commit: cab362d71396a6f4b451962ac310a408f4d2e14d Author: Michał Górny <mgorny <AT> gentoo <DOT> org> AuthorDate: Tue Aug 22 04:05:12 2023 +0000 Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> CommitDate: Tue Aug 22 04:05:26 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cab362d7
dev-python/numpy: Backport segfault fix to 1.26.0_beta1 Signed-off-by: Michał Górny <mgorny <AT> gentoo.org> .../files/numpy-1.26.0_beta1-npy_cast_info.patch | 44 ++++++ dev-python/numpy/numpy-1.26.0_beta1-r1.ebuild | 154 +++++++++++++++++++++ 2 files changed, 198 insertions(+) diff --git a/dev-python/numpy/files/numpy-1.26.0_beta1-npy_cast_info.patch b/dev-python/numpy/files/numpy-1.26.0_beta1-npy_cast_info.patch new file mode 100644 index 000000000000..cd09573deb7f --- /dev/null +++ b/dev-python/numpy/files/numpy-1.26.0_beta1-npy_cast_info.patch @@ -0,0 +1,44 @@ +From 9cfb416aad45260e1cc837029638d6b39cea9e38 Mon Sep 17 00:00:00 2001 +From: Nathan Goldbaum <[email protected]> +Date: Mon, 21 Aug 2023 15:45:11 -0600 +Subject: [PATCH] BUG: fix NPY_cast_info error handling in choose + +--- + numpy/core/src/multiarray/item_selection.c | 2 +- + numpy/core/tests/test_multiarray.py | 6 ++++++ + 2 files changed, 7 insertions(+), 1 deletion(-) + +diff --git a/numpy/core/src/multiarray/item_selection.c b/numpy/core/src/multiarray/item_selection.c +index e935a27edb6..c1d4a950815 100644 +--- a/numpy/core/src/multiarray/item_selection.c ++++ b/numpy/core/src/multiarray/item_selection.c +@@ -968,6 +968,7 @@ PyArray_Choose(PyArrayObject *ip, PyObject *op, PyArrayObject *out, + PyArrayObject **mps, *ap; + PyArrayMultiIterObject *multi = NULL; + npy_intp mi; ++ NPY_cast_info cast_info = {.func = NULL}; + ap = NULL; + + /* +@@ -1045,7 +1046,6 @@ PyArray_Choose(PyArrayObject *ip, PyObject *op, PyArrayObject *out, + npy_intp transfer_strides[2] = {elsize, elsize}; + npy_intp one = 1; + NPY_ARRAYMETHOD_FLAGS transfer_flags = 0; +- NPY_cast_info cast_info = {.func = NULL}; + if (PyDataType_REFCHK(dtype)) { + int is_aligned = IsUintAligned(obj); + PyArray_GetDTypeTransferFunction( +diff --git a/numpy/core/tests/test_multiarray.py b/numpy/core/tests/test_multiarray.py +index 966b75cc122..2836c8985c9 100644 +--- a/numpy/core/tests/test_multiarray.py ++++ b/numpy/core/tests/test_multiarray.py +@@ -10043,3 +10043,9 @@ def test_gh_22683(): + np.choose(np.zeros(10000, dtype=int), [a], out=a) + refc_end = sys.getrefcount(b) + assert refc_end - refc_start < 10 ++ ++ ++def test_gh_24459(): ++ a = np.zeros((50, 3), dtype=np.float64) ++ with pytest.raises(TypeError): ++ np.choose(a, [3, -1]) diff --git a/dev-python/numpy/numpy-1.26.0_beta1-r1.ebuild b/dev-python/numpy/numpy-1.26.0_beta1-r1.ebuild new file mode 100644 index 000000000000..1072d42ba823 --- /dev/null +++ b/dev-python/numpy/numpy-1.26.0_beta1-r1.ebuild @@ -0,0 +1,154 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=meson-python +PYTHON_COMPAT=( python3_{10..12} pypy3 ) +PYTHON_REQ_USE="threads(+)" +FORTRAN_NEEDED=lapack + +inherit distutils-r1 flag-o-matic fortran-2 multiprocessing pypi toolchain-funcs + +DESCRIPTION="Fast array and numerical python library" +HOMEPAGE=" + https://numpy.org/ + https://github.com/numpy/numpy/ + https://pypi.org/project/numpy/ +" + +LICENSE="BSD" +SLOT="0" +IUSE="lapack" +if [[ ${PV} != *_[rab]* ]] ; then + KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86" +fi + +RDEPEND=" + lapack? ( + >=virtual/cblas-3.8 + >=virtual/lapack-3.8 + ) +" +BDEPEND=" + ${RDEPEND} + >=dev-util/meson-1.1.0 + >=dev-python/cython-3.0.0[${PYTHON_USEDEP}] + lapack? ( + virtual/pkgconfig + ) + test? ( + $(python_gen_cond_dep ' + >=dev-python/cffi-1.14.0[${PYTHON_USEDEP}] + ' 'python*') + dev-python/charset-normalizer[${PYTHON_USEDEP}] + >=dev-python/hypothesis-5.8.0[${PYTHON_USEDEP}] + dev-python/pytest-xdist[${PYTHON_USEDEP}] + >=dev-python/pytz-2019.3[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_prepare_all() { + local PATCHES=( + # https://github.com/numpy/numpy/pull/24484 + "${FILESDIR}/${P}-npy_cast_info.patch" + ) + + append-flags -fno-strict-aliasing + + distutils-r1_python_prepare_all +} + +python_configure_all() { + DISTUTILS_ARGS=( + -Dblas=$(usev lapack cblas) + -Dlapack=$(usev lapack lapack) + # TODO: cpu-* options + ) +} + +python_test() { + local EPYTEST_DESELECT=( + # Very disk-and-memory-hungry + lib/tests/test_io.py::TestSaveTxt::test_large_zip + lib/tests/test_io.py::TestSavezLoad::test_closing_fid + lib/tests/test_io.py::TestSavezLoad::test_closing_zipfile_after_load + + # Precision problems + core/tests/test_umath_accuracy.py::TestAccuracy::test_validate_transcendentals + + # Runs the whole test suite recursively, that's just crazy + core/tests/test_mem_policy.py::test_new_policy + + typing/tests/test_typing.py + # Uses huge amount of memory + core/tests/test_mem_overlap.py + + # TODO: crashes + lib/tests/test_histograms.py::TestHistogram::test_big_arrays + ) + + if use arm && [[ $(uname -m || echo "unknown") == "armv8l" ]] ; then + # Degenerate case of arm32 chroot on arm64, bug #774108 + EPYTEST_DESELECT+=( + core/tests/test_cpu_features.py::Test_ARM_Features::test_features + ) + fi + + if use x86 ; then + EPYTEST_DESELECT+=( + # https://github.com/numpy/numpy/issues/18388 + core/tests/test_umath.py::TestRemainder::test_float_remainder_overflow + # https://github.com/numpy/numpy/issues/18387 + random/tests/test_generator_mt19937.py::TestRandomDist::test_pareto + # more precision problems + core/tests/test_einsum.py::TestEinsum::test_einsum_sums_int16 + ) + fi + + if use hppa ; then + EPYTEST_DESELECT+=( + # TODO: Get selectedrealkind updated! + # bug #907228 + # https://github.com/numpy/numpy/issues/3424 (https://github.com/numpy/numpy/issues/3424#issuecomment-412369029) + # https://github.com/numpy/numpy/pull/21785 + f2py/tests/test_kind.py::TestKind::test_real + f2py/tests/test_kind.py::TestKind::test_quad_precision + ) + fi + + if [[ $(tc-endian) == "big" ]] ; then + # https://github.com/numpy/numpy/issues/11831 and bug #707116 + EPYTEST_DESELECT+=( + 'f2py/tests/test_return_character.py::TestFReturnCharacter::test_all_f77[s1]' + 'f2py/tests/test_return_character.py::TestFReturnCharacter::test_all_f90[t1]' + 'f2py/tests/test_return_character.py::TestFReturnCharacter::test_all_f90[s1]' + 'f2py/tests/test_return_character.py::TestFReturnCharacter::test_all_f77[t1]' + f2py/tests/test_kind.py::TestKind::test_int + ) + fi + + case "${ABI}" in + alpha|arm|hppa|m68k|o32|ppc|s390|sh|sparc|x86) + EPYTEST_DESELECT+=( + # too large for 32-bit platforms + core/tests/test_ufunc.py::TestUfunc::test_identityless_reduction_huge_array + 'core/tests/test_multiarray.py::TestDot::test_huge_vectordot[float64]' + 'core/tests/test_multiarray.py::TestDot::test_huge_vectordot[complex128]' + ) + ;; + *) + ;; + esac + + rm -rf numpy || die + epytest -n "$(makeopts_jobs)" --pyargs numpy +} + +python_install_all() { + local DOCS=( LICENSE.txt README.md THANKS.txt ) + distutils-r1_python_install_all +}
