commit: 95bc234cf4f8d823d890a17571c7d517b42e6c4e Author: Sam James <sam <AT> gentoo <DOT> org> AuthorDate: Mon Jun 12 00:44:01 2023 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Mon Jun 12 00:44:06 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=95bc234c
dev-python/numpy: fix build/link with libcxx New revision as this pretty much only worked by chance before and could affect the installed files as a result. Closes: https://bugs.gentoo.org/893962 Signed-off-by: Sam James <sam <AT> gentoo.org> .../numpy/files/numpy-1.24.3-fix-c++-linkage.patch | 25 +++ dev-python/numpy/numpy-1.24.3-r1.ebuild | 176 +++++++++++++++++++++ 2 files changed, 201 insertions(+) diff --git a/dev-python/numpy/files/numpy-1.24.3-fix-c++-linkage.patch b/dev-python/numpy/files/numpy-1.24.3-fix-c++-linkage.patch new file mode 100644 index 000000000000..ae7d5ba0ea49 --- /dev/null +++ b/dev-python/numpy/files/numpy-1.24.3-fix-c++-linkage.patch @@ -0,0 +1,25 @@ +https://bugs.gentoo.org/893962 +https://github.com/numpy/numpy/issues/23122 +https://github.com/numpy/numpy/pull/23601 + +From 0a0240bcdad5daa0b84781719b3f8a002ef0f82b Mon Sep 17 00:00:00 2001 +From: Ralf Gommers <[email protected]> +Date: Sun, 16 Apr 2023 22:23:38 +0100 +Subject: [PATCH] BLD: use the C++ linker to link `_multiarray_umath.so` + +This gets rid of undefined symbol issues for `assert`. + +Closes gh-23122 +Closes gh-23595 +--- a/numpy/core/setup.py ++++ b/numpy/core/setup.py +@@ -1010,9 +1010,6 @@ def generate_umath_doc_header(ext, build_dir): + svml_objs.sort() + + config.add_extension('_multiarray_umath', +- # Forcing C language even though we have C++ sources. +- # It forces the C linker and don't link C++ runtime. +- language = 'c', + sources=multiarray_src + umath_src + + common_src + + [generate_config_h, diff --git a/dev-python/numpy/numpy-1.24.3-r1.ebuild b/dev-python/numpy/numpy-1.24.3-r1.ebuild new file mode 100644 index 000000000000..7abf863915aa --- /dev/null +++ b/dev-python/numpy/numpy-1.24.3-r1.ebuild @@ -0,0 +1,176 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{9..11} pypy3 ) +PYTHON_REQ_USE="threads(+)" + +FORTRAN_NEEDED=lapack + +inherit distutils-r1 flag-o-matic fortran-2 multiprocessing pypi +inherit toolchain-funcs + +DOC_PV=${PV} +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" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~loong ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x64-solaris" +IUSE="lapack" + +RDEPEND=" + lapack? ( + >=virtual/cblas-3.8 + >=virtual/lapack-3.8 + ) +" +BDEPEND=" + ${RDEPEND} + <dev-python/cython-3[${PYTHON_USEDEP}] + >=dev-python/cython-0.29.30[${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}] + ) +" + +PATCHES=( + "${FILESDIR}"/numpy-1.22.0-no-hardcode-blasv2.patch + "${FILESDIR}"/numpy-1.24.3-fix-c++-linkage.patch +) + +distutils_enable_tests pytest + +python_prepare_all() { + # Allow use with setuptools 60.x + # See numpy-1.22.1-revert-setuptools-upper-bound.patch for details + export SETUPTOOLS_USE_DISTUTILS=stdlib + + if use lapack; then + local incdir="${EPREFIX}"/usr/include + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = ${incdir} + library_dirs = ${libdir} + blas_libs = cblas,blas + [lapack] + library_dirs = ${libdir} + lapack_libs = lapack + EOF + else + export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None + fi + + export CC="$(tc-getCC) ${CFLAGS}" + + append-flags -fno-strict-aliasing + + # See progress in http://projects.scipy.org/scipy/numpy/ticket/573 + # with the subtle difference that we don't want to break Darwin where + # -shared is not a valid linker argument + if [[ ${CHOST} != *-darwin* ]]; then + append-ldflags -shared + fi + + # only one fortran to link with: + # linking with cblas and lapack library will force + # autodetecting and linking to all available fortran compilers + append-fflags -fPIC + if use lapack; then + NUMPY_FCONFIG="config_fc --noopt --noarch" + # workaround bug 335908 + [[ $(tc-getFC) == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95" + fi + + # don't version f2py, we will handle it. + sed -i -e '/f2py_exe/s: + os\.path.*$::' numpy/f2py/setup.py || die + + distutils-r1_python_prepare_all +} + +python_compile() { + local -x MAKEOPTS=-j1 #660754 + + distutils-r1_python_compile ${NUMPY_FCONFIG} +} + +python_test() { + local EPYTEST_DESELECT=( + # very disk- and memory-hungry + numpy/lib/tests/test_histograms.py::TestHistogram::test_big_arrays + numpy/lib/tests/test_io.py::test_large_zip + + # precision problems + numpy/core/tests/test_umath_accuracy.py::TestAccuracy::test_validate_transcendentals + + # runs the whole test suite recursively, that's just crazy + numpy/core/tests/test_mem_policy.py::test_new_policy + + # very slow, unlikely to be practically useful + numpy/typing/tests/test_typing.py + ) + + if use arm && [[ $(uname -m || echo "unknown") == "armv8l" ]] ; then + # Degenerate case. arm32 chroot on arm64. + # bug #774108 + EPYTEST_DESELECT+=( + numpy/core/tests/test_cpu_features.py::Test_ARM_Features::test_features + ) + fi + + if use x86 ; then + EPYTEST_DESELECT+=( + # https://github.com/numpy/numpy/issues/18388 + numpy/core/tests/test_umath.py::TestRemainder::test_float_remainder_overflow + # https://github.com/numpy/numpy/issues/18387 + numpy/random/tests/test_generator_mt19937.py::TestRandomDist::test_pareto + # more precision problems + numpy/core/tests/test_einsum.py::TestEinsum::test_einsum_sums_int16 + ) + fi + + case "${ABI}" in + alpha|arm|hppa|m68k|o32|ppc|s390|sh|sparc|x86) + EPYTEST_DESELECT+=( + # too large for 32-bit platforms + numpy/core/tests/test_ufunc.py::TestUfunc::test_identityless_reduction_huge_array + ) + ;; + *) + ;; + esac + + distutils_install_for_testing --single-version-externally-managed \ + --record "${TMPDIR}/record.txt" ${NUMPY_FCONFIG} + + cd "${TEST_DIR}/lib" || die + epytest -k "not _fuzz" -n "$(makeopts_jobs)" +} + +python_install() { + # https://github.com/numpy/numpy/issues/16005 + local mydistutilsargs=( build_src ) + distutils-r1_python_install ${NUMPY_FCONFIG} + python_optimize +} + +python_install_all() { + local DOCS=( LICENSE.txt README.md THANKS.txt ) + distutils-r1_python_install_all +}
