dev-python/scipy: Bump to 1.8.0

Signed-off-by: Michał Górny <mgorny@gentoo.org>

3 files changed, 211 insertions, 0 deletions

diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index 88d145b73116..a902c4b4014b 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,6 +1,7 @@
 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-1.7.3.tar.gz 36102562 BLAKE2B 9a605a45d8f03aae3411a6fa92e32c7f6d10373455493ead847d4ad01429b55dbbc33c1a0309d6c9d76d3e9ab1a06772df59c08d393377896c4b534599f9eb9b SHA512 83fe00cf708a13a08d28af7022ec645d8976c177f2fefb56e0a47bfcbec726330b973d1f44364e23c939ae708e239a05904346f515ea1a37e8b70ad160b81cee
+DIST scipy-1.8.0.tar.gz 38313602 BLAKE2B 3f071ad3dfa350bba7eaf8e06c8bdb660f9dc1ef0e0bfc1eb1be2c400f947b2b26d62066a4b0f603ae56244131aff6e4c5b7e87cfd2aa7b278e3071062a4bf02 SHA512 674652728ae76479d17189e6974895bb838a8e83b17b9fb91c5f86faebf2a1387e1466555ac5b51d05c293f9b31b9a72e634f5858105ea984ca94bd2f05bbb4c
 DIST scipy-html-1.6.2.zip 23947380 BLAKE2B e4616a157c037b0830fc32d23678fb7e8ebe023d1fd9f0f762695a0d93bc56e432e441e675ec3c7a7d6586a665f6127ce49d570f1716876e58afb402761f8e95 SHA512 119a2227a808c752a751bc7bec6463da739c68391ebac8d2451998d90ebe03b2af401adbf987f0b694244e715c0ef1fd86c2f4a36c48dbb1ff7cdf4d914875df
 DIST scipy-html-1.7.1.zip 32435246 BLAKE2B fd8173da41aba95a14b1376f848bc668c4659bf1bbbdd0f87d926633d36f29c039957d38be145a5583010ebd83f6458090f75bdad773cc0f1591664e13c04c20 SHA512 ee59722878f6ef2d2319cdf4e6a60d3d1184f7c22752f9a8859eaa46fb677ebac9e8eef9c0826998e12bac9399e336799843341ef203224a82c9101347149672
 DIST scipy-ref-1.6.2.pdf 34599668 BLAKE2B 9ae3221c814eb0d1b1e9191e08000955af503f6448cf8b5841e400fad106c658670339219f4838bd312023601776fe0b0d123ebbd41460c478145da2ac3e9989 SHA512 9aecb7ca760805c470c41121268281c9547aef35ddf078816c5e48f7cf4912a67cf622e267152c6cc823df9d82be1f3a875d97469169d0d91d6219164c130c88
diff --git a/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch b/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch
new file mode 100644
index 000000000000..caefc334a973
--- /dev/null
+++ b/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch
@@ -0,0 +1,22 @@
+From 2b6392eeeb8ef5225ace15e8a1553fa87409272f Mon Sep 17 00:00:00 2001
+From: Ralf Gommers <ralf.gommers@gmail.com>
+Date: Wed, 29 Dec 2021 22:47:13 +0100
+Subject: [PATCH] Revert "BLD Respect the --skip-build flag in setup.py"
+
+---
+ setup.py | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index 002531fcc00..d91916e5894 100755
+--- a/setup.py
++++ b/setup.py
+@@ -488,8 +488,6 @@ def setup_package():
+     if "--force" in sys.argv:
+         run_build = True
+         sys.argv.remove('--force')
+-    elif "--skip-build" in sys.argv:
+-        run_build = False
+     else:
+         # Raise errors for unsupported commands, improve help output, etc.
+         run_build = check_setuppy_command()
diff --git a/dev-python/scipy/scipy-1.8.0.ebuild b/dev-python/scipy/scipy-1.8.0.ebuild
new file mode 100644
index 000000000000..103ff10d567e
--- /dev/null
+++ b/dev-python/scipy/scipy-1.8.0.ebuild
@@ -0,0 +1,188 @@
+# Copyright 1999-2022 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 multiprocessing 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-${DOC_PV}.pdf
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 -hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
+IUSE="doc +pythran sparse"
+
+DEPEND="
+	>=dev-python/numpy-1.17.3[lapack,${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[${PYTHON_USEDEP}]
+	)"
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+distutils_enable_tests pytest
+
+PATCHES=(
+	"${FILESDIR}"/${P}-skip-build-revert.patch
+)
+
+src_unpack() {
+	default
+	if use doc; then
+		unzip -qo "${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 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"
+}