commit: b35dd378c21b892038747fba6e58fb67442be4ac
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 29 03:08:02 2025 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Oct 29 18:33:55 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b35dd378
dev-python/scipy: Bump to 1.16.3
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
dev-python/scipy/Manifest | 1 +
dev-python/scipy/scipy-1.16.3.ebuild | 191 +++++++++++++++++++++++++++++++++++
2 files changed, 192 insertions(+)
diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index 7474a88874e8..f6680752bd67 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,2 +1,3 @@
DIST scipy-1.16.2.tar.gz 30580599 BLAKE2B
aec4039fe5798365fbe5147a4d6acea61e408ad0a533da4a3602e3c03a5a495f693b9b998a0417524621e6414e3bc847339364d6536e6b489cff43931253c87d
SHA512
6b5c1ab6236af5d40850f8b77f8d47494dda9bccf814908ba306b4b3710359d18eb0dd880c05dc4f334cc298d0a2d54d271d5cd5b519190fcfba58524b1d8dce
+DIST scipy-1.16.3.tar.gz 30597883 BLAKE2B
ba026013ecfdc9329ec6140bf32f8de61e141b645c5a35ad5dc38276ac4df296fce0091675177daaf3d65f2cb797783365df306397e1643d50508e343daaa325
SHA512
7386670d2be598f46425a5f2ac0194748c83ec006be0b0395a850a613bc12731669469aefe503c9db2521aba956325d44e7a75fa82e4c1e629202cafd1966aa5
DIST scipy-html-1.16.2.zip 71516578 BLAKE2B
244537f823e39b52e0b00df63f8f36088f5ef17e365f98415d1573883e9c0eee3f4376b149eaea9b70b34b34a294aeafae9f849050ab8161a8ecdb24172c2876
SHA512
15df0c7211cc4d32007b54015efc17edd1c9b23e8892b748ab946c5c1ea3e1840a00d9005b585cc0c6416bcef1e490f54ff919d3c0140ed95d8e469836751d5c
diff --git a/dev-python/scipy/scipy-1.16.3.ebuild
b/dev-python/scipy/scipy-1.16.3.ebuild
new file mode 100644
index 000000000000..9d8d3160e3e4
--- /dev/null
+++ b/dev-python/scipy/scipy-1.16.3.ebuild
@@ -0,0 +1,191 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+FORTRAN_NEEDED=fortran
+DISTUTILS_EXT=1
+DISTUTILS_USE_PEP517=meson-python
+PYTHON_COMPAT=( pypy3_11 python3_{11..14} )
+PYTHON_REQ_USE="threads(+)"
+
+inherit flag-o-matic fortran-2 distutils-r1
+
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="
+ https://scipy.org/
+ https://github.com/scipy/scipy/
+ https://pypi.org/project/scipy/
+"
+
+if [[ ${PV} == *9999* ]] ; then
+ inherit git-r3
+
+ # Need submodules, so git for now.
+ EGIT_REPO_URI="https://github.com/scipy/scipy";
+ EGIT_BRANCH="maintenance/$(ver_cut 1-2).x"
+ EGIT_SUBMODULES=( '*' )
+else
+ inherit pypi
+
+ # Upstream is often behind with doc updates
+ DOC_PV=1.16.2
+
+ SRC_URI+="
+ doc? (
+
https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip
+ )
+ "
+
+ if [[ ${PV} != *rc* ]] ; then
+ KEYWORDS="~amd64 ~arm ~arm64 ~loong ~ppc ~ppc64 ~riscv ~s390
~sparc ~x86"
+ fi
+fi
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+IUSE="doc +fortran test-rust"
+
+# pythran is needed in both BDEPEND (for /usr/bin/pythran) and in DEPEND
+# to actually compile code generated by pythran (headers and such needed).
+#
+# umfpack is technically optional but it's preferred to have it available.
+COMMON_DEPEND="
+ >=dev-python/numpy-1.23.5:=[lapack,${PYTHON_USEDEP}]
+ >=media-libs/qhull-2020.2:=
+ virtual/cblas
+ >=virtual/lapack-3.8
+"
+# Only boost.math is used, and meson.build doesn't even look up specific boost
modules.
+DEPEND="
+ ${COMMON_DEPEND}
+ >=dev-libs/boost-1.88.0
+"
+RDEPEND="
+ ${COMMON_DEPEND}
+ dev-python/pillow[${PYTHON_USEDEP}]
+"
+DEPEND+="
+ fortran? (
+ >=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
+ )
+"
+BDEPEND="
+ dev-lang/swig
+ >=dev-python/cython-3.0.8[${PYTHON_USEDEP}]
+ >=dev-python/meson-python-0.15.0[${PYTHON_USEDEP}]
+ >=dev-python/pybind11-2.13.2[${PYTHON_USEDEP}]
+ >=dev-python/pytest-8.0.0[${PYTHON_USEDEP}]
+ >=dev-build/meson-1.5.0
+ !kernel_Darwin? ( dev-util/patchelf )
+ virtual/pkgconfig
+ doc? ( app-arch/unzip )
+ fortran? (
+ >=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
+ )
+ test-rust? (
+ dev-python/pooch[${PYTHON_USEDEP}]
+ )
+"
+
+EPYTEST_PLUGINS=( hypothesis )
+EPYTEST_XDIST=1
+distutils_enable_tests pytest
+
+src_unpack() {
+ default
+
+ if use doc; then
+ unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die
+ fi
+}
+
+src_prepare() {
+ distutils-r1_src_prepare
+
+ # unpin system dependencies
+ sed -i -e "s@version : '@&>=@" meson.build || die
+}
+
+python_configure_all() {
+ DISTUTILS_ARGS=(
+ -Dblas=blas
+ -Dlapack=lapack
+ -Duse-pythran=$(usex fortran true false)
+ -Duse-system-libraries=all
+ )
+
+ # https://bugs.gentoo.org/932721
+ has_version '>=dev-python/numpy-2.0.0' && filter-lto
+}
+
+python_test() {
+ # We run tests in parallel, so avoid having n^2 threads in lapack
+ # tests.
+ local -x BLIS_NUM_THREADS=1
+ local -x MKL_NUM_THREADS=1
+ local -x OMP_NUM_THREADS=1
+ local -x OPENBLAS_NUM_THREADS=1
+
+ cd "${BUILD_DIR}/install$(python_get_sitedir)" || die
+
+ local EPYTEST_DESELECT=(
+ # Network
+
scipy/datasets/tests/test_data.py::TestDatasets::test_existence_all
+ scipy/datasets/tests/test_data.py::TestDatasets::test_ascent
+ scipy/datasets/tests/test_data.py::TestDatasets::test_face
+
scipy/datasets/tests/test_data.py::TestDatasets::test_electrocardiogram
+
+ # Crashes with assertion, not a regression
+ # https://github.com/scipy/scipy/issues/19321
+ scipy/signal/tests/test_signaltools.py::test_lfilter_bad_object
+
+ # Awfully slow tests
+ scipy/interpolate/tests/test_bsplines.py::TestBatch::test_batch
+
scipy/linalg/tests/test_basic.py::TestLstsq::test_random_complex_exact
+
scipy/sparse/linalg/_eigen/tests/test_svds.py::test_small_sigma_sparse
+
+ # TODO: minor precision errors
+
'scipy/linalg/tests/test_batch.py::TestBatch::test_solve[float32-bdim2]'
+
'scipy/linalg/tests/test_batch.py::TestBatch::test_lu_solve[float32-bdim2]'
+
'scipy/stats/tests/test_continuous.py::TestDistributions::test_funcs[cdf-methods11-x-Normal]['
+
+ # Crashes, probably too big
+
'scipy/interpolate/tests/test_fitpack2.py::TestRectBivariateSpline::test_spline_large_2d_maxit'
+ )
+ local EPYTEST_IGNORE=()
+
+ if ! has_version -b "dev-python/pooch[${PYTHON_USEDEP}]" ; then
+ EPYTEST_IGNORE+=(
+ scipy/datasets/tests/test_data.py
+ )
+ fi
+
+ if has_version -b "sys-libs/zlib-ng[compat]"; then
+ EPYTEST_DESELECT+=(
+ # https://github.com/scipy/scipy/issues/23185
+
scipy/io/matlab/tests/test_streams.py::TestZlibInputStream::test_all_data_read_bad_checksum
+
scipy/io/matlab/tests/test_streams.py::TestZlibInputStream::test_all_data_read_overlap
+ )
+ fi
+
+ case ${EPYTHON} in
+ pypy3*)
+ EPYTEST_DESELECT+=(
+ # TODO
+ scipy/special/tests/test_data.py::test_boost
+
scipy/_lib/tests/test_ccallback.py::test_callbacks
+ )
+ ;;
+ esac
+
+ # avoid other stuff being multithreaded when using xdist
+ local -x PYTHON_CPU_COUNT=1
+ epytest scipy
+}
+
+python_install_all() {
+ use doc && local HTML_DOCS=( "${WORKDIR}"/html/. )
+
+ distutils-r1_python_install_all
+}
