[gentoo-commits] repo/gentoo:master commit in: dev-python/numpy/files/, dev-python/numpy/

["Sam James" <sam@gentoo.org>]

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 <ralf.gommers@gmail.com>
+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
+}