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

[Sam James]

commit:     1e9653dd0688577b64da7071962cce1c76abc8c5
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Thu May 19 03:01:07 2022 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Thu May 19 03:01:07 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e9653dd

dev-python/scipy: add 1.8.1

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

 dev-python/scipy/Manifest           |   3 +
 dev-python/scipy/scipy-1.8.1.ebuild | 189 ++++++++++++++++++++++++++++++++++++
 2 files changed, 192 insertions(+)

diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index d49ac5272be8..76487212a3c9 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,3 +1,6 @@
 DIST scipy-1.8.0.tar.gz 38313602 BLAKE2B 3f071ad3dfa350bba7eaf8e06c8bdb660f9dc1ef0e0bfc1eb1be2c400f947b2b26d62066a4b0f603ae56244131aff6e4c5b7e87cfd2aa7b278e3071062a4bf02 SHA512 674652728ae76479d17189e6974895bb838a8e83b17b9fb91c5f86faebf2a1387e1466555ac5b51d05c293f9b31b9a72e634f5858105ea984ca94bd2f05bbb4c
+DIST scipy-1.8.1.tar.gz 38196215 BLAKE2B 180ae646adba2031a4bf99cd4feefe652b8e340110b3b2872e61aa1083054aadf369c7e3b3e3fd8fb71fcd831c95841d2dadd1c71e35e5f7d95800e5551173f0 SHA512 f6fc71c209991fe82baa4b10d8ade0deb1057f6f5942a91dfb7ae45f3eb78a4535efa2861badf5e2d37239fa99dbd99de760aa7e4854b95991ade0263004e7ea
 DIST scipy-html-1.7.1.zip 32435246 BLAKE2B fd8173da41aba95a14b1376f848bc668c4659bf1bbbdd0f87d926633d36f29c039957d38be145a5583010ebd83f6458090f75bdad773cc0f1591664e13c04c20 SHA512 ee59722878f6ef2d2319cdf4e6a60d3d1184f7c22752f9a8859eaa46fb677ebac9e8eef9c0826998e12bac9399e336799843341ef203224a82c9101347149672
+DIST scipy-html-1.8.1.zip 37060661 BLAKE2B 2fa617c58eb47463f8a61f9798b32c6da255d26b8e86c1558e427a715093f5a29ced3847ab6ecfe88ce1017664f36ac3e9fa9bbf72ede7e0fd3812b5f41fe933 SHA512 95153dc1f404aa64898a700c94c0deea3ca842c3152167d0987edabcf4a8eba16b6c8e6bc38a6775a849dc621e6a21434baf53d1669b1865fa5049cffa4387ac
 DIST scipy-ref-1.7.1.pdf 33542025 BLAKE2B 6c978f06b770805f0fae06db740e8596658d98bbbc93c865127eae909957503bb38e02a9c97319aed07608718f8f373374b1cf3a8c3bd624aa3143f1d21bc428 SHA512 45720dc299594bac5c7539f950a0ff135b125d86bfe9847032cbff1f294601fefd0a1ac3fd7e3928b2702390c318ae2f8adca6403ba06ea1ded705fcff94ab79
+DIST scipy-ref-1.8.1.pdf 35025868 BLAKE2B 9221755d2dc69b8623271f75ff3078a0a4410fe9ff69ee317b40bf145af7da21a7f5f4b6b67820d8bb2878f83b7014f1ea7c2f0e026afb716da0479d394505e2 SHA512 8f27dcb9dd1030e15266389af21a1475ecfec5ea777fb2dbcf8db8d3398ac6e45c7040b8d6dbaffd29be3920925427be7c55efdc8094d670c857edfdab7f7728

diff --git a/dev-python/scipy/scipy-1.8.1.ebuild b/dev-python/scipy/scipy-1.8.1.ebuild
new file mode 100644
index 000000000000..81edc28b8dca
--- /dev/null
+++ b/dev-python/scipy/scipy-1.8.1.ebuild
@@ -0,0 +1,189 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs
+
+# Upstream is often behind with doc updates
+DOC_PV=1.8.1
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="
+	https://scipy.org/
+	https://github.com/scipy/scipy/
+	https://pypi.org/project/scipy/
+"
+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-${DOC_PV}.pdf
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 -hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+IUSE="doc +pythran sparse"
+
+DEPEND="
+	>=dev-python/numpy-1.17.3[lapack,${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}]
+		dev-python/pytest-xdist[${PYTHON_USEDEP}]
+	)"
+
+distutils_enable_tests pytest
+
+src_unpack() {
+	default
+
+	if use doc; then
+		unzip -qo "${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 = $(pc_libs lapack)
+	EOF
+	cat >> setup.cfg <<-EOF || die
+		[options]
+		zip_safe = False
+	EOF
+
+	# TODO
+	sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \
+		-i scipy/stats/tests/test_continuous_basic.py || die
+
+	# Skip known-failing test. Broken on all versions in Gentoo for years.
+	# bug #743295
+	sed -e 's:test_bisplev_integer_overflow:_&:' \
+			-i scipy/interpolate/tests/test_fitpack.py || die
+
+	# Skip a few 32-bit related failures
+	if use x86 ; then
+		# TODO: Tidy this up and switch to epytest
+		sed -i -e 's:test_nd_axis_m1:_&:' \
+			-e 's:test_nd_axis_0:_&:' \
+			-e 's:test_maxiter_worsening:_&:' \
+			-e 's:test_pdist_jensenshannon_iris:_&:' \
+			-e 's:test_align_vectors_single_vector:_&:' \
+			scipy/signal/tests/test_spectral.py \
+			scipy/spatial/tests/test_distance.py \
+			scipy/spatial/transform/tests/test_rotation.py || die
+	fi
+
+	if has_version ">=sci-libs/lapack-3.10"; then
+		sed -e 's:test_sort(:_&:' \
+			-i scipy/linalg/tests/test_decomp.py || die
+		sed -e 's:test_solve_discrete_are:_&:' \
+			-i scipy/linalg/tests/test_solvers.py || die
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_configure_all() {
+	export SCIPY_USE_PYTHRAN=$(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 ORIGINAL_MAKEOPTS="${MAKEOPTS}"
+	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 ${TEST_DIR} available"
+
+	# Let's try using pytest again with xdist to speed things up.
+	# Note that using pytest is required to avoid dying b/c of a
+	# deprecation warning with distutils in Python 3.01.
+	epytest -n "$(makeopts_jobs "${ORIGINAL_MAKEOPTS}" "$(get_nproc)")"
+}
+
+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"
+}