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.coll...@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 <mhabe...@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
+}
