[gentoo-commits] repo/gentoo:master commit in: dev-python/scipy/

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

commit:     51d4183bcebc56b75332e0a6da4d844a09c9c010
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 25 00:32:22 2021 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu Nov 25 00:32:22 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=51d4183b

dev-python/scipy: add 1.7.3

Signed-off-by: Sam James <sam <AT> gentoo.org>

 dev-python/scipy/Manifest           |   1 +
 dev-python/scipy/scipy-1.7.3.ebuild | 185 ++++++++++++++++++++++++++++++++++++
 2 files changed, 186 insertions(+)

diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index 8219933ad788..ab7dc2d11b63 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -2,6 +2,7 @@ DIST scipy-1.6.2.tar.gz 27187804 BLAKE2B af3578bc029c3af548c04144d7405ac8e6f8e05
 DIST scipy-1.6.3.tar.gz 27187987 BLAKE2B 30f7171ca0dc0842f254472f4b52c0b0ad4389964a140cc4b94f9d85437c5a7da238c082be503242d433f1d3c65c3fd4afeb2f7831eea39ce303077406e718df SHA512 10ff25da84ce09ae231e781873902d8040d79868721d75a3f9facee177e7f46f7c9c34374feee6fe2253ddd968716d2993658ce514c4ac0c98d255c06a6ef808
 DIST scipy-1.7.1.tar.gz 36102628 BLAKE2B 67a414d863c61bf419fa907b9bed53b57beedc20d71d0630fac9719f02e951ea79b893d0803b385936a7c04a6c2f723d3870f0498f71e3c210ccd6ee75a009dc SHA512 81fea7e4f5fbcd537d662273507b6ac75bd4cf900567da8083ac86fb06d9f96b010d01a1697db53211440f0fdb2d89510313bafd3d383284d0ab9a08311dd102
 DIST scipy-1.7.2.tar.gz 36104529 BLAKE2B 8e31a71e8cd69a83e1b60747a01e34f79e42664089a2c41aa263c1697a689464fde0b467063e0ae3bafa37721294a79e21d0eedc6023c1558aea6e0105aefeae SHA512 87596430571ff2a43f067eaaf3254c0841dac82b9152cb64040f1a4d9bc5429aebc31c619ce55d74727f2a79567dfef4acbc6252c24c46d3c8849f97e6e8cfef
+DIST scipy-1.7.3.tar.gz 36102562 BLAKE2B 9a605a45d8f03aae3411a6fa92e32c7f6d10373455493ead847d4ad01429b55dbbc33c1a0309d6c9d76d3e9ab1a06772df59c08d393377896c4b534599f9eb9b SHA512 83fe00cf708a13a08d28af7022ec645d8976c177f2fefb56e0a47bfcbec726330b973d1f44364e23c939ae708e239a05904346f515ea1a37e8b70ad160b81cee
 DIST scipy-html-1.6.1.zip 23946591 BLAKE2B d3464c342b1d4f43e17e214c7557737913bf4131f88b9d569cff106c75dc7ebf0d065283792fddc189e2a3ddc322f1b2b4f38c6d313569f28395e79680060b58 SHA512 73561f9daa303c6e967f9b11952c6239dea7ff1a2fa02434354ac78fcffe7a552aa0f1043a17cb5c35a442def499eff199856cca8efa1415449cbf54f0d4913b
 DIST scipy-html-1.6.2.zip 23947380 BLAKE2B e4616a157c037b0830fc32d23678fb7e8ebe023d1fd9f0f762695a0d93bc56e432e441e675ec3c7a7d6586a665f6127ce49d570f1716876e58afb402761f8e95 SHA512 119a2227a808c752a751bc7bec6463da739c68391ebac8d2451998d90ebe03b2af401adbf987f0b694244e715c0ef1fd86c2f4a36c48dbb1ff7cdf4d914875df
 DIST scipy-html-1.7.1.zip 32435246 BLAKE2B fd8173da41aba95a14b1376f848bc668c4659bf1bbbdd0f87d926633d36f29c039957d38be145a5583010ebd83f6458090f75bdad773cc0f1591664e13c04c20 SHA512 ee59722878f6ef2d2319cdf4e6a60d3d1184f7c22752f9a8859eaa46fb677ebac9e8eef9c0826998e12bac9399e336799843341ef203224a82c9101347149672

diff --git a/dev-python/scipy/scipy-1.7.3.ebuild b/dev-python/scipy/scipy-1.7.3.ebuild
new file mode 100644
index 000000000000..cdc137b1517c
--- /dev/null
+++ b/dev-python/scipy/scipy-1.7.3.ebuild
@@ -0,0 +1,185 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit fortran-2 distutils-r1 flag-o-matic toolchain-funcs
+
+# upstream is slacking forever with doc updates
+DOC_PV=1.7.1
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="https://www.scipy.org/"
+SRC_URI="
+	mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz
+	doc? (
+		https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip
+		https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 -hppa ~ia64 ~riscv ~s390 ~sparc ~x86"
+IUSE="doc +pythran sparse"
+
+DEPEND="
+	>=dev-python/numpy-1.16.5[lapack,${PYTHON_USEDEP}]
+	sci-libs/arpack:0=
+	virtual/cblas
+	virtual/lapack
+	sparse? ( sci-libs/umfpack:0= )"
+RDEPEND="${DEPEND}
+	dev-python/pillow[${PYTHON_USEDEP}]"
+BDEPEND="
+	dev-lang/swig
+	>=dev-python/cython-0.29.18[${PYTHON_USEDEP}]
+	dev-python/pybind11[${PYTHON_USEDEP}]
+	virtual/pkgconfig
+	doc? ( app-arch/unzip )
+	pythran? ( dev-python/pythran[${PYTHON_USEDEP}] )
+	test? (
+		dev-python/nose[${PYTHON_USEDEP}]
+	)"
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+distutils_enable_tests pytest
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.7.1-pythran-tests-32-bit.patch
+)
+
+src_unpack() {
+	default
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die
+	fi
+}
+
+pc_incdir() {
+	$(tc-getPKG_CONFIG) --cflags-only-I $@ | \
+		sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||'
+}
+
+pc_libdir() {
+	$(tc-getPKG_CONFIG) --libs-only-L $@ | \
+		sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||'
+}
+
+pc_libs() {
+	$(tc-getPKG_CONFIG) --libs-only-l $@ | \
+		sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \
+		-e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \
+		| tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||'
+}
+
+python_prepare_all() {
+	# scipy automatically detects libraries by default
+	export {FFTW,FFTW3,UMFPACK}=None
+	use sparse && unset UMFPACK
+	# the missing symbols are in -lpythonX.Y, but since the version can
+	# differ, we just introduce the same scaryness as on Linux/ELF
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+	[[ -z ${FC}  ]] && export FC="$(tc-getFC)"
+	# hack to force F77 to be FC until bug #278772 is fixed
+	[[ -z ${F77} ]] && export F77="$(tc-getFC)"
+	export F90="${FC}"
+	export SCIPY_FCONFIG="config_fc --noopt --noarch"
+	append-fflags -fPIC
+
+	local libdir="${EPREFIX}"/usr/$(get_libdir)
+	cat >> site.cfg <<-EOF || die
+		[blas]
+		include_dirs = $(pc_incdir cblas)
+		library_dirs = $(pc_libdir cblas blas):${libdir}
+		blas_libs = $(pc_libs cblas blas)
+		[lapack]
+		library_dirs = $(pc_libdir lapack):${libdir}
+		lapack_libs = $(pc_libs lapack)
+	EOF
+	cat >> setup.cfg <<-EOF || die
+		[options]
+		zip_safe = False
+	EOF
+
+	# TODO
+	sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \
+		-i scipy/stats/tests/test_continuous_basic.py || die
+
+	# Skip known-failing test. Broken on all versions in Gentoo for years.
+	# bug #743295
+	sed -e 's:test_bisplev_integer_overflow:_&:' \
+			-i scipy/interpolate/tests/test_fitpack.py || die
+
+	# Skip a few 32-bit related failures
+	if use x86 ; then
+		# TODO: Tidy this up and switch to epytest
+		sed -i -e 's:test_nd_axis_m1:_&:' \
+			-e 's:test_nd_axis_0:_&:' \
+			-e 's:test_maxiter_worsening:_&:' \
+			-e 's:test_pdist_jensenshannon_iris:_&:' \
+			-e 's:test_align_vectors_single_vector:_&:' \
+			scipy/signal/tests/test_spectral.py \
+			scipy/sparse/linalg/isolve/tests/test_iterative.py \
+			scipy/spatial/tests/test_distance.py \
+			scipy/spatial/transform/tests/test_rotation.py || die
+	fi
+
+	if has_version ">=sci-libs/lapack-3.10"; then
+		sed -e 's:test_sort(:_&:' \
+			-i scipy/linalg/tests/test_decomp.py || die
+		sed -e 's:test_solve_discrete_are:_&:' \
+			-i scipy/linalg/tests/test_solvers.py || die
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_configure_all() {
+	export SCIPY_USE_PYTHRAN=$(usex pythran 1 0)
+
+	# bug 721860
+	test-flag-FC -fallow-argument-mismatch &&
+		append-fflags -fallow-argument-mismatch
+}
+
+python_compile() {
+	# FIXME: parallel python building fails, bug #614464
+	export MAKEOPTS=-j1
+
+	${EPYTHON} tools/cythonize.py || die
+	distutils-r1_python_compile \
+		${SCIPY_FCONFIG}
+}
+
+python_test() {
+	# fails with bdist_egg. should it be fixed in distutils-r1 eclass?
+	distutils_install_for_testing ${SCIPY_FCONFIG}
+	cd "${TEST_DIR}/lib" || die "no ${TEST_DIR} available"
+	PYTHONPATH=. "${EPYTHON}" -c "
+import scipy, sys
+r = scipy.test('fast', verbose=2)
+sys.exit(0 if r else 1)" || die "Tests fail with ${EPYTHON}"
+}
+
+python_install_all() {
+	use doc && \
+		local DOCS=( "${DISTDIR}"/${PN}-ref-${DOC_PV}.pdf ) \
+		local HTML_DOCS=( "${WORKDIR}"/html/. )
+	distutils-r1_python_install_all
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+	python_optimize
+}
+
+pkg_postinst() {
+	elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER"
+	elog "to your prefered image viewer. Example:"
+	elog "    echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc"
+}