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 <[email protected]> -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 <[email protected]> -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 -}
