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

["Michał Górny" <mgorny@gentoo.org>]

commit:     86fbcb4a46c77c4f56c05f94a3cf17e170f13fb8
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 22 01:39:54 2024 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Sep 22 02:22:55 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=86fbcb4a

dev-python/scipy: Remove old

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

 dev-python/scipy/Manifest                     |   1 -
 dev-python/scipy/files/scipy-1.14.0-np2.patch |  68 ----------
 dev-python/scipy/scipy-1.14.0-r1.ebuild       | 173 --------------------------
 dev-python/scipy/scipy-1.14.0.ebuild          | 167 -------------------------
 4 files changed, 409 deletions(-)

diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest
index 6416455905f3..282cd531d647 100644
--- a/dev-python/scipy/Manifest
+++ b/dev-python/scipy/Manifest
@@ -1,3 +1,2 @@
-DIST scipy-1.14.0.tar.gz 58618870 BLAKE2B bf9ed05628b02dc058555402995caae722cf6802bde80387d4e4477ec533589a66ca70b5dd44a32ddac652c7c69300406434b80e7cbc9aee2a78ae6b26ee4c2b SHA512 6579d988a2093602f5fc82203bbb5dc5690a95032484b5d5bd843d1e7995b3b89d802c7b38ec0345c1f3d8e22c98fb92b3982a1eadfcdf63607f929a52b56abf
 DIST scipy-1.14.1.tar.gz 58620554 BLAKE2B 5cb383648a5f3b8d0d321efcd66992212c59ce3fc3dbf812a2fa97c09cb18831b280af6c7689553644f83c531a266e9152e2a139a12aed08307e1ed64deea78e SHA512 20e3cf13590f76dfdc40ca8f90e6d5a68502e74415f37fa24fdb8169098e1d7f0aa631ae742c8c3e9573fa7d63da61986d51f35f090a3785873ae0761f7fcfa6
 DIST scipy-html-1.14.0.zip 65723829 BLAKE2B ba47dbf00a5d2a53a9addc5ea68ab18b42f211a018b89aa4b0b57ff0dee02e410a3effc59ddf8fbbc5aa33075d45d86880aed3a14068da5bd7b62ee526199967 SHA512 93be0bafcc64cea1ba130bbcc77c0741acc4f819c84a5030391a22657a1bc63abe8434a2723f66b7ad04c0809dc6d02e3a97ffb8d94bd3d4a4bb759ee796b475

diff --git a/dev-python/scipy/files/scipy-1.14.0-np2.patch b/dev-python/scipy/files/scipy-1.14.0-np2.patch
deleted file mode 100644
index fdb81baa68a6..000000000000
--- a/dev-python/scipy/files/scipy-1.14.0-np2.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-From 87c4932ca0e4dbe10f918bc5e8096e30fc6557e7 Mon Sep 17 00:00:00 2001
-From: Lucas Colley <lucas.colley8@gmail.com>
-Date: Mon, 29 Jul 2024 17:57:11 +0100
-Subject: [PATCH 1/2] BUG: stats: adapt to `np.floor` type promotion removal
-
-`rv_discrete._cdf` relied on `np.floor` promoting its integer input to `np.float64`. This is no longer the case since numpy/numpy#26766.
-
-[skip cirrus] [skip circle]
----
- scipy/stats/_distn_infrastructure.py     |  2 +-
- scipy/stats/tests/test_discrete_basic.py | 12 ++++++++++++
- 2 files changed, 13 insertions(+), 1 deletion(-)
-
-diff --git a/scipy/stats/_distn_infrastructure.py b/scipy/stats/_distn_infrastructure.py
-index a7a0bb66b396..83954af2c11f 100644
---- a/scipy/stats/_distn_infrastructure.py
-+++ b/scipy/stats/_distn_infrastructure.py
-@@ -3392,7 +3392,7 @@ def _cdf_single(self, k, *args):
-         return np.sum(self._pmf(m, *args), axis=0)
- 
-     def _cdf(self, x, *args):
--        k = floor(x)
-+        k = floor(x).astype(np.float64)
-         return self._cdfvec(k, *args)
- 
-     # generic _logcdf, _sf, _logsf, _ppf, _isf, _rvs defined in rv_generic
-diff --git a/scipy/stats/tests/test_discrete_basic.py b/scipy/stats/tests/test_discrete_basic.py
-index 1ebc9371c075..3db2f0666dbd 100644
---- a/scipy/stats/tests/test_discrete_basic.py
-+++ b/scipy/stats/tests/test_discrete_basic.py
-@@ -549,3 +549,15 @@ def test_rv_sample():
-     rng = np.random.default_rng(98430143469)
-     rvs0 = dist.ppf(rng.random(size=100))
-     assert_allclose(rvs, rvs0)
-+
-+def test__pmf_float_input():
-+    # gh-21272
-+    # test that `rvs()` can be computed when `_pmf` requires float input
-+    
-+    class rv_exponential(stats.rv_discrete):
-+        def _pmf(self, i):
-+            return (2/3)*3**(1 - i)
-+    
-+    rv = rv_exponential(a=0.0, b=float('inf'))
-+    rvs = rv.rvs() # should not crash due to integer input to `_pmf`
-+    assert_allclose(rvs, 0)
-
-From fe924edb6564358df24de8b915861d6754c6e94d Mon Sep 17 00:00:00 2001
-From: Matt Haberland <mhaberla@calpoly.edu>
-Date: Sat, 10 Aug 2024 12:15:56 -0700
-Subject: [PATCH 2/2] Update scipy/stats/tests/test_discrete_basic.py
-
-[skip ci]
----
- scipy/stats/tests/test_discrete_basic.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/scipy/stats/tests/test_discrete_basic.py b/scipy/stats/tests/test_discrete_basic.py
-index 3db2f0666dbd..2bc53d95228a 100644
---- a/scipy/stats/tests/test_discrete_basic.py
-+++ b/scipy/stats/tests/test_discrete_basic.py
-@@ -559,5 +559,5 @@ def _pmf(self, i):
-             return (2/3)*3**(1 - i)
-     
-     rv = rv_exponential(a=0.0, b=float('inf'))
--    rvs = rv.rvs() # should not crash due to integer input to `_pmf`
-+    rvs = rv.rvs(random_state=42)  # should not crash due to integer input to `_pmf`
-     assert_allclose(rvs, 0)

diff --git a/dev-python/scipy/scipy-1.14.0-r1.ebuild b/dev-python/scipy/scipy-1.14.0-r1.ebuild
deleted file mode 100644
index 1352c9c3bfbd..000000000000
--- a/dev-python/scipy/scipy-1.14.0-r1.ebuild
+++ /dev/null
@@ -1,173 +0,0 @@
-# Copyright 1999-2024 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 python3_{10..13} )
-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=${PV}
-
-	SRC_URI+="
-		doc? (
-			https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip
-		)"
-
-	if [[ ${PV} != *rc* ]] ; then
-		KEYWORDS="~amd64 ~arm ~arm64 ~loong ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86"
-	fi
-fi
-
-LICENSE="BSD LGPL-2"
-SLOT="0"
-IUSE="doc +fortran test-rust"
-
-# umfpack is technically optional but it's preferred to have it available.
-DEPEND="
-	>=dev-python/numpy-1.23.5:=[lapack,${PYTHON_USEDEP}]
-	sci-libs/arpack:=
-	sci-libs/umfpack
-	virtual/cblas
-	>=virtual/lapack-3.8
-"
-RDEPEND="
-	${DEPEND}
-	dev-python/pillow[${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/pybind11-2.12.0[${PYTHON_USEDEP}]
-	>=dev-build/meson-1.1.0
-	!kernel_Darwin? ( dev-util/patchelf )
-	virtual/pkgconfig
-	doc? ( app-arch/unzip )
-	fortran? (
-		>=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
-	)
-	test? (
-		>=dev-python/hypothesis-6.30[${PYTHON_USEDEP}]
-	)
-	test-rust? (
-		dev-python/pooch[${PYTHON_USEDEP}]
-	)
-"
-
-EPYTEST_XDIST=1
-distutils_enable_tests pytest
-
-PATCHES=(
-	# https://github.com/scipy/scipy/pull/21283
-	# (breaks test_sample_scipy in dev-python/sympy)
-	"${FILESDIR}/${P}-np2.patch"
-)
-
-src_unpack() {
-	default
-
-	if use doc; then
-		unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die
-	fi
-}
-
-python_configure_all() {
-	DISTUTILS_ARGS=(
-		-Dblas=blas
-		-Dlapack=lapack
-		-Duse-pythran=$(usex fortran true false)
-	)
-
-	# https://bugs.gentoo.org/932721
-	has_version '>=dev-python/numpy-2.0.0' && filter-lto
-}
-
-python_test() {
-	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
-
-		# Precision issue with diff. blas?
-		scipy/optimize/tests/test__basinhopping.py::Test_Metropolis::test_gh7799
-
-		# Crashes with assertion, not a regression
-		# https://github.com/scipy/scipy/issues/19321
-		scipy/signal/tests/test_signaltools.py::test_lfilter_bad_object
-
-		# timeouts
-		scipy/sparse/linalg/tests/test_propack.py::test_examples
-		# hang or incredibly slow
-		scipy/optimize/tests/test_lsq_linear.py::TestBVLS::test_large_rank_deficient
-		scipy/optimize/tests/test_lsq_linear.py::TestTRF::test_large_rank_deficient
-
-		# TODO
-		scipy/optimize/tests/test_minimize_constrained.py::TestTrustRegionConstr::test_list_of_problems
-	)
-	local EPYTEST_IGNORE=()
-
-	if ! has_version -b "dev-python/pooch[${PYTHON_USEDEP}]" ; then
-		EPYTEST_IGNORE+=(
-			scipy/datasets/tests/test_data.py
-		)
-	fi
-
-	case ${EPYTHON} in
-		pypy3)
-			EPYTEST_DESELECT+=(
-				# fd leaks in tests
-				# https://github.com/scipy/scipy/issues/19553
-				scipy/fft/_pocketfft/tests/test_real_transforms.py
-				# TODO
-				'scipy/special/tests/test_data.py::test_boost[<Data for expi: expinti_data_long_ipp-expinti_data_long>]'
-				# missing dict.__ror__
-				# https://github.com/pypy/pypy/issues/4934
-				'scipy/sparse/tests/test_dok.py::test_dunder_ror[dok_matrix]'
-				# mismatched exception message
-				scipy/optimize/tests/test_hessian_update_strategy.py::TestHessianUpdateStrategy::test_initialize_catch_illegal
-			)
-			;;
-		python3.13)
-			EPYTEST_DESELECT+=(
-				# docstring formatting
-				scipy/misc/tests/test_doccer.py::test_decorator
-			)
-			;;
-	esac
-
-	local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
-	epytest scipy
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( "${WORKDIR}"/html/. )
-
-	distutils-r1_python_install_all
-}

diff --git a/dev-python/scipy/scipy-1.14.0.ebuild b/dev-python/scipy/scipy-1.14.0.ebuild
deleted file mode 100644
index d92a8af88f7a..000000000000
--- a/dev-python/scipy/scipy-1.14.0.ebuild
+++ /dev/null
@@ -1,167 +0,0 @@
-# Copyright 1999-2024 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 python3_{10..13} )
-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=${PV}
-
-	SRC_URI+="
-		doc? (
-			https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip
-		)"
-
-	if [[ ${PV} != *rc* ]] ; then
-		KEYWORDS="amd64 arm arm64 ~loong ~ppc ppc64 ~riscv ~s390 ~sparc x86"
-	fi
-fi
-
-LICENSE="BSD LGPL-2"
-SLOT="0"
-IUSE="doc +fortran test-rust"
-
-# umfpack is technically optional but it's preferred to have it available.
-DEPEND="
-	>=dev-python/numpy-1.23.5:=[lapack,${PYTHON_USEDEP}]
-	sci-libs/arpack:=
-	sci-libs/umfpack
-	virtual/cblas
-	>=virtual/lapack-3.8
-"
-RDEPEND="
-	${DEPEND}
-	dev-python/pillow[${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/pybind11-2.12.0[${PYTHON_USEDEP}]
-	>=dev-build/meson-1.1.0
-	!kernel_Darwin? ( dev-util/patchelf )
-	virtual/pkgconfig
-	doc? ( app-arch/unzip )
-	fortran? (
-		>=dev-python/pythran-0.16.0[${PYTHON_USEDEP}]
-	)
-	test? (
-		>=dev-python/hypothesis-6.30[${PYTHON_USEDEP}]
-	)
-	test-rust? (
-		dev-python/pooch[${PYTHON_USEDEP}]
-	)
-"
-
-EPYTEST_XDIST=1
-distutils_enable_tests pytest
-
-src_unpack() {
-	default
-
-	if use doc; then
-		unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die
-	fi
-}
-
-python_configure_all() {
-	DISTUTILS_ARGS=(
-		-Dblas=blas
-		-Dlapack=lapack
-		-Duse-pythran=$(usex fortran true false)
-	)
-
-	# https://bugs.gentoo.org/932721
-	has_version '>=dev-python/numpy-2.0.0' && filter-lto
-}
-
-python_test() {
-	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
-
-		# Precision issue with diff. blas?
-		scipy/optimize/tests/test__basinhopping.py::Test_Metropolis::test_gh7799
-
-		# Crashes with assertion, not a regression
-		# https://github.com/scipy/scipy/issues/19321
-		scipy/signal/tests/test_signaltools.py::test_lfilter_bad_object
-
-		# timeouts
-		scipy/sparse/linalg/tests/test_propack.py::test_examples
-		# hang or incredibly slow
-		scipy/optimize/tests/test_lsq_linear.py::TestBVLS::test_large_rank_deficient
-		scipy/optimize/tests/test_lsq_linear.py::TestTRF::test_large_rank_deficient
-
-		# TODO
-		scipy/optimize/tests/test_minimize_constrained.py::TestTrustRegionConstr::test_list_of_problems
-	)
-	local EPYTEST_IGNORE=()
-
-	if ! has_version -b "dev-python/pooch[${PYTHON_USEDEP}]" ; then
-		EPYTEST_IGNORE+=(
-			scipy/datasets/tests/test_data.py
-		)
-	fi
-
-	case ${EPYTHON} in
-		pypy3)
-			EPYTEST_DESELECT+=(
-				# fd leaks in tests
-				# https://github.com/scipy/scipy/issues/19553
-				scipy/fft/_pocketfft/tests/test_real_transforms.py
-				# TODO
-				'scipy/special/tests/test_data.py::test_boost[<Data for expi: expinti_data_long_ipp-expinti_data_long>]'
-				# missing dict.__ror__
-				# https://github.com/pypy/pypy/issues/4934
-				'scipy/sparse/tests/test_dok.py::test_dunder_ror[dok_matrix]'
-				# mismatched exception message
-				scipy/optimize/tests/test_hessian_update_strategy.py::TestHessianUpdateStrategy::test_initialize_catch_illegal
-			)
-			;;
-		python3.13)
-			EPYTEST_DESELECT+=(
-				# docstring formatting
-				scipy/misc/tests/test_doccer.py::test_decorator
-			)
-			;;
-	esac
-
-	local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
-	epytest scipy
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( "${WORKDIR}"/html/. )
-
-	distutils-r1_python_install_all
-}