Merge updates from master

4 files changed, 246 insertions, 0 deletions

diff --git a/dev-python/nanobind/Manifest b/dev-python/nanobind/Manifest
index 8e37a87bc11d..f6ac22e33129 100644
--- a/dev-python/nanobind/Manifest
+++ b/dev-python/nanobind/Manifest
@@ -1 +1,2 @@
+DIST nanobind-2.10.2.gh.tar.gz 931057 BLAKE2B aa682523097c4459142b989557d73d98a44ee58797a2cc1d4e783aeacbe0ba2839b1d8c83f80bce203400f4a88a4ae9862b638976908cd86178a5d132c7f42b4 SHA512 8b9a98f659a2b852946247b5ab415432715e19d7be3932b401f9a9c65c68a0e8e513bc785b77114b1c43c2eb2b932858981156a4b850c8a5160c1bd47f5ac337
 DIST nanobind-2.9.2.gh.tar.gz 922360 BLAKE2B 0f8685698e61e72e2b939c0646da0e71ee12af33a2e61c17edc9eb8fcb74f2e47bbb55d34cafff2c0f0175416ff4b4ea66f36cacd32a1ebf4cb93248533c81c4 SHA512 05b2541896e64bb513f915ebc09820b2d3659efa9a1a4bdda9da79a761a23d84e41db22031c02ae816b1f729dab95efcb7c888e926dbb89fb4b34c8a329d59bf
diff --git a/dev-python/nanobind/nanobind-2.10.2.ebuild b/dev-python/nanobind/nanobind-2.10.2.ebuild
new file mode 100644
index 000000000000..9a77fc8442ce
--- /dev/null
+++ b/dev-python/nanobind/nanobind-2.10.2.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=scikit-build-core
+PYTHON_COMPAT=( python3_{11..14} )
+
+inherit cmake distutils-r1
+
+DESCRIPTION="Tiny and efficient C++/Python bindings"
+HOMEPAGE="
+	https://github.com/wjakob/nanobind/
+	https://pypi.org/project/nanobind/
+"
+SRC_URI="
+	https://github.com/wjakob/nanobind/archive/refs/tags/v${PV}.tar.gz
+		-> ${P}.gh.tar.gz
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64 ~ppc64 ~riscv ~x86"
+
+DEPEND="
+	>=dev-cpp/robin-map-1.3.0
+"
+RDEPEND="
+	${DEPEND}
+"
+
+EPYTEST_PLUGINS=()
+EPYTEST_XDIST=1
+distutils_enable_tests pytest
+
+src_prepare() {
+	cmake_src_prepare
+	distutils-r1_src_prepare
+}
+
+src_configure() {
+	# XXX: nanobind installs a CMake config file which by default passes -Os
+	# We currently patch around it in dev-python/pyopencl. In future, we
+	# may want to add some override with Gentoo specific environment vars.
+	DISTUTILS_ARGS=(
+		-DNB_CREATE_INSTALL_RULES=ON
+		-DNB_USE_SUBMODULE_DEPS=OFF
+		-DNB_TEST=OFF
+	)
+}
+
+python_test() {
+	local mycmakeargs=(
+		-DNB_CREATE_INSTALL_RULES=OFF
+		-DNB_USE_SUBMODULE_DEPS=OFF
+		-DNB_TEST=ON
+	)
+	cmake_src_configure
+	cmake_src_compile
+
+	cd "${BUILD_DIR}/tests" || die
+	epytest
+}
diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index f6680752bd67..25438172e16a 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,3 +1,4 @@
 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-1.17.0rc1.tar.gz 30393241 BLAKE2B aa98c2df9c10a456a47eda9cbeebded3e2a7c46e881fce6a8ede10ba232d5101392994e9f7a75f1312e7f7601eded977e803423fa60ee7b1ab0325c11b5683ae SHA512 91ecca179ad61ed7e584d90cdf4a2d918d86cc75a45ed12c761d1840a7cd1b2265d442e67de19dc271355c37f9bead00c3d55d4c9011eb9b898cd3ff6d9fd167
 DIST scipy-html-1.16.2.zip 71516578 BLAKE2B 244537f823e39b52e0b00df63f8f36088f5ef17e365f98415d1573883e9c0eee3f4376b149eaea9b70b34b34a294aeafae9f849050ab8161a8ecdb24172c2876 SHA512 15df0c7211cc4d32007b54015efc17edd1c9b23e8892b748ab946c5c1ea3e1840a00d9005b585cc0c6416bcef1e490f54ff919d3c0140ed95d8e469836751d5c
diff --git a/dev-python/scipy/scipy-1.17.0_rc1.ebuild b/dev-python/scipy/scipy-1.17.0_rc1.ebuild
new file mode 100644
index 000000000000..acd01ac0947f
--- /dev/null
+++ b/dev-python/scipy/scipy-1.17.0_rc1.ebuild
@@ -0,0 +1,181 @@
+# 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=( 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-1.89.0
+"
+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
+
+	# 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
+}