From 0f558761aa2dee1017b4751e4017205e015a9560 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 29 Jun 2022 12:04:12 +0100 Subject: gentoo resync : 29.12.2022 --- dev-python/scipy/Manifest | 16 +- .../files/scipy-1.7.1-pythran-tests-32-bit.patch | 31 ---- .../files/scipy-1.8.0-skip-build-revert.patch | 22 --- .../scipy-1.9.9999-meson-options-lapack.patch | 28 +++ dev-python/scipy/scipy-1.7.3.ebuild | 194 --------------------- dev-python/scipy/scipy-1.8.0.ebuild | 187 -------------------- dev-python/scipy/scipy-1.8.1.ebuild | 189 ++++++++++++++++++++ dev-python/scipy/scipy-1.9.0_rc1.ebuild | 78 +++++++++ dev-python/scipy/scipy-1.9.9999.ebuild | 73 ++++++++ 9 files changed, 376 insertions(+), 442 deletions(-) delete mode 100644 dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch delete mode 100644 dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch create mode 100644 dev-python/scipy/files/scipy-1.9.9999-meson-options-lapack.patch delete mode 100644 dev-python/scipy/scipy-1.7.3.ebuild delete mode 100644 dev-python/scipy/scipy-1.8.0.ebuild create mode 100644 dev-python/scipy/scipy-1.8.1.ebuild create mode 100644 dev-python/scipy/scipy-1.9.0_rc1.ebuild create mode 100644 dev-python/scipy/scipy-1.9.9999.ebuild (limited to 'dev-python/scipy') diff --git a/dev-python/scipy/Manifest b/dev-python/scipy/Manifest index bcb543e85532..ad84673471ec 100644 --- a/dev-python/scipy/Manifest +++ b/dev-python/scipy/Manifest @@ -1,9 +1,9 @@ -AUX scipy-1.7.1-pythran-tests-32-bit.patch 1201 BLAKE2B 5db911d23e45556cbcf84fec40a3abdaa3fd9859e2cb8cd08c77a8016aa798338b48dc7b4459b36702a94a94cb4d5ef3bf9ed35f7e4e6f97911a96a35e9e7179 SHA512 613db1a48864d6cd0d1c07c8e1fe898f0aa6db6030d843e2e7580e0d03d5c958be9b9341cd311e47a62f78c6f4114fa293d9beae9cb00042fe3894a98576359a -AUX scipy-1.8.0-skip-build-revert.patch 712 BLAKE2B 3637bfe30dc1bc4caf9ed9c8eb24e8d92d6a715218ff472d72cb2ddef895309a95307e18f38524045ca8010c7ba2e0d5359c36e08d427244a5cc684accd89158 SHA512 3ca5fb6c44c5a20c09292b91aaf0a74464e4caaba628f97306a805a64aa2f5ef5bb4c1c5886735503d4859df9a1c30d4827d3359a1820f955ad992275a4dc306 -DIST scipy-1.7.3.tar.gz 36102562 BLAKE2B 9a605a45d8f03aae3411a6fa92e32c7f6d10373455493ead847d4ad01429b55dbbc33c1a0309d6c9d76d3e9ab1a06772df59c08d393377896c4b534599f9eb9b SHA512 83fe00cf708a13a08d28af7022ec645d8976c177f2fefb56e0a47bfcbec726330b973d1f44364e23c939ae708e239a05904346f515ea1a37e8b70ad160b81cee -DIST scipy-1.8.0.tar.gz 38313602 BLAKE2B 3f071ad3dfa350bba7eaf8e06c8bdb660f9dc1ef0e0bfc1eb1be2c400f947b2b26d62066a4b0f603ae56244131aff6e4c5b7e87cfd2aa7b278e3071062a4bf02 SHA512 674652728ae76479d17189e6974895bb838a8e83b17b9fb91c5f86faebf2a1387e1466555ac5b51d05c293f9b31b9a72e634f5858105ea984ca94bd2f05bbb4c -DIST scipy-html-1.7.1.zip 32435246 BLAKE2B fd8173da41aba95a14b1376f848bc668c4659bf1bbbdd0f87d926633d36f29c039957d38be145a5583010ebd83f6458090f75bdad773cc0f1591664e13c04c20 SHA512 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f7c45d801c3344b3d8de3fabad26a95814cfdf92b604e8215bfac2cfd1cfb181cc8a9a9fa46c0b95c7fb55a34e44bab51c2d1cd7a5adcf421cd965a755722e73 diff --git a/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch b/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch deleted file mode 100644 index 206d1d9fa3b2..000000000000 --- a/dev-python/scipy/files/scipy-1.7.1-pythran-tests-32-bit.patch +++ /dev/null @@ -1,31 +0,0 @@ -https://github.com/scipy/scipy/commit/5b3a3b440525aa5038e2cead1f9b4f23a610cd9f - -From: serge-sans-paille -Date: Sun, 18 Jul 2021 11:14:29 +0200 -Subject: [PATCH] Extra pythran annotation for i686 support - -Bug spotted on Fedora, see https://src.fedoraproject.org/rpms/scipy/pull-request/22 - -The `int[::]` annotation is used to accept non-contiguous views. ---- a/scipy/optimize/_group_columns.py -+++ b/scipy/optimize/_group_columns.py -@@ -54,6 +54,8 @@ def group_dense(m, n, A): - - #pythran export group_sparse(int, int, intc[], intc[]) - #pythran export group_sparse(int, int, int[], int[]) -+#pythran export group_sparse(int, int, intc[::], intc[::]) -+#pythran export group_sparse(int, int, int[::], int[::]) - def group_sparse(m, n, indices, indptr): - groups = -np.ones(n, dtype=np.intp) - current_group = 0 ---- a/scipy/signal/_max_len_seq_inner.py -+++ b/scipy/signal/_max_len_seq_inner.py -@@ -4,6 +4,7 @@ - import numpy as np - - #pythran export _max_len_seq_inner(intp[], int8[], int, int, int8[]) -+#pythran export _max_len_seq_inner(int[], int8[], int, int, int8[]) - - # Fast inner loop of max_len_seq. - def _max_len_seq_inner(taps, state, nbits, length, seq): - diff --git a/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch b/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch deleted file mode 100644 index caefc334a973..000000000000 --- a/dev-python/scipy/files/scipy-1.8.0-skip-build-revert.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 2b6392eeeb8ef5225ace15e8a1553fa87409272f Mon Sep 17 00:00:00 2001 -From: Ralf Gommers -Date: Wed, 29 Dec 2021 22:47:13 +0100 -Subject: [PATCH] Revert "BLD Respect the --skip-build flag in setup.py" - ---- - setup.py | 2 -- - 1 file changed, 2 deletions(-) - -diff --git a/setup.py b/setup.py -index 002531fcc00..d91916e5894 100755 ---- a/setup.py -+++ b/setup.py -@@ -488,8 +488,6 @@ def setup_package(): - if "--force" in sys.argv: - run_build = True - sys.argv.remove('--force') -- elif "--skip-build" in sys.argv: -- run_build = False - else: - # Raise errors for unsupported commands, improve help output, etc. - run_build = check_setuppy_command() diff --git a/dev-python/scipy/files/scipy-1.9.9999-meson-options-lapack.patch b/dev-python/scipy/files/scipy-1.9.9999-meson-options-lapack.patch new file mode 100644 index 000000000000..23d29c31c2cb --- /dev/null +++ b/dev-python/scipy/files/scipy-1.9.9999-meson-options-lapack.patch @@ -0,0 +1,28 @@ +diff --git a/meson_options.txt b/meson_options.txt +index 5935bb8..f8c14ce 100644 +--- a/meson_options.txt ++++ b/meson_options.txt +@@ -1,6 +1,6 @@ +-option('blas', type: 'string', value: 'openblas', ++option('blas', type: 'string', value: 'blas', + description: 'option for BLAS library switching') +-option('lapack', type: 'string', value: 'openblas', ++option('lapack', type: 'string', value: 'lapack', + description: 'option for LAPACK library switching') + option('use-g77-abi', type: 'boolean', value: 'false', + description: 'If set to true, forces using g77 compatibility wrappers ' + +diff --git a/meson.build b/meson.build +index d80ebc93e..c0c92c00f 100644 +--- a/meson.build ++++ b/meson.build +@@ -16,8 +16,8 @@ project( + 'c_args=-Wno-unused-function -Wno-conversion -Wno-misleading-indentation -Wno-incompatible-pointer-types', + 'fortran_args=-Wno-conversion', + 'fortran_std=legacy', +- 'blas=openblas', +- 'lapack=openblas' ++ 'blas=blas', ++ 'lapack=lapack' + ], + ) + diff --git a/dev-python/scipy/scipy-1.7.3.ebuild b/dev-python/scipy/scipy-1.7.3.ebuild deleted file mode 100644 index 3a3cfc929a8b..000000000000 --- a/dev-python/scipy/scipy-1.7.3.ebuild +++ /dev/null @@ -1,194 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..10} ) -PYTHON_REQ_USE="threads(+)" - -inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs - -# upstream is slacking forever with doc updates -DOC_PV=1.7.1 -DESCRIPTION="Scientific algorithms library for Python" -HOMEPAGE="https://www.scipy.org/" -SRC_URI=" - mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz - doc? ( - https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip - https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf - )" - -LICENSE="BSD LGPL-2" -SLOT="0" -KEYWORDS="amd64 arm arm64 -hppa ~ia64 ppc ppc64 ~riscv ~s390 ~sparc x86" -IUSE="doc +pythran sparse" - -DEPEND=" - >=dev-python/numpy-1.16.5[lapack,${PYTHON_USEDEP}] - sci-libs/arpack:0= - virtual/cblas - virtual/lapack - sparse? ( sci-libs/umfpack:0= )" -RDEPEND="${DEPEND} - dev-python/pillow[${PYTHON_USEDEP}]" -BDEPEND=" - dev-lang/swig - >=dev-python/cython-0.29.18[${PYTHON_USEDEP}] - dev-python/pybind11[${PYTHON_USEDEP}] - virtual/pkgconfig - doc? ( app-arch/unzip ) - pythran? ( dev-python/pythran[${PYTHON_USEDEP}] ) - test? ( - dev-python/nose[${PYTHON_USEDEP}] - dev-python/pytest-xdist[${PYTHON_USEDEP}] - )" - -DISTUTILS_IN_SOURCE_BUILD=1 - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}"/${PN}-1.7.1-pythran-tests-32-bit.patch -) - -src_unpack() { - default - if use doc; then - unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die - fi -} - -pc_incdir() { - $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ - sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' -} - -pc_libdir() { - $(tc-getPKG_CONFIG) --libs-only-L $@ | \ - sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' -} - -pc_libs() { - $(tc-getPKG_CONFIG) --libs-only-l $@ | \ - sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ - -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ - | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' -} - -python_prepare_all() { - # scipy automatically detects libraries by default - export {FFTW,FFTW3,UMFPACK}=None - use sparse && unset UMFPACK - # the missing symbols are in -lpythonX.Y, but since the version can - # differ, we just introduce the same scaryness as on Linux/ELF - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - [[ -z ${FC} ]] && export FC="$(tc-getFC)" - # hack to force F77 to be FC until bug #278772 is fixed - [[ -z ${F77} ]] && export F77="$(tc-getFC)" - export F90="${FC}" - export SCIPY_FCONFIG="config_fc --noopt --noarch" - append-fflags -fPIC - - local libdir="${EPREFIX}"/usr/$(get_libdir) - cat >> site.cfg <<-EOF || die - [blas] - include_dirs = $(pc_incdir cblas) - library_dirs = $(pc_libdir cblas blas):${libdir} - blas_libs = $(pc_libs cblas blas) - [lapack] - library_dirs = $(pc_libdir lapack):${libdir} - lapack_libs = $(pc_libs lapack) - EOF - cat >> setup.cfg <<-EOF || die - [options] - zip_safe = False - EOF - - # TODO - sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \ - -i scipy/stats/tests/test_continuous_basic.py || die - - # Skip known-failing test. Broken on all versions in Gentoo for years. - # bug #743295 - sed -e 's:test_bisplev_integer_overflow:_&:' \ - -i scipy/interpolate/tests/test_fitpack.py || die - - # Skip a few 32-bit related failures - if use x86 ; then - # TODO: Tidy this up and switch to epytest - sed -i -e 's:test_nd_axis_m1:_&:' \ - -e 's:test_nd_axis_0:_&:' \ - -e 's:test_maxiter_worsening:_&:' \ - -e 's:test_pdist_jensenshannon_iris:_&:' \ - -e 's:test_align_vectors_single_vector:_&:' \ - scipy/signal/tests/test_spectral.py \ - scipy/sparse/linalg/isolve/tests/test_iterative.py \ - scipy/spatial/tests/test_distance.py \ - scipy/spatial/transform/tests/test_rotation.py || die - fi - - if has_version ">=sci-libs/lapack-3.10"; then - sed -e 's:test_sort(:_&:' \ - -i scipy/linalg/tests/test_decomp.py || die - sed -e 's:test_solve_discrete_are:_&:' \ - -i scipy/linalg/tests/test_solvers.py || die - fi - - distutils-r1_python_prepare_all -} - -python_configure_all() { - export SCIPY_USE_PYTHRAN=$(usex pythran 1 0) - - # bug 721860 - test-flag-FC -fallow-argument-mismatch && - append-fflags -fallow-argument-mismatch -} - -python_compile() { - # FIXME: parallel python building fails, bug #614464 - export ORIGINAL_MAKEOPTS="${MAKEOPTS}" - export MAKEOPTS=-j1 - - ${EPYTHON} tools/cythonize.py || die - distutils-r1_python_compile \ - ${SCIPY_FCONFIG} -} - -python_test() { - # fails with bdist_egg. should it be fixed in distutils-r1 eclass? - distutils_install_for_testing ${SCIPY_FCONFIG} - cd "${TEST_DIR}/lib" || die "no ${TEST_DIR} available" - - # Let's try using pytest again with xdist to speed things up. - # Note that using pytest is required to avoid dying b/c of a - # deprecation warning with distutils in Python 3.01. - epytest -n "$(makeopts_jobs "${ORIGINAL_MAKEOPTS}" "$(get_nproc)")" - - # Old test runner -# PYTHONPATH=. "${EPYTHON}" -c " -#import scipy, sys -#r = scipy.test('fast', verbose=2) -#sys.exit(0 if r else 1)" || die "Tests fail with ${EPYTHON}" -} - -python_install_all() { - use doc && \ - local DOCS=( "${DISTDIR}"/${PN}-ref-${DOC_PV}.pdf ) \ - local HTML_DOCS=( "${WORKDIR}"/html/. ) - distutils-r1_python_install_all -} - -python_install() { - distutils-r1_python_install ${SCIPY_FCONFIG} - python_optimize -} - -pkg_postinst() { - elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" - elog "to your prefered image viewer. Example:" - elog " echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" -} diff --git a/dev-python/scipy/scipy-1.8.0.ebuild b/dev-python/scipy/scipy-1.8.0.ebuild deleted file mode 100644 index a3e3314b5819..000000000000 --- a/dev-python/scipy/scipy-1.8.0.ebuild +++ /dev/null @@ -1,187 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..10} ) -PYTHON_REQ_USE="threads(+)" - -inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs - -# upstream is slacking forever with doc updates -DOC_PV=1.7.1 -DESCRIPTION="Scientific algorithms library for Python" -HOMEPAGE="https://www.scipy.org/" -SRC_URI=" - mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz - doc? ( - https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip - https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf - )" - -LICENSE="BSD LGPL-2" -SLOT="0" -KEYWORDS="amd64 arm arm64 -hppa ~ia64 ppc ppc64 ~riscv ~s390 ~sparc ~x86" -IUSE="doc +pythran sparse" - -DEPEND=" - >=dev-python/numpy-1.17.3[lapack,${PYTHON_USEDEP}] - sci-libs/arpack:0= - virtual/cblas - virtual/lapack - sparse? ( sci-libs/umfpack:0= )" -RDEPEND="${DEPEND} - dev-python/pillow[${PYTHON_USEDEP}]" -BDEPEND=" - dev-lang/swig - >=dev-python/cython-0.29.18[${PYTHON_USEDEP}] - dev-python/pybind11[${PYTHON_USEDEP}] - virtual/pkgconfig - doc? ( app-arch/unzip ) - pythran? ( dev-python/pythran[${PYTHON_USEDEP}] ) - test? ( - dev-python/nose[${PYTHON_USEDEP}] - dev-python/pytest-xdist[${PYTHON_USEDEP}] - )" - -DISTUTILS_IN_SOURCE_BUILD=1 - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}"/${P}-skip-build-revert.patch -) - -src_unpack() { - default - if use doc; then - unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die - fi -} - -pc_incdir() { - $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ - sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' -} - -pc_libdir() { - $(tc-getPKG_CONFIG) --libs-only-L $@ | \ - sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' -} - -pc_libs() { - $(tc-getPKG_CONFIG) --libs-only-l $@ | \ - sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ - -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ - | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' -} - -python_prepare_all() { - # scipy automatically detects libraries by default - export {FFTW,FFTW3,UMFPACK}=None - use sparse && unset UMFPACK - # the missing symbols are in -lpythonX.Y, but since the version can - # differ, we just introduce the same scaryness as on Linux/ELF - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - [[ -z ${FC} ]] && export FC="$(tc-getFC)" - # hack to force F77 to be FC until bug #278772 is fixed - [[ -z ${F77} ]] && export F77="$(tc-getFC)" - export F90="${FC}" - export SCIPY_FCONFIG="config_fc --noopt --noarch" - append-fflags -fPIC - - local libdir="${EPREFIX}"/usr/$(get_libdir) - cat >> site.cfg <<-EOF || die - [blas] - include_dirs = $(pc_incdir cblas) - library_dirs = $(pc_libdir cblas blas):${libdir} - blas_libs = $(pc_libs cblas blas) - [lapack] - library_dirs = $(pc_libdir lapack):${libdir} - lapack_libs = $(pc_libs lapack) - EOF - cat >> setup.cfg <<-EOF || die - [options] - zip_safe = False - EOF - - # TODO - sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \ - -i scipy/stats/tests/test_continuous_basic.py || die - - # Skip known-failing test. Broken on all versions in Gentoo for years. - # bug #743295 - sed -e 's:test_bisplev_integer_overflow:_&:' \ - -i scipy/interpolate/tests/test_fitpack.py || die - - # Skip a few 32-bit related failures - if use x86 ; then - # TODO: Tidy this up and switch to epytest - sed -i -e 's:test_nd_axis_m1:_&:' \ - -e 's:test_nd_axis_0:_&:' \ - -e 's:test_maxiter_worsening:_&:' \ - -e 's:test_pdist_jensenshannon_iris:_&:' \ - -e 's:test_align_vectors_single_vector:_&:' \ - scipy/signal/tests/test_spectral.py \ - scipy/spatial/tests/test_distance.py \ - scipy/spatial/transform/tests/test_rotation.py || die - fi - - if has_version ">=sci-libs/lapack-3.10"; then - sed -e 's:test_sort(:_&:' \ - -i scipy/linalg/tests/test_decomp.py || die - sed -e 's:test_solve_discrete_are:_&:' \ - -i scipy/linalg/tests/test_solvers.py || die - fi - - distutils-r1_python_prepare_all -} - -python_configure_all() { - export SCIPY_USE_PYTHRAN=$(usex pythran 1 0) - - # bug 721860 - test-flag-FC -fallow-argument-mismatch && - append-fflags -fallow-argument-mismatch -} - -python_compile() { - # FIXME: parallel python building fails, bug #614464 - export ORIGINAL_MAKEOPTS="${MAKEOPTS}" - export MAKEOPTS=-j1 - - ${EPYTHON} tools/cythonize.py || die - distutils-r1_python_compile \ - ${SCIPY_FCONFIG} -} - -python_test() { - # fails with bdist_egg. should it be fixed in distutils-r1 eclass? - distutils_install_for_testing ${SCIPY_FCONFIG} - cd "${TEST_DIR}/lib" || die "no ${TEST_DIR} available" - - # Let's try using pytest again with xdist to speed things up. - # Note that using pytest is required to avoid dying b/c of a - # deprecation warning with distutils in Python 3.01. - epytest -n "$(makeopts_jobs "${ORIGINAL_MAKEOPTS}" "$(get_nproc)")" -} - -python_install_all() { - use doc && \ - local DOCS=( "${DISTDIR}"/${PN}-ref-${DOC_PV}.pdf ) \ - local HTML_DOCS=( "${WORKDIR}"/html/. ) - distutils-r1_python_install_all -} - -python_install() { - distutils-r1_python_install ${SCIPY_FCONFIG} - python_optimize -} - -pkg_postinst() { - elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" - elog "to your prefered image viewer. Example:" - elog " echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" -} diff --git a/dev-python/scipy/scipy-1.8.1.ebuild b/dev-python/scipy/scipy-1.8.1.ebuild new file mode 100644 index 000000000000..df38fbcc3ec2 --- /dev/null +++ b/dev-python/scipy/scipy-1.8.1.ebuild @@ -0,0 +1,189 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_REQ_USE="threads(+)" + +inherit fortran-2 distutils-r1 flag-o-matic multiprocessing toolchain-funcs + +# Upstream is often behind with doc updates +DOC_PV=1.8.1 +DESCRIPTION="Scientific algorithms library for Python" +HOMEPAGE=" + https://scipy.org/ + https://github.com/scipy/scipy/ + https://pypi.org/project/scipy/ +" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf + )" + +LICENSE="BSD LGPL-2" +SLOT="0" +KEYWORDS="amd64 arm arm64 -hppa ~ia64 ppc ppc64 ~riscv ~s390 ~sparc x86" +IUSE="doc +pythran sparse" + +DEPEND=" + >=dev-python/numpy-1.17.3[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +RDEPEND="${DEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" +BDEPEND=" + dev-lang/swig + >=dev-python/cython-0.29.18[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + virtual/pkgconfig + doc? ( app-arch/unzip ) + pythran? ( dev-python/pythran[${PYTHON_USEDEP}] ) + test? ( + dev-python/nose[${PYTHON_USEDEP}] + dev-python/pytest-xdist[${PYTHON_USEDEP}] + )" + +distutils_enable_tests pytest + +src_unpack() { + default + + if use doc; then + unzip -qo "${DISTDIR}"/${PN}-html-${DOC_PV}.zip -d html || die + fi +} + +pc_incdir() { + $(tc-getPKG_CONFIG) --cflags-only-I $@ | \ + sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libdir() { + $(tc-getPKG_CONFIG) --libs-only-L $@ | \ + sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||' +} + +pc_libs() { + $(tc-getPKG_CONFIG) --libs-only-l $@ | \ + sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ + -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ + | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' +} + +python_prepare_all() { + # scipy automatically detects libraries by default + export {FFTW,FFTW3,UMFPACK}=None + use sparse && unset UMFPACK + + # the missing symbols are in -lpythonX.Y, but since the version can + # differ, we just introduce the same scaryness as on Linux/ELF + [[ ${CHOST} == *-darwin* ]] \ + && append-ldflags -bundle "-undefined dynamic_lookup" \ + || append-ldflags -shared + + [[ -z ${FC} ]] && export FC="$(tc-getFC)" + # hack to force F77 to be FC until bug #278772 is fixed + [[ -z ${F77} ]] && export F77="$(tc-getFC)" + export F90="${FC}" + export SCIPY_FCONFIG="config_fc --noopt --noarch" + append-fflags -fPIC + + local libdir="${EPREFIX}"/usr/$(get_libdir) + cat >> site.cfg <<-EOF || die + [blas] + include_dirs = $(pc_incdir cblas) + library_dirs = $(pc_libdir cblas blas):${libdir} + blas_libs = $(pc_libs cblas blas) + [lapack] + library_dirs = $(pc_libdir lapack):${libdir} + lapack_libs = $(pc_libs lapack) + EOF + cat >> setup.cfg <<-EOF || die + [options] + zip_safe = False + EOF + + # TODO + sed -e "s:== 'levy_stable':in ('levy_stable', 'crystalball', 'ncf'):" \ + -i scipy/stats/tests/test_continuous_basic.py || die + + # Skip known-failing test. Broken on all versions in Gentoo for years. + # bug #743295 + sed -e 's:test_bisplev_integer_overflow:_&:' \ + -i scipy/interpolate/tests/test_fitpack.py || die + + # Skip a few 32-bit related failures + if use x86 ; then + # TODO: Tidy this up and switch to epytest + sed -i -e 's:test_nd_axis_m1:_&:' \ + -e 's:test_nd_axis_0:_&:' \ + -e 's:test_maxiter_worsening:_&:' \ + -e 's:test_pdist_jensenshannon_iris:_&:' \ + -e 's:test_align_vectors_single_vector:_&:' \ + scipy/signal/tests/test_spectral.py \ + scipy/spatial/tests/test_distance.py \ + scipy/spatial/transform/tests/test_rotation.py || die + fi + + if has_version ">=sci-libs/lapack-3.10"; then + sed -e 's:test_sort(:_&:' \ + -i scipy/linalg/tests/test_decomp.py || die + sed -e 's:test_solve_discrete_are:_&:' \ + -i scipy/linalg/tests/test_solvers.py || die + fi + + distutils-r1_python_prepare_all +} + +python_configure_all() { + export SCIPY_USE_PYTHRAN=$(usex pythran 1 0) + + # bug 721860 + test-flag-FC -fallow-argument-mismatch && + append-fflags -fallow-argument-mismatch +} + +python_compile() { + # FIXME: parallel python building fails, bug #614464 + export ORIGINAL_MAKEOPTS="${MAKEOPTS}" + export MAKEOPTS=-j1 + + ${EPYTHON} tools/cythonize.py || die + distutils-r1_python_compile \ + ${SCIPY_FCONFIG} +} + +python_test() { + # fails with bdist_egg. should it be fixed in distutils-r1 eclass? + distutils_install_for_testing ${SCIPY_FCONFIG} + cd "${TEST_DIR}/lib" || die "no ${TEST_DIR} available" + + # Let's try using pytest again with xdist to speed things up. + # Note that using pytest is required to avoid dying b/c of a + # deprecation warning with distutils in Python 3.01. + epytest -n "$(makeopts_jobs "${ORIGINAL_MAKEOPTS}" "$(get_nproc)")" +} + +python_install_all() { + use doc && \ + local DOCS=( "${DISTDIR}"/${PN}-ref-${DOC_PV}.pdf ) \ + local HTML_DOCS=( "${WORKDIR}"/html/. ) + distutils-r1_python_install_all +} + +python_install() { + distutils-r1_python_install ${SCIPY_FCONFIG} + python_optimize +} + +pkg_postinst() { + elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER" + elog "to your prefered image viewer. Example:" + elog " echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc" +} diff --git a/dev-python/scipy/scipy-1.9.0_rc1.ebuild b/dev-python/scipy/scipy-1.9.0_rc1.ebuild new file mode 100644 index 000000000000..aa0db9c53032 --- /dev/null +++ b/dev-python/scipy/scipy-1.9.0_rc1.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=meson-python +PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_REQ_USE="threads(+)" + +inherit fortran-2 distutils-r1 multiprocessing + +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 + # Upstream is often behind with doc updates + DOC_PV=1.8.1 + MY_PV=${PV/_rc/rc} + MY_P=${PN}-${MY_PV} + + SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${MY_P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf + )" + S="${WORKDIR}"/${MY_P} + + if [[ ${PV} != *rc* ]] ; then + KEYWORDS="~amd64 ~arm ~arm64 -hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86" + fi +fi + +LICENSE="BSD LGPL-2" +SLOT="0" +IUSE="doc +sparse" + +DEPEND=" + >=dev-python/numpy-1.17.3[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +RDEPEND="${DEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" +# TODO: restore pythran optionality? +BDEPEND=" + dev-lang/swig + >=dev-python/cython-0.29.18[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-python/pythran[${PYTHON_USEDEP}] + dev-util/patchelf + virtual/pkgconfig + doc? ( app-arch/unzip ) + test? ( dev-python/pytest-xdist[${PYTHON_USEDEP}] )" + +PATCHES=( + "${FILESDIR}"/${PN}-1.9.9999-meson-options-lapack.patch +) + +distutils_enable_tests pytest + +python_test() { + cd "${T}" || die + + epytest -n "$(makeopts_jobs)" --pyargs scipy +} diff --git a/dev-python/scipy/scipy-1.9.9999.ebuild b/dev-python/scipy/scipy-1.9.9999.ebuild new file mode 100644 index 000000000000..a25a63827ff7 --- /dev/null +++ b/dev-python/scipy/scipy-1.9.9999.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=meson-python +PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_REQ_USE="threads(+)" + +inherit fortran-2 distutils-r1 multiprocessing + +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 + # Upstream is often behind with doc updates + DOC_PV=1.8.1 + + SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-html-${DOC_PV}.zip + https://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref-${DOC_PV}.pdf + )" + + KEYWORDS="~amd64 ~arm ~arm64 -hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86" +fi + +LICENSE="BSD LGPL-2" +SLOT="0" +IUSE="doc +sparse" + +DEPEND=" + >=dev-python/numpy-1.17.3[lapack,${PYTHON_USEDEP}] + sci-libs/arpack:0= + virtual/cblas + virtual/lapack + sparse? ( sci-libs/umfpack:0= )" +RDEPEND="${DEPEND} + dev-python/pillow[${PYTHON_USEDEP}]" +# TODO: restore pythran optionality? +BDEPEND=" + dev-lang/swig + >=dev-python/cython-0.29.18[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-python/pythran[${PYTHON_USEDEP}] + dev-util/patchelf + virtual/pkgconfig + doc? ( app-arch/unzip ) + test? ( dev-python/pytest-xdist[${PYTHON_USEDEP}] )" + +PATCHES=( + "${FILESDIR}"/${PN}-1.9.9999-meson-options-lapack.patch +) + +distutils_enable_tests pytest + +python_test() { + cd "${T}" || die + + epytest -n "$(makeopts_jobs)" --pyargs scipy +} -- cgit v1.2.3