From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id AB115159C9C for ; Tue, 13 Aug 2024 20:41:50 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 9B8D72BC029; Tue, 13 Aug 2024 20:41:49 +0000 (UTC) Received: from smtp.gentoo.org (dev.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 823FA2BC02E for ; Tue, 13 Aug 2024 20:41:49 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id AFE75343064 for ; Tue, 13 Aug 2024 20:41:48 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id F007D1C57 for ; Tue, 13 Aug 2024 20:41:46 +0000 (UTC) From: "Michał Górny" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Michał Górny" Message-ID: <1723579667.68ed3fe84fdbab8d929e70efe749d5c38fe77814.mgorny@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: dev-python/scipy/files/, dev-python/scipy/ X-VCS-Repository: repo/gentoo X-VCS-Files: dev-python/scipy/files/scipy-1.14.0-np2.patch dev-python/scipy/scipy-1.14.0-r1.ebuild X-VCS-Directories: dev-python/scipy/files/ dev-python/scipy/ X-VCS-Committer: mgorny X-VCS-Committer-Name: Michał Górny X-VCS-Revision: 68ed3fe84fdbab8d929e70efe749d5c38fe77814 X-VCS-Branch: master Date: Tue, 13 Aug 2024 20:41:46 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 4d0289fd-eba0-498c-88c5-76dbcb7ff3e0 X-Archives-Hash: 51e6f9cb69045e189f9bf9a07ff0f5b2 commit: 68ed3fe84fdbab8d929e70efe749d5c38fe77814 Author: Michał Górny gentoo org> AuthorDate: Tue Aug 13 18:44:04 2024 +0000 Commit: Michał Górny gentoo 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 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 +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 +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 ${EPYTHON} in + pypy3) + EPYTEST_DESELECT+=( + # fd leaks in tests + # https://github.com/scipy/scipy/issues/19553 + scipy/fft/_pocketfft/tests/test_real_transforms.py + # TODO + 'scipy/special/tests/test_data.py::test_boost[]' + # missing dict.__ror__ + # https://github.com/pypy/pypy/issues/4934 + 'scipy/sparse/tests/test_dok.py::test_dunder_ror[dok_matrix]' + # mismatched exception message + scipy/optimize/tests/test_hessian_update_strategy.py::TestHessianUpdateStrategy::test_initialize_catch_illegal + ) + ;; + python3.13) + EPYTEST_DESELECT+=( + # docstring formatting + scipy/misc/tests/test_doccer.py::test_decorator + ) + ;; + esac + + local -x PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 + epytest scipy +} + +python_install_all() { + use doc && local HTML_DOCS=( "${WORKDIR}"/html/. ) + + distutils-r1_python_install_all +}