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

["Michał Górny" <mgorny@gentoo.org>]

commit:     68ed3fe84fdbab8d929e70efe749d5c38fe77814
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 13 18:44:04 2024 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Tue Aug 13 20:07:47 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=68ed3fe8

dev-python/scipy: Backport a patch related to numpy-2

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

 dev-python/scipy/files/scipy-1.14.0-np2.patch |  68 ++++++++++
 dev-python/scipy/scipy-1.14.0-r1.ebuild       | 173 ++++++++++++++++++++++++++
 2 files changed, 241 insertions(+)

diff --git a/dev-python/scipy/files/scipy-1.14.0-np2.patch b/dev-python/scipy/files/scipy-1.14.0-np2.patch
new file mode 100644
index 000000000000..fdb81baa68a6
--- /dev/null
+++ b/dev-python/scipy/files/scipy-1.14.0-np2.patch
@@ -0,0 +1,68 @@
+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
new file mode 100644
index 000000000000..1352c9c3bfbd
--- /dev/null
+++ b/dev-python/scipy/scipy-1.14.0-r1.ebuild
@@ -0,0 +1,173 @@
+# 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
+}