From 520a5b56dff7c24c9d42eafec142cb78b44f8e3e Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 21 Jul 2018 18:59:32 +0100 Subject: gentoo resync : 21.07.2018 --- dev-python/numpy/Manifest | 9 +- .../files/numpy-1.14.5-no-hardcode-blas.patch | 75 +++++++++++ dev-python/numpy/files/numpy-1.14.5-py37.patch | 135 +++++++++++++++++++ dev-python/numpy/numpy-1.14.5.ebuild | 148 +++++++++++++++++++++ dev-python/numpy/numpy-9999.ebuild | 2 +- 5 files changed, 367 insertions(+), 2 deletions(-) create mode 100644 dev-python/numpy/files/numpy-1.14.5-no-hardcode-blas.patch create mode 100644 dev-python/numpy/files/numpy-1.14.5-py37.patch create mode 100644 dev-python/numpy/numpy-1.14.5.ebuild (limited to 'dev-python/numpy') diff --git a/dev-python/numpy/Manifest b/dev-python/numpy/Manifest index 060d62c13ae0..b02ed455618e 100644 --- a/dev-python/numpy/Manifest +++ b/dev-python/numpy/Manifest @@ -1,26 +1,33 @@ AUX numpy-1.10.2-no-hardcode-blas.patch 3295 BLAKE2B 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5e257d6ea3c59c5819d854db7b7db3ebff53b5c87b5ce9348786085f09db12aa6fc8fa86393b9e6c06760ac0d9f36a52fdfb1865c9d1d9ad5526d74d3d53e8b1 SHA512 d35d0954ff8f21e370edeab3ce3e5ab501bf216c93399e807ede6f1910ba0ea41359425bf894d813a39442fb92a724fe83ec8a5c64e6bd97de9422f67700d549 diff --git a/dev-python/numpy/files/numpy-1.14.5-no-hardcode-blas.patch b/dev-python/numpy/files/numpy-1.14.5-no-hardcode-blas.patch new file mode 100644 index 000000000000..39777ec55afb --- /dev/null +++ b/dev-python/numpy/files/numpy-1.14.5-no-hardcode-blas.patch @@ -0,0 +1,75 @@ +diff --git a/numpy/distutils/system_info.py b/numpy/distutils/system_info.py +index 93a8e6f..df3f3f8 100644 +--- a/numpy/distutils/system_info.py ++++ b/numpy/distutils/system_info.py +@@ -364,28 +364,7 @@ def get_info(name, notfound_action=0): + 1 - display warning message + 2 - raise error + """ +- cl = {'atlas': atlas_info, # use lapack_opt or blas_opt instead +- 'atlas_threads': atlas_threads_info, # ditto +- 'atlas_blas': atlas_blas_info, +- 'atlas_blas_threads': atlas_blas_threads_info, +- 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead +- 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto +- 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead +- 'atlas_3_10_threads': atlas_3_10_threads_info, # ditto +- 'atlas_3_10_blas': atlas_3_10_blas_info, +- 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info, +- 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt instead +- 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, # ditto +- 'mkl': mkl_info, +- # openblas which may or may not have embedded lapack +- 'openblas': openblas_info, # use blas_opt instead +- # openblas with embedded lapack +- 'openblas_lapack': openblas_lapack_info, # use blas_opt instead +- 'openblas_clapack': openblas_clapack_info, # use blas_opt instead +- 'blis': blis_info, # use blas_opt instead +- 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead +- 'blas_mkl': blas_mkl_info, # use blas_opt instead +- 'x11': x11_info, ++ cl = {'x11': x11_info, + 'fft_opt': fft_opt_info, + 'fftw': fftw_info, + 'fftw2': fftw2_info, +@@ -730,10 +709,7 @@ class system_info(object): + return [b for b in [a.strip() for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): +- if hasattr(self, '_lib_names'): +- return self.get_libs(key, default=self._lib_names) +- else: +- return self.get_libs(key, '') ++ return self.get_libs(key, '') + + def library_extensions(self): + c = customized_ccompiler() +@@ -1740,7 +1716,7 @@ class blas_info(system_info): + lib = self.has_cblas(info) + if lib is not None: + info['language'] = 'c' +- info['libraries'] = [lib] ++ info['libraries'] = lib + info['define_macros'] = [('HAVE_CBLAS', None)] + self.set_info(**info) + +@@ -1772,16 +1748,16 @@ class blas_info(system_info): + # check for cblas lib, and if not present check for blas lib. + try: + c.link_executable(obj, os.path.join(tmpdir, "a.out"), +- libraries=["cblas"], ++ libraries=info["libraries"], + library_dirs=info['library_dirs'], + extra_postargs=info.get('extra_link_args', [])) +- res = "cblas" ++ res = info["libraries"] + except distutils.ccompiler.LinkError: + c.link_executable(obj, os.path.join(tmpdir, "a.out"), + libraries=["blas"], + library_dirs=info['library_dirs'], + extra_postargs=info.get('extra_link_args', [])) +- res = "blas" ++ res = ["blas"] + except distutils.ccompiler.CompileError: + res = None + finally: diff --git a/dev-python/numpy/files/numpy-1.14.5-py37.patch b/dev-python/numpy/files/numpy-1.14.5-py37.patch new file mode 100644 index 000000000000..c53b3acf6966 --- /dev/null +++ b/dev-python/numpy/files/numpy-1.14.5-py37.patch @@ -0,0 +1,135 @@ +From dce7f20e95e6bd3fc07517c0b2daf3942a34ddf7 Mon Sep 17 00:00:00 2001 +From: Charles Harris +Date: Wed, 14 Mar 2018 12:52:26 -0600 +Subject: [PATCH] MAINT: Fix test_utils.py for Python 3.7. + +The contents of the module warnings registries was made more module +specific in Python 3.7 and consequently the tests of the context +managers clear_and_catch_warnings and suppress_warnings need updating. +--- + numpy/testing/tests/test_utils.py | 43 +++++++++++++++++++++---------- + 1 file changed, 29 insertions(+), 14 deletions(-) + +diff --git a/numpy/testing/tests/test_utils.py b/numpy/testing/tests/test_utils.py +index a97b627f9..33b3555b0 100644 +--- a/numpy/testing/tests/test_utils.py ++++ b/numpy/testing/tests/test_utils.py +@@ -1114,18 +1114,28 @@ class TestStringEqual(unittest.TestCase): + lambda: assert_string_equal("foo", "hello")) + + +-def assert_warn_len_equal(mod, n_in_context, py3_n_in_context=None): ++def assert_warn_len_equal(mod, n_in_context, py34=None, py37=None): + mod_warns = mod.__warningregistry__ ++ num_warns = len(mod_warns) + # Python 3.4 appears to clear any pre-existing warnings of the same type, + # when raising warnings inside a catch_warnings block. So, there is a + # warning generated by the tests within the context manager, but no + # previous warnings. + if 'version' in mod_warns: +- if py3_n_in_context is None: +- py3_n_in_context = n_in_context +- assert_equal(len(mod_warns) - 1, py3_n_in_context) +- else: +- assert_equal(len(mod_warns), n_in_context) ++ # Python 3 adds a 'version' entry to the registry, ++ # do not count it. ++ num_warns -= 1 ++ ++ # Behavior of warnings is Python version dependent. Adjust the ++ # expected result to compensate. In particular, Python 3.7 does ++ # not make an entry for ignored warnings. ++ if sys.version_info[:2] >= (3, 7): ++ if py37 is not None: ++ n_in_context = py37 ++ elif sys.version_info[:2] >= (3, 4): ++ if py34 is not None: ++ n_in_context = py34 ++ assert_equal(num_warns, n_in_context) + + + def _get_fresh_mod(): +@@ -1134,6 +1144,8 @@ def _get_fresh_mod(): + try: + my_mod.__warningregistry__.clear() + except AttributeError: ++ # will not have a __warningregistry__ unless warning has been ++ # raised in the module at some point + pass + return my_mod + +@@ -1147,21 +1159,23 @@ def test_clear_and_catch_warnings(): + warnings.warn('Some warning') + assert_equal(my_mod.__warningregistry__, {}) + # Without specified modules, don't clear warnings during context ++ # Python 3.7 catch_warnings doesn't make an entry for 'ignore'. + with clear_and_catch_warnings(): + warnings.simplefilter('ignore') + warnings.warn('Some warning') +- assert_warn_len_equal(my_mod, 1) ++ assert_warn_len_equal(my_mod, 1, py37=0) + # Confirm that specifying module keeps old warning, does not add new + with clear_and_catch_warnings(modules=[my_mod]): + warnings.simplefilter('ignore') + warnings.warn('Another warning') +- assert_warn_len_equal(my_mod, 1) ++ assert_warn_len_equal(my_mod, 1, py37=0) + # Another warning, no module spec does add to warnings dict, except on + # Python 3.4 (see comments in `assert_warn_len_equal`) ++ # Python 3.7 catch_warnings doesn't make an entry for 'ignore'. + with clear_and_catch_warnings(): + warnings.simplefilter('ignore') + warnings.warn('Another warning') +- assert_warn_len_equal(my_mod, 2, 1) ++ assert_warn_len_equal(my_mod, 2, py34=1, py37=0) + + + def test_suppress_warnings_module(): +@@ -1178,6 +1192,7 @@ def test_suppress_warnings_module(): + np.apply_along_axis(warn, 0, [0]) + + # Test module based warning suppression: ++ assert_warn_len_equal(my_mod, 0) + with suppress_warnings() as sup: + sup.record(UserWarning) + # suppress warning from other module (may have .pyc ending), +@@ -1189,8 +1204,7 @@ def test_suppress_warnings_module(): + # got filtered) + assert_(len(sup.log) == 1) + assert_(sup.log[0].message.args[0] == "Some warning") +- +- assert_warn_len_equal(my_mod, 0) ++ assert_warn_len_equal(my_mod, 0, py37=0) + sup = suppress_warnings() + # Will have to be changed if apply_along_axis is moved: + sup.filter(module=my_mod) +@@ -1204,11 +1218,11 @@ def test_suppress_warnings_module(): + assert_warn_len_equal(my_mod, 0) + + # Without specified modules, don't clear warnings during context ++ # Python 3.7 does not add ignored warnings. + with suppress_warnings(): + warnings.simplefilter('ignore') + warnings.warn('Some warning') +- assert_warn_len_equal(my_mod, 1) +- ++ assert_warn_len_equal(my_mod, 1, py37=0) + + def test_suppress_warnings_type(): + # Initial state of module, no warnings +@@ -1232,10 +1246,11 @@ def test_suppress_warnings_type(): + assert_warn_len_equal(my_mod, 0) + + # Without specified modules, don't clear warnings during context ++ # Python 3.7 does not add ignored warnings. + with suppress_warnings(): + warnings.simplefilter('ignore') + warnings.warn('Some warning') +- assert_warn_len_equal(my_mod, 1) ++ assert_warn_len_equal(my_mod, 1, py37=0) + + + def test_suppress_warnings_decorate_no_record(): +-- +2.18.0 + diff --git a/dev-python/numpy/numpy-1.14.5.ebuild b/dev-python/numpy/numpy-1.14.5.ebuild new file mode 100644 index 000000000000..69028b40de6f --- /dev/null +++ b/dev-python/numpy/numpy-1.14.5.ebuild @@ -0,0 +1,148 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6,7} ) +PYTHON_REQ_USE="threads(+)" + +FORTRAN_NEEDED=lapack + +inherit distutils-r1 flag-o-matic fortran-2 multiprocessing toolchain-funcs + +DOC_PV="${PV}" +DOC_P="${PN}-${DOC_PV}" + +DESCRIPTION="Fast array and numerical python library" +HOMEPAGE="https://www.numpy.org" +SRC_URI=" + mirror://pypi/${PN:0:1}/${PN}/${P}.zip + doc? ( + http://docs.scipy.org/doc/${DOC_P}/${PN}-html-${DOC_PV}.zip + http://docs.scipy.org/doc/${DOC_P}/${PN}-ref-${DOC_PV}.pdf + http://docs.scipy.org/doc/${DOC_P}/${PN}-user-${DOC_PV}.pdf + )" +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~arm-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" +IUSE="doc lapack test" + +RDEPEND="lapack? ( virtual/cblas virtual/lapack )" +DEPEND="${RDEPEND} + app-arch/unzip + dev-python/setuptools[${PYTHON_USEDEP}] + lapack? ( virtual/pkgconfig ) + test? ( >=dev-python/nose-1.0[${PYTHON_USEDEP}] )" + +PATCHES=( + "${FILESDIR}"/${PN}-1.14.5-no-hardcode-blas.patch + # backport a fix for py3.7 test failures + "${FILESDIR}"/numpy-1.14.5-py37.patch +) + +src_unpack() { + default + if use doc; then + unzip -qo "${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() { + if use lapack; then + append-ldflags "$($(tc-getPKG_CONFIG) --libs-only-other cblas lapack)" + 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 = $(pc_libs lapack) + EOF + else + export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None + fi + + export CC="$(tc-getCC) ${CFLAGS}" + + append-flags -fno-strict-aliasing + + # See progress in http://projects.scipy.org/scipy/numpy/ticket/573 + # with the subtle difference that we don't want to break Darwin where + # -shared is not a valid linker argument + if [[ ${CHOST} != *-darwin* ]]; then + append-ldflags -shared + fi + + # only one fortran to link with: + # linking with cblas and lapack library will force + # autodetecting and linking to all available fortran compilers + append-fflags -fPIC + if use lapack; then + NUMPY_FCONFIG="config_fc --noopt --noarch" + # workaround bug 335908 + [[ $(tc-getFC) == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95" + fi + + # don't version f2py, we will handle it. + sed -i -e '/f2py_exe/s: + os\.path.*$::' numpy/f2py/setup.py || die + + # we don't have f2py-3.3 + sed \ + -e 's:test_f2py:_&:g' \ + -i numpy/tests/test_scripts.py || die + + distutils-r1_python_prepare_all +} + +python_compile() { + local python_makeopts_jobs="" + python_is_python3 || python_makeopts_jobs="-j $(makeopts_jobs)" + distutils-r1_python_compile \ + ${python_makeopts_jobs} \ + ${NUMPY_FCONFIG} +} + +python_test() { + distutils_install_for_testing --single-version-externally-managed --record "${TMPDIR}/record.txt" ${NUMPY_FCONFIG} + + cd "${TMPDIR}" || die + + ${EPYTHON} -c " +import numpy, sys +r = numpy.test(label='full', verbose=3) +sys.exit(0 if r.wasSuccessful() else 1)" || die "Tests fail with ${EPYTHON}" +} + +python_install() { + distutils-r1_python_install ${NUMPY_FCONFIG} +} + +python_install_all() { + local DOCS=( THANKS.txt ) + + if use doc; then + local HTML_DOCS=( "${WORKDIR}"/html/. ) + DOCS+=( "${DISTDIR}"/${PN}-{user,ref}-${DOC_PV}.pdf ) + fi + + distutils-r1_python_install_all +} diff --git a/dev-python/numpy/numpy-9999.ebuild b/dev-python/numpy/numpy-9999.ebuild index a930c5a32ab4..aa2a3abfa0ef 100644 --- a/dev-python/numpy/numpy-9999.ebuild +++ b/dev-python/numpy/numpy-9999.ebuild @@ -3,7 +3,7 @@ EAPI=5 -PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) +PYTHON_COMPAT=( python2_7 python3_{4,5,6,7} ) PYTHON_REQ_USE="threads(+)" FORTRAN_NEEDED=lapack -- cgit v1.2.3