_WITHOUT_ASSERT = has_option('without-assert')
+ OPTION_WITHOUT_THREADING = has_option('without-threading')
+ OPTION_WITHOUT_CYTHON = has_option('without-cython')
+-OPTION_WITH_CYTHON = has_option('with-cython')
++OPTION_WITH_CYTHON = True
+ OPTION_WITH_CYTHON_GDB = has_option('cython-gdb')
+ OPTION_WITH_REFNANNY = has_option('with-refnanny')
+ OPTION_WITH_COVERAGE = has_option('with-coverage')

graalpython/lib-graalpython/patches/lxml-5.1.1.patch

@@ -0,0 +1,24 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index 1720657..b3cd9ab 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -1,5 +1,6 @@
+ [build-system]
+ requires = ["Cython>=3.0.10", "setuptools", "wheel"]
++build-backend = "setuptools.build_meta:__legacy__"
+ 
+ [tool.cibuildwheel]
+ build-verbosity = 2
+diff --git a/setupinfo.py b/setupinfo.py
+index 97e3399..9079171 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -563,7 +563,7 @@ OPTION_WITH_UNICODE_STRINGS = has_option('with-unicode-strings')
+ OPTION_WITHOUT_ASSERT = has_option('without-assert')
+ OPTION_WITHOUT_THREADING = has_option('without-threading')
+ OPTION_WITHOUT_CYTHON = has_option('without-cython')
+-OPTION_WITH_CYTHON = has_option('with-cython')
++OPTION_WITH_CYTHON = True
+ OPTION_WITH_CYTHON_GDB = has_option('cython-gdb')
+ OPTION_WITH_REFNANNY = has_option('with-refnanny')
+ OPTION_WITH_COVERAGE = has_option('with-coverage')

graalpython/lib-graalpython/patches/lxml-5.2.patch

@@ -0,0 +1,24 @@
+diff --git a/pyproject.toml b/pyproject.toml
+index f2edb28..259ed3c 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -1,5 +1,6 @@
+ [build-system]
+ requires = ["Cython>=3.0.11, < 3.1.0", "setuptools", "wheel"]
++build-backend = "setuptools.build_meta:__legacy__"
+ 
+ [tool.cibuildwheel]
+ build-verbosity = 1
+diff --git a/setupinfo.py b/setupinfo.py
+index 2aa3dca..e715c86 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -557,7 +557,7 @@ OPTION_WITH_UNICODE_STRINGS = has_option('with-unicode-strings')
+ OPTION_WITHOUT_ASSERT = has_option('without-assert')
+ OPTION_WITHOUT_THREADING = has_option('without-threading')
+ OPTION_WITHOUT_CYTHON = has_option('without-cython')
+-OPTION_WITH_CYTHON = has_option('with-cython')
++OPTION_WITH_CYTHON = True
+ OPTION_WITH_CYTHON_GDB = has_option('cython-gdb')
+ OPTION_WITH_REFNANNY = has_option('with-refnanny')
+ OPTION_WITH_COVERAGE = has_option('with-coverage')

graalpython/lib-graalpython/patches/lxml-5.4.0.patch

@@ -48,9 +48,6 @@ version = '== 2.2.1'
 patch = 'cloudpickle-2.2.1.patch'
 license = 'BSD-3-Clause'
 
-[[cppy.rules]]
-version = '==1.2.1'
-
 [[cramjam.rules]]
 version = '== 2.7.0'
 patch = 'cramjam-2.7.0.patch'
@@ -236,13 +233,38 @@ patch = 'llvmlite.patch'
 license = 'BSD-2-Clause'
 
 [[lxml.rules]]
-version = '== 5.3.0'
+version = '>= 5.3.2, <= 5.4.0'
+patch = 'lxml-5.4.0.patch'
+license = 'BSD-3-Clause'
+
+[[lxml.rules]]
+version = '>= 5.3.0, < 5.3.2'
 patch = 'lxml-5.3.0.patch'
 license = 'BSD-3-Clause'
 
 [[lxml.rules]]
-version = '== 4.9.1'
-patch = 'lxml-4.9.1.patch'
+version = '== 5.2.*'
+patch = 'lxml-5.2.patch'
+license = 'BSD-3-Clause'
+
+[[lxml.rules]]
+version = '== 5.1.1'
+patch = 'lxml-5.1.1.patch'
+license = 'BSD-3-Clause'
+
+[[lxml.rules]]
+version = '== 5.1.0'
+patch = 'lxml-5.1.0.patch'
+license = 'BSD-3-Clause'
+
+[[lxml.rules]]
+version = '== 5.0.*'
+patch = 'lxml-5.0.patch'
+license = 'BSD-3-Clause'
+
+[[lxml.rules]]
+version = '>= 4.9, < 5'
+patch = 'lxml-4.9.patch'
 license = 'BSD-3-Clause'
 
 # Patch already upstreamed, keeping it around for older versions
@@ -260,10 +282,6 @@ install-priority = 0
 patch = 'meson-python.patch'
 license = 'MIT'
 
-[[ml_dtypes.rules]]
-# 0.4.0 requires numpy==2.0rc1
-version = "< 0.4.0"
-
 [[mlx.rules]]
 patch = 'mlx.patch'
 license = 'MIT'
@@ -301,13 +319,6 @@ patch = 'numpy-2.0.0.patch'
 license = 'BSD-3-Clause'
 dist-type = 'sdist'
 
-[[numpy.rules]]
-version = '== 2.2.3'
-patch = 'numpy-2.2.3.patch'
-license = 'BSD-3-Clause'
-dist-type = 'sdist'
-install-priority = 0
-
 [[numpy.rules]]
 version = '== 1.26.4'
 patch = 'numpy-1.26.4.patch'
@@ -402,7 +413,6 @@ version = '== 3.0.0'
 patch = 'pendulum-3.0.0.patch'
 license = 'MIT'
 
-
 [[pip.rules]]
 version = '== 23.2.1'
 patch = 'pip-23.2.1.patch'
@@ -482,32 +492,33 @@ version = '>= 2.10.1, < 2.11.0'
 patch = 'pybind11-2.10.1.patch'
 license = 'BSD-3-Clause'
 
-[[pydantic.rules]]
-# Pin to match our pinned pydantic-core
-version = '== 2.10.3'
-
 [[pydantic-core.rules]]
 version = '== 2.10.1'
+install-priority = 0
 patch = 'pydantic-core-2.10.1.patch'
 license = 'MIT'
 
 [[pydantic-core.rules]]
 version = '== 2.23.4'
+install-priority = 0
 patch = 'pydantic-core-2.23.4.patch'
 license = 'MIT'
 
 [[pydantic-core.rules]]
 version = '== 2.27.1'
+install-priority = 0
 patch = 'pydantic-core-2.27.1.patch'
 license = 'MIT'
 
 [[pydantic-core.rules]]
 version = '== 2.27.2'
+install-priority = 0
 patch = 'pydantic-core-2.27.1.patch'
 license = 'MIT'
 
 [[pydantic-core.rules]]
 version = '== 2.26.0'
+install-priority = 0
 patch = 'pydantic-core-2.26.0.patch'
 license = 'MIT'
 
@@ -539,26 +550,18 @@ patch = "pymupdf.patch"
 # of the AGPL'd codebase
 license = 'UPL'
 
-[[pyOpenSSL.rules]]
-# Pin this version to avoid pulling newer cryptography than we have patch for
-version = "== 23.2.0"
-
-[[pyparsing.rules]]
-version = '== 3.0.8'
-
 [[pyperf.rules]]
 version = '== 2.3.0'
+install-priority = 0
 patch = 'pyperf-2.3.0.patch'
 license = 'MIT'
 
 [[pyperf.rules]]
 version = '== 2.3.1'
+install-priority = 0
 patch = 'pyperf-2.3.1.patch'
 license = 'MIT'
 
-[[pyperf.rules]]
-version = '== 2.5.0'
-
 [[pyperformance.rules]]
 version = '== 1.0.5'
 patch = 'pyperformance-1.0.5.patch'
@@ -591,8 +594,8 @@ patch = 'pythran-0.16.patch'
 license = 'BSD-3-Clause'
 
 [[pyzmq.rules]]
-# 26+ needs Cython 3
 version = '< 26'
+install-priority = 0
 # The patch just makes it re-cythonize to pick up our cython changes
 patch = 'pyzmq.patch'
 license = 'BSD-3-Clause'
@@ -634,10 +637,6 @@ license = 'Apache-2.0'
 version = '2.9.1'
 url = 'https://github.com/ray-project/ray/archive/refs/tags/ray-2.9.1.tar.gz'
 
-[[readme-renderer.rules]]
-# Newer version depends nh3 which is built with maturin, which is currently broken
-version = '< 42'
-
 [[rpds_py.rules]]
 # Patch not needed anymore in recent version since pyo3 changes have been upstreamed
 install-priority = 0
@@ -675,11 +674,9 @@ patch = 'scikit-learn-1.1.3.patch'
 license = 'BSD-3-Clause'
 dist-type = 'sdist'
 
-[[scipy.rules]]
-version = '== 1.13.1'
-
 [[scipy.rules]]
 version = '== 1.10.1'
+install-priority = 0
 patch = 'scipy-1.10.1.patch'
 license = 'BSD-3-Clause'
 dist-type = 'sdist'
@@ -689,10 +686,6 @@ version = '>= 1.2.2'
 patch = 'setproctitle-1.2.2.patch'
 license = 'BSD-3-Clause'
 
-[[statsmodels.rules]]
-# Pin older versions for now, the new ones require numpy-2rc1 and cython 3
-version = '<= 0.14.1'
-
 [[tensorflow.rules]]
 version = '== 2.15.0'
 patch = 'tensorflow-2.15.0.patch'
@@ -731,21 +724,19 @@ url = 'https://github.com/tensorflow/io/archive/refs/tags/v0.34.0.tar.gz'
 
 [[tiktoken.rules]]
 version = '== 0.7.0'
+install-priority = 0
 patch = 'tiktoken-0.7.0.patch'
 license = 'MIT'
 
-[[tokenizers.rules]]
-version = '>= 0.19'
-patch = 'tokenizers-0.19-plus.patch'
-license = 'Apache-2.0'
-
 [[tokenizers.rules]]
 version = '== 0.13.3'
+install-priority = 0
 patch = 'tokenizers-0.13.3.patch'
 license = 'Apache-2.0'
 
 [[tokenizers.rules]]
 version = '== 0.15.0'
+install-priority = 0
 patch = 'tokenizers-0.15.0.patch'
 license = 'Apache-2.0'
 
@@ -797,13 +788,6 @@ license = 'BSD-3-Clause'
 version = '0.17.1'
 url = 'https://github.com/pytorch/vision/archive/refs/tags/v0.17.1.tar.gz'
 
-[[tox.rules]]
-version = '== 3.*'
-
-[[transformers.rules]]
-# transformers tends to depend on a specific version of tokenizers. Pin it to avoid pulling unpatched tokenizers
-version = '== 4.33.3'
-
 [[trio.rules]]
 patch = 'trio.patch'
 license = 'Apache-2.0 OR MIT'
@@ -890,6 +874,13 @@ license = 'MIT'
 subdir = 'src'
 install-priority = 0
 
+[[xmlschema.rules]]
+version = '>= 4.0.0, <= 4.0.1'
+# Submitted upstream, optimistically assuming it'll get merged before the next release
+install-priority = 0
+patch = 'xmlschema.patch'
+license = 'MIT'
+
 [[zstandard.rules]]
 patch = 'zstandard.patch'
 license = 'BSD-3-Clause'