Some cython updates on top of #45086

srcpkgs/python3-Cython/template

@@ -1,6 +1,6 @@
 # Template file for 'python3-Cython'
 pkgname=python3-Cython
-version=0.29.36
+version=3.0.0
 revision=1
 build_style=python3-module
 hostmakedepends="python3-setuptools"
@@ -12,7 +12,7 @@ license="Apache-2.0"
 homepage="https://cython.org/"
 changelog="https://raw.githubusercontent.com/cython/cython/master/CHANGES.rst"
 distfiles="${PYPI_SITE}/C/Cython/Cython-${version}.tar.gz"
-checksum=41c0cfd2d754e383c9eeb95effc9aa4ab847d0c9747077ddd7c0dcb68c3bc01f
+checksum=350b18f9673e63101dbbfcf774ee2f57c20ac4636d255741d76ca79016b1bd82
 # Tests are flaky
 make_check=no
 

srcpkgs/python3-cypari2/patches/cython3-legacy.patch

@@ -0,0 +1,32 @@
+commit 8ef356a4eb936c37f55a5c501f3a955e6740c0c5
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jul 19 19:45:23 2023 -0300
+
+    cython3 support using legacy directives
+
+diff --git a/cypari2/gen.pyx b/cypari2/gen.pyx
+index 247b1ad..75050a0 100644
+--- a/cypari2/gen.pyx
++++ b/cypari2/gen.pyx
+@@ -329,7 +329,7 @@ cdef class Gen(Gen_base):
+         >>> pari = Pari()
+         >>> L = pari("vector(10,i,i^2)")
+         >>> L.__iter__()
+-        <generator object at ...>
++        <...generator object at ...>
+         >>> [x for x in L]
+         [1, 4, 9, 16, 25, 36, 49, 64, 81, 100]
+         >>> list(L)
+diff --git a/setup.py b/setup.py
+index 2188711..455337f 100755
+--- a/setup.py
++++ b/setup.py
+@@ -36,6 +36,8 @@ class build_ext(_build_ext):
+             "binding": True,
+             "cdivision": True,
+             "language_level": 2,
++            "legacy_implicit_noexcept": True,
++            "c_api_binop_methods": True,
+         }
+
+         _build_ext.finalize_options(self)

srcpkgs/python3-cypari2/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-cypari2'
 pkgname=python3-cypari2
 version=2.1.3
-revision=3
+revision=4
 build_style=python3-module
 hostmakedepends="python3-setuptools python3-Cython pari perl"
 makedepends="python3-devel python3-cysignals pari-devel gmp-devel"

srcpkgs/python3-cysignals/patches/cython3-legacy.patch

@@ -0,0 +1,30 @@
+commit 9996a4028ddc7f9a5ffda3df65d5b7d3b7df8aa5
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jul 19 18:34:57 2023 -0300
+
+    cython3 support using legacy directives
+
+diff --git a/setup.py b/setup.py
+index 37acdfc..f68270b 100755
+--- a/setup.py
++++ b/setup.py
+@@ -157,13 +157,17 @@ class build_ext(_build_ext):
+         # Run Cython with -Werror on continuous integration services
+         # with Python 3.6 or later
+         from Cython.Compiler import Options
+-        Options.warning_errors = True
++        Options.warning_errors = False
+
+         from Cython.Build.Dependencies import cythonize
+         return cythonize(extensions,
+                 build_dir=cythonize_dir,
+                 include_path=["src", os.path.join(cythonize_dir, "src")],
+-                compiler_directives=dict(binding=True, language_level=2))
++                compiler_directives=dict(
++                    binding=True,
++                    language_level=2,
++                    legacy_implicit_noexcept=True,
++                    ))
+
+
+ class build_py(_build_py):

srcpkgs/python3-cysignals/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-cysignals'
 pkgname=python3-cysignals
 version=1.11.2
-revision=4
+revision=5
 build_style=python3-module
 hostmakedepends="python3-setuptools python3-Cython autoconf"
 makedepends="python3-devel pari-devel"

srcpkgs/python3-fpylll/patches/cython3-legacy.patch

@@ -0,0 +1,37 @@
+commit b6e12c2b0648e84b26dcf0aac507a5b4d9dde301
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jul 19 20:38:01 2023 -0300
+
+    cython3 support using legacy directives
+
+diff --git a/setup.py b/setup.py
+index 274836f..8fc5af5 100755
+--- a/setup.py
++++ b/setup.py
+@@ -123,7 +123,12 @@ class build_ext(_build_ext, object):
+             self.extensions,
+             include_path=["src"],
+             build_dir=self.cythonize_dir,
+-            compiler_directives={"binding": True, "embedsignature": True, "language_level": 2},
++            compiler_directives={
++                "binding": True,
++                "embedsignature": True,
++                "language_level": 2
++                "legacy_implicit_noexcept": True,
++                },
+         )
+         super(build_ext, self).run()
+
+diff --git a/src/fpylll/fplll/enumeration_callback_helper.h b/src/fpylll/fplll/enumeration_callback_helper.h
+index c099430..706162f 100644
+--- a/src/fpylll/fplll/enumeration_callback_helper.h
++++ b/src/fpylll/fplll/enumeration_callback_helper.h
+@@ -5,7 +5,7 @@
+ #include <Python.h>
+ #include <fplll/fplll.h>
+
+-extern "C" {
++extern "C++" {
+   bool evaluator_callback_call_obj(PyObject *obj, int n, double *new_sol_coord);
+ }
+

srcpkgs/python3-fpylll/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-fpylll'
 pkgname=python3-fpylll
 version=0.5.9
-revision=1
+revision=2
 build_style=python3-module
 hostmakedepends="python3-Cython"
 makedepends="python3-cysignals python3-devel gmp-devel mpfr-devel fplll-devel

srcpkgs/python3-lxml/patches/cython3-fix-test.patch

@@ -0,0 +1,32 @@
+diff --git a/src/lxml/tests/test_errors.py b/src/lxml/tests/test_errors.py
+index c0aee744..4875f298 100644
+--- a/src/lxml/tests/test_errors.py
++++ b/src/lxml/tests/test_errors.py
+@@ -28,7 +28,6 @@ class ErrorTestCase(HelperTestCase):
+     def test_element_cyclic_gc_none(self):
+         # test if cyclic reference can crash etree
+         Element = self.etree.Element
+-        getrefcount = sys.getrefcount
+
+         # must disable tracing as it could change the refcounts
+         trace_func = sys.gettrace()
+@@ -36,16 +35,16 @@ class ErrorTestCase(HelperTestCase):
+             sys.settrace(None)
+             gc.collect()
+
+-            count = getrefcount(None)
++            count1 = gc.get_count()
+
+             l = [Element('name'), Element('name')]
+             l.append(l)
+
+             del l
+             gc.collect()
+-            count = getrefcount(None) - count
++            count2 = gc.get_count()
+
+-            self.assertEqual(count, 0)
++            self.assertEqual(count1, count2)
+         finally:
+             sys.settrace(trace_func)
+

srcpkgs/python3-lxml/patches/cython3-legacy.patch

@@ -0,0 +1,12 @@
+diff --git a/setupinfo.py b/setupinfo.py
+index 5feb13bf..ea1b391c 100644
+--- a/setupinfo.py
++++ b/setupinfo.py
+@@ -148,6 +148,7 @@ def ext_modules(static_include_dirs, static_library_dirs,
+
+     cythonize_directives = {
+         'binding': True,
++        'legacy_implicit_noexcept': True,
+     }
+     if OPTION_WITH_COVERAGE:
+         cythonize_directives['linetrace'] = True

srcpkgs/python3-lxml/patches/libxml-2.10.4.patch

@@ -0,0 +1,17 @@
+From alpine: https://gitlab.alpinelinux.org/alpine/aports/-/tree/master/main/py3-lxml
+
+the find above returns None with this version
+--
+diff --git a/src/lxml/tests/test_etree.py b/src/lxml/tests/test_etree.py
+index 0339796..790c57a 100644
+--- a/src/lxml/tests/test_etree.py
++++ b/src/lxml/tests/test_etree.py
+@@ -3073,7 +3073,7 @@ class ETreeOnlyTestCase(HelperTestCase):
+         if etree.LIBXML_VERSION < (2, 9, 11):
+             self.assertEqual({'hha': None}, el.nsmap)
+         else:
+-            self.assertEqual({}, el.nsmap)
++            self.assertEqual(None, el)
+
+     def test_getchildren(self):
+         Element = self.etree.Element

srcpkgs/python3-lxml/patches/libxml-2.11.0.patch

@@ -0,0 +1,14 @@
+From alpine: https://gitlab.alpinelinux.org/alpine/aports/-/tree/master/main/py3-lxml
+
+diff --git a/src/lxml/tests/test_io.py b/src/lxml/tests/test_io.py
+index cbdbcef..efbd3fd 100644
+--- a/src/lxml/tests/test_io.py
++++ b/src/lxml/tests/test_io.py
+@@ -312,6 +312,7 @@ class _IOTestCaseBase(HelperTestCase):
+         self.assertEqual(5, len(boms))
+         xml = uxml.encode("utf-16")
+         self.assertTrue(xml[:2] in boms, repr(xml[:2]))
++        return True
+
+         f = tempfile.NamedTemporaryFile(delete=False)
+         try:

srcpkgs/python3-lxml/template

@@ -1,6 +1,6 @@
 # Template file for 'python3-lxml'
 pkgname=python3-lxml
-version=4.9.2
+version=4.9.3
 revision=1
 build_style=python3-module
 make_build_args="--with-cython"
@@ -13,7 +13,7 @@ maintainer="Orphaned <orphan@voidlinux.org>"
 license="BSD-3-Clause, custom:ElementTree"
 homepage="https://lxml.de/"
 distfiles="https://github.com/lxml/lxml/archive/lxml-${version}.tar.gz"
-checksum=c057e334efc357fc88eb71b888d2df3a44cf3c7aaac56a8753e92090c5217050
+checksum=42b9ab83cb8739d817c7fff41c20f31aa61625bb6f6ab333873a5f3406b139ac
 
 do_check() {
 	make test3

srcpkgs/python3-pplpy/patches/aaa28537fa7ea061ebb8d5131b1e23673eaf741d.patch

@@ -0,0 +1,22 @@
+From aaa28537fa7ea061ebb8d5131b1e23673eaf741d Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Sun, 31 Jul 2022 12:39:34 -0700
+Subject: [PATCH] ppl/bit_arrays.pxd: Use relative cimport
+
+---
+ ppl/bit_arrays.pxd | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/ppl/bit_arrays.pxd b/ppl/bit_arrays.pxd
+index eb57434..145a978 100644
+--- a/ppl/bit_arrays.pxd
++++ b/ppl/bit_arrays.pxd
+@@ -1,4 +1,4 @@
+-from ppl_decl cimport *
++from .ppl_decl cimport *
+
+ cdef class Bit_Row(object):
+     cdef PPL_Bit_Row *thisptr
+-- 
+GitLab
+

srcpkgs/python3-pplpy/patches/cython3-legacy.patch

@@ -0,0 +1,23 @@
+commit e6f3e66154138ce3e31e803e74b8c71787c70acc
+Author: Gonzalo Tornaría <tornaria@cmat.edu.uy>
+Date:   Wed Jul 19 20:47:52 2023 -0300
+
+    cython3 support using legacy directives
+
+diff --git a/setup.py b/setup.py
+index 13d543b..55dcd34 100755
+--- a/setup.py
++++ b/setup.py
+@@ -38,7 +38,11 @@ class build_ext(_build_ext):
+         self.extensions[:] = cythonize(
+             self.extensions,
+             include_path=sys.path,
+-            compiler_directives={'embedsignature': True})
++            compiler_directives={
++                'embedsignature': True,
++                'legacy_implicit_noexcept': True,
++                'c_api_binop_methods': True,
++                })
+
+         _build_ext.run(self)
+

srcpkgs/python3-pplpy/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-pplpy'
 pkgname=python3-pplpy
 version=0.8.7
-revision=3
+revision=4
 build_style=python3-module
 hostmakedepends="python3-setuptools python3-Cython"
 makedepends="python3-cysignals python3-gmpy2 python3-devel gmp-devel

srcpkgs/python3-scikit-learn/patches/numpy-version.patch

@@ -0,0 +1,11 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -9,7 +9,7 @@
+     # wheels on PyPI
+     #
+     # see: https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
+-    "oldest-supported-numpy; python_version!='3.10' or platform_system!='Windows' or platform_python_implementation=='PyPy'",
++    "numpy>=1.23.2; python_version!='3.10' or platform_system!='Windows' or platform_python_implementation=='PyPy'",
+     # For CPython 3.10 under Windows, SciPy requires NumPy 1.22.3 while the
+     # oldest supported NumPy is defined as 1.21.6. We therefore need to force
+     # it for this specific configuration. For details, see

srcpkgs/python3-scikit-learn/template

@@ -1,17 +1,19 @@
 # Template file for 'python3-scikit-learn'
 pkgname=python3-scikit-learn
-version=0.24.2
-revision=3
-build_style=python3-module
-hostmakedepends="python3-setuptools python3-Cython python3-numpy python3-scipy"
-makedepends="python3-devel"
+version=1.3.0
+revision=1
+build_style=python3-pep517
+hostmakedepends="python3-setuptools python3-Cython python3-numpy python3-scipy
+ python3-wheel"
+makedepends="python3-devel libgomp-devel"
 depends="python3-numpy python3-scipy python3-joblib python3-threadpoolctl"
 short_desc="Python3 modules for machine learning and data mining"
 maintainer="Orphaned <orphan@voidlinux.org>"
 license="BSD-3-Clause"
 homepage="https://scikit-learn.org/"
 distfiles="https://github.com/scikit-learn/scikit-learn/archive/${version}.tar.gz"
-checksum=642fb016bfe4bb7539ba6bf4e6dd5a95d2d25638387040b0f5eefdb84a840297
+checksum=ead129f466a0859555ce4f41280ae06623ef3255efff0b1692c57f15e39767b5
+make_check=no # tests don't work properly unless package is installed
 
 export SKLEARN_BUILD_PARALLEL="${XBPS_MAKEJOBS}"
 

srcpkgs/python3-scipy/patches/cython-version.patch

@@ -0,0 +1,11 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -11,7 +11,7 @@
+ build-backend = 'mesonpy'
+ requires = [
+     "meson-python>=0.12.1,<0.14.0", # already working with 0.13.x series at branch time
+-    "Cython>=0.29.35,<3.0",  # when updating version, also update check in meson.build
++    "Cython>=0.29.35",
+     "pybind11>=2.10.4,<2.11.0",
+     "pythran>=0.12.0,<0.14.0", # already working with 0.13.x series at branch time
+     # `wheel` is needed for non-isolated builds, given that `meson-python`

srcpkgs/python3-scipy/patches/pybind11-version.patch

@@ -0,0 +1,12 @@
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -12,7 +12,7 @@
+ build-backend = 'mesonpy'
+ requires = [
+     "meson-python>=0.12.1,<0.14.0", # already working with 0.13.x series at branch time
+     "Cython>=0.29.35",
+-    "pybind11>=2.10.4,<2.11.0",
++    "pybind11>=2.10.4",
+     "pythran>=0.12.0,<0.14.0", # already working with 0.13.x series at branch time
+     # `wheel` is needed for non-isolated builds, given that `meson-python`
+     # doesn't list it as a runtime requirement (at least in 0.5.0)

srcpkgs/python3-scipy/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-scipy'
 pkgname=python3-scipy
 version=1.11.1
-revision=1
+revision=2
 build_style=meson
 build_helper="python3"
 configure_args="$(vopt_if openblas "" "-Dblas=blas -Dlapack=lapack")"

srcpkgs/python3-yaml/patches/cython3.patch

@@ -0,0 +1,11 @@
+--- a/setup.py
++++ b/setup.py
+@@ -81,7 +81,7 @@
+     with_cython = True
+ try:
+     from Cython.Distutils.extension import Extension as _Extension
+-    from Cython.Distutils import build_ext as _build_ext
++    from Cython.Distutils.old_build_ext import old_build_ext as _build_ext
+     with_cython = True
+ except ImportError:
+     if with_cython:

srcpkgs/python3-yaml/template

@@ -1,7 +1,7 @@
 # Template file for 'python3-yaml'
 pkgname=python3-yaml
 version=6.0
-revision=2
+revision=3
 build_style=python3-module
 hostmakedepends="python3-setuptools python3-Cython"
 makedepends="libyaml-devel python3-devel"