gentoo resync : 13.11.2021

6 files changed, 257 insertions, 6 deletions

diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index 980dcc7155d6..d7efd67cd1bd 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,11 +1,16 @@
+AUX scipy-1.7.1-pythran-tests-32-bit.patch 1201 BLAKE2B 5db911d23e45556cbcf84fec40a3abdaa3fd9859e2cb8cd08c77a8016aa798338b48dc7b4459b36702a94a94cb4d5ef3bf9ed35f7e4e6f97911a96a35e9e7179 SHA512 613db1a48864d6cd0d1c07c8e1fe898f0aa6db6030d843e2e7580e0d03d5c958be9b9341cd311e47a62f78c6f4114fa293d9beae9cb00042fe3894a98576359a
 DIST scipy-1.6.2.tar.gz 27187804 BLAKE2B af3578bc029c3af548c04144d7405ac8e6f8e057f870394e124f24aea9989120275407e5a7fdd29fbe1019d2acc295c1ce00872461ecf3a325000e8817cd559f SHA512 18b03f32e8343c5a6c6148ac0bfd4b5f2cc9ff5f74d5d41761ae9e773d6af8774c7b09a3fcc47122864eccce1dbbc17e9325819885d3fc3ab2baf98e7d3befa4
 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-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
 DIST scipy-ref-1.6.1.pdf 34594740 BLAKE2B 905ddcd7a3d462b09ded688f0818204d7684fa18058d0dac480d0a000e9ea0b7ebcdd33c01adae17234dcdf630d4aef9078174127af46f1db55d5c14b3245346 SHA512 355f4681439c1720f45dca6badfe72d77edfca0962fd9b42df34f1cd8fff7121fa6e7f60570bb638abd3ba9693930fa46b25af862d8fc1568b508c6fdd785479
 DIST scipy-ref-1.6.2.pdf 34599668 BLAKE2B 9ae3221c814eb0d1b1e9191e08000955af503f6448cf8b5841e400fad106c658670339219f4838bd312023601776fe0b0d123ebbd41460c478145da2ac3e9989 SHA512 9aecb7ca760805c470c41121268281c9547aef35ddf078816c5e48f7cf4912a67cf622e267152c6cc823df9d82be1f3a875d97469169d0d91d6219164c130c88
+DIST scipy-ref-1.7.1.pdf 33542025 BLAKE2B 6c978f06b770805f0fae06db740e8596658d98bbbc93c865127eae909957503bb38e02a9c97319aed07608718f8f373374b1cf3a8c3bd624aa3143f1d21bc428 SHA512 45720dc299594bac5c7539f950a0ff135b125d86bfe9847032cbff1f294601fefd0a1ac3fd7e3928b2702390c318ae2f8adca6403ba06ea1ded705fcff94ab79
 EBUILD scipy-1.6.2.ebuild 4145 BLAKE2B ad4da15044f02436a9b736ecc41761b4700f2c35b57bbbb4c82cc78219c3bdee7024e4370b4c2627c484b0cc29bca26d6b6178abe19c6320532632966b451fa7 SHA512 eeeaa9bfb5312992d7d9528d60ac0831c5502b051783b85455c230a01fc889baa24ab44bac272c44e7dfc4072fd083fb5fb18c525c58c58c1657be5db9e37c5e
-EBUILD scipy-1.6.3.ebuild 4364 BLAKE2B 703ffd70ff12fbcfb37b3ac73d5f99c233a92f5965e601cb7aebb96c721e25b523472284760ad04718df551bd3732a07d00aeb26b80b31662b0cb777fcdc6f62 SHA512 8b963e5b2f04ccbb3df374fee0939bd6f9ebf1eccb9e5cf026169c106141377c7420eb49b1754fd0ab443cb56cfb03077ebedcc6bd8f9b175757662c6d9c93d1
-EBUILD scipy-1.7.1.ebuild 4264 BLAKE2B 8e3154cd9e27f288678c5e6596e70213d87bd33986cbc354fca83bc135f9437174f8920bfa40b8462ff92d63fcaeeea731ccf6842ff97008e6913319d0678b5b SHA512 ef4b2a84c08c587bf70da636211b43ecfe6cb187b9356e12493a3a10b50dca66b2e2a1c636953b9ee036746e56d849a8a194821ed8e353670a049e15a909b9d3
-MISC metadata.xml 1039 BLAKE2B 74d7919c947e4efbeb597dba51ce74b9e2ef995a1e06c0db7fc7c13dcfd0c175afd0b9bce04907274e4eeab2dfcc49f0eca81ab71f76873817f3b9a1ca8ca196 SHA512 c0024d9accbb563f13ba22b32c95881118fec0ec0a68ce498a39d6bc63e13cf2c7db903132481e3b4d085757c5aba8bb4959780d67fd33db5b161a149e18c643
+EBUILD scipy-1.6.3.ebuild 4515 BLAKE2B afba6911ab5aaca626944be8d91b10c9994aade23631a2f4c5df8bdb455811506e005021b75257e5858f7d2488a1e494d1f61ed73ea4b1a0b3fde7c3a7076cc7 SHA512 a723b4d93f30a57aa9ccd012248e24b364b2c1c1a7698d6e80ceb1f46eddcd814f77e0610e4f9ff9344e28f709e9cef3dd9572f41f6b8f56e580b75a9ee190da
+EBUILD scipy-1.7.1-r1.ebuild 5109 BLAKE2B eab04d4c65fa9c95504921a7bcd14c01f15fb247f54b2380a3c11a7485dae3f111784e554b4872782eb2ade5b7139db0b03e841bfcd1bac77f132360860a2bd4 SHA512 a5c750d40817d8212f224de29b3b3eafc0f6977a079f4dcf65c9f29daaf278a093e5b23df4e1f202f9757e746e955dd19ab409bfd2addf055acc019672228e06
+EBUILD scipy-1.7.2.ebuild 5119 BLAKE2B c06fb283a5c8444db4439f94a138995d693aeba9c75f348539166195ece54e79e8c6cbee39a7f570671890a7681365ad41a0e19418a1d4a7e49fdc87c48c8b84 SHA512 d0b978ca0e738b8e4475b3ca971e0f2f614e9526c2fb3e7a918cbf180ecbcb4918eccf05362bdc9776f80485a8169df2cdfff7bef48316c9f3f2207f5f33520c
+MISC metadata.xml 1127 BLAKE2B 6019c7fe056a0198db927c1b149d5a60bd583a523d749e57c86ad899a880fd83e688e040cb693ec3f34be63cae1e5b785d5f6f7a378b98e992d6cb9368ea1b2c SHA512 f7c45d801c3344b3d8de3fabad26a95814cfdf92b604e8215bfac2cfd1cfb181cc8a9a9fa46c0b95c7fb55a34e44bab51c2d1cd7a5adcf421cd965a755722e73
diff --git a/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch b/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch
new file mode 100644
index 000000000000..206d1d9fa3b2
--- /dev/null
+++ b/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch
@@ -0,0 +1,31 @@
+https://github.com/scipy/scipy/commit/5b3a3b440525aa5038e2cead1f9b4f23a610cd9f
+
+From: serge-sans-paille <serge.guelton@telecom-bretagne.eu>
+Date: Sun, 18 Jul 2021 11:14:29 +0200
+Subject: [PATCH] Extra pythran annotation for i686 support
+
+Bug spotted on Fedora, see https://src.fedoraproject.org/rpms/scipy/pull-request/22
+
+The `int[::]` annotation is used to accept non-contiguous views.
+--- a/scipy/optimize/_group_columns.py
++++ b/scipy/optimize/_group_columns.py
+@@ -54,6 +54,8 @@ def group_dense(m, n, A):
+ 
+ #pythran export group_sparse(int, int, intc[], intc[])
+ #pythran export group_sparse(int, int, int[], int[])
++#pythran export group_sparse(int, int, intc[::], intc[::])
++#pythran export group_sparse(int, int, int[::], int[::])
+ def group_sparse(m, n, indices, indptr):
+     groups = -np.ones(n, dtype=np.intp)
+     current_group = 0
+--- a/scipy/signal/_max_len_seq_inner.py
++++ b/scipy/signal/_max_len_seq_inner.py
+@@ -4,6 +4,7 @@
+ import numpy as np
+ 
+ #pythran export _max_len_seq_inner(intp[], int8[], int, int, int8[])
++#pythran export _max_len_seq_inner(int[], int8[], int, int, int8[])
+ 
+ # Fast inner loop of max_len_seq.
+ def _max_len_seq_inner(taps, state, nbits, length, seq):
+
diff --git a/dev-python/scipy/metadata.xml b/dev-python/scipy/metadata.xml
index 9e4a6eb32f2e..0192620473a3 100644
--- a/dev-python/scipy/metadata.xml
+++ b/dev-python/scipy/metadata.xml
@@ -18,6 +18,7 @@
   algorithms, ODE solvers, and others.
 </longdescription>
   <use>
+    <flag name="pythran">Use <pkg>dev-python/pythran</pkg> to accelerate runtime</flag>
     <flag name="sparse">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag>
   </use>
   <upstream>
diff --git a/dev-python/scipy/scipy-1.6.3.ebuild b/dev-python/scipy/scipy-1.6.3.ebuild
index d4b29952702d..169b23036823 100644
--- a/dev-python/scipy/scipy-1.6.3.ebuild
+++ b/dev-python/scipy/scipy-1.6.3.ebuild
@@ -108,6 +108,10 @@ python_prepare_all() {
 	sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \
 		-i scipy/stats/tests/test_continuous_basic.py || die
 
+	# Skip broken test causing segfault, bug #743295
+	sed -e 's:test_bisplev_integer_overflow:_&:' \
+		-i scipy/interpolate/tests/test_fitpack.py || die
+
 	if has_version ">=sci-libs/lapack-3.10"; then
 		sed -e 's:test_sort(:_&:' \
 			-i scipy/linalg/tests/test_decomp.py || die
diff --git a/dev-python/scipy/scipy-1.7.1.ebuild b/dev-python/scipy/scipy-1.7.1-r1.ebuild
index d2dc22464cf4..004da6ad0a63 100644
--- a/dev-python/scipy/scipy-1.7.1.ebuild
+++ b/dev-python/scipy/scipy-1.7.1-r1.ebuild
@@ -21,8 +21,8 @@ SRC_URI="
 
 LICENSE="BSD LGPL-2"
 SLOT="0"
-KEYWORDS="~amd64 ~arm64 ~riscv ~x86"
-IUSE="doc sparse"
+KEYWORDS="amd64 ~arm arm64 ~ia64 ~riscv ~s390 ~sparc x86"
+IUSE="doc +pythran sparse"
 
 DEPEND="
 	>=dev-python/numpy-1.16.5[lapack,${PYTHON_USEDEP}]
@@ -36,9 +36,9 @@ BDEPEND="
 	dev-lang/swig
 	>=dev-python/cython-0.29.18[${PYTHON_USEDEP}]
 	dev-python/pybind11[${PYTHON_USEDEP}]
-	dev-python/pythran[${PYTHON_USEDEP}]
 	virtual/pkgconfig
 	doc? ( app-arch/unzip )
+	pythran? ( dev-python/pythran[${PYTHON_USEDEP}] )
 	test? (
 		dev-python/nose[${PYTHON_USEDEP}]
 	)"
@@ -47,6 +47,10 @@ DISTUTILS_IN_SOURCE_BUILD=1
 
 distutils_enable_tests pytest
 
+PATCHES=(
+	"${FILESDIR}"/${P}-pythran-tests-32-bit.patch
+)
+
 src_unpack() {
 	default
 	if use doc; then
@@ -106,6 +110,25 @@ python_prepare_all() {
 	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
@@ -117,6 +140,8 @@ python_prepare_all() {
 }
 
 python_configure_all() {
+	export SCIPY_USE_PYTHRAN=$(usex pythran 1 0)
+
 	# bug 721860
 	test-flag-FC -fallow-argument-mismatch &&
 		append-fflags -fallow-argument-mismatch
diff --git a/dev-python/scipy/scipy-1.7.2.ebuild b/dev-python/scipy/scipy-1.7.2.ebuild
new file mode 100644
index 000000000000..7290265e9ab7
--- /dev/null
+++ b/dev-python/scipy/scipy-1.7.2.ebuild
@@ -0,0 +1,185 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit fortran-2 distutils-r1 flag-o-matic toolchain-funcs
+
+# upstream is slacking forever with doc updates
+DOC_PV=1.7.1
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="https://www.scipy.org/"
+SRC_URI="
+	mirror://pypi/${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 ~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"
+}