commit: bb027200ad8cf7ae8453902a014b367456586a61 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Tue Oct 20 19:24:34 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Oct 21 13:40:24 2015 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bb027200
dev-python/numpy: Backport several fixes from 0.10.2 fixing regression in pandas, statsmodel and bottleneck Package-Manager: portage-2.2.23 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> .../numpy/files/numpy-1.10.1-backport-1.patch | 127 +++++++++++++++++ .../numpy/files/numpy-1.10.1-backport-2.patch | 73 ++++++++++ dev-python/numpy/numpy-1.10.1-r1.ebuild | 154 +++++++++++++++++++++ 3 files changed, 354 insertions(+) diff --git a/dev-python/numpy/files/numpy-1.10.1-backport-1.patch b/dev-python/numpy/files/numpy-1.10.1-backport-1.patch new file mode 100644 index 0000000..77a3c01 --- /dev/null +++ b/dev-python/numpy/files/numpy-1.10.1-backport-1.patch @@ -0,0 +1,127 @@ +From 3a816a4db9b498eb64eb837fdcca0fa8ddbe063e Mon Sep 17 00:00:00 2001 +From: Allan Haldane <[email protected]> +Date: Sat, 17 Oct 2015 14:00:36 -0400 +Subject: [PATCH] BUG: recarrays viewed as subarrays don't convert to np.record + type + +Record array views were updated in #5943 to return np.record dtype +where possible, but forgot about the case of sub-arrays. + +That's fixed here, so accessing subarray fields by attribute or index +works sensibly, as well as viewing a record array as a subarray dtype, +and printing subarrays. + +This also happens to fix #6459, since it affects the same lines. + +Fixes #6497 #6459 +--- + numpy/core/records.py | 30 +++++++++++++++++++----------- + numpy/core/tests/test_records.py | 23 +++++++++++++++++++++++ + 2 files changed, 42 insertions(+), 11 deletions(-) + +diff --git a/numpy/core/records.py b/numpy/core/records.py +index 4a99553..4ce3fe9 100644 +--- a/numpy/core/records.py ++++ b/numpy/core/records.py +@@ -448,12 +448,14 @@ def __getattribute__(self, attr): + + # At this point obj will always be a recarray, since (see + # PyArray_GetField) the type of obj is inherited. Next, if obj.dtype is +- # non-structured, convert it to an ndarray. If obj is structured leave +- # it as a recarray, but make sure to convert to the same dtype.type (eg +- # to preserve numpy.record type if present), since nested structured +- # fields do not inherit type. ++ # non-structured, convert it to an ndarray. Then if obj is structured ++ # with void type convert it to the same dtype.type (eg to preserve ++ # numpy.record type if present), since nested structured fields do not ++ # inherit type. Don't do this for non-void structures though. + if obj.dtype.fields: +- return obj.view(dtype=(self.dtype.type, obj.dtype.fields)) ++ if issubclass(obj.dtype.type, nt.void): ++ return obj.view(dtype=(self.dtype.type, obj.dtype)) ++ return obj + else: + return obj.view(ndarray) + +@@ -463,8 +465,9 @@ def __getattribute__(self, attr): + # Thus, you can't create attributes on-the-fly that are field names. + def __setattr__(self, attr, val): + +- # Automatically convert (void) dtypes to records. +- if attr == 'dtype' and issubclass(val.type, nt.void): ++ # Automatically convert (void) structured types to records ++ # (but not non-void structures, subarrays, or non-structured voids) ++ if attr == 'dtype' and issubclass(val.type, nt.void) and val.fields: + val = sb.dtype((record, val)) + + newattr = attr not in self.__dict__ +@@ -499,7 +502,9 @@ def __getitem__(self, indx): + # we might also be returning a single element + if isinstance(obj, ndarray): + if obj.dtype.fields: +- return obj.view(dtype=(self.dtype.type, obj.dtype.fields)) ++ if issubclass(obj.dtype.type, nt.void): ++ return obj.view(dtype=(self.dtype.type, obj.dtype)) ++ return obj + else: + return obj.view(type=ndarray) + else: +@@ -519,11 +524,14 @@ def __repr__(self): + # If this is a full record array (has numpy.record dtype), + # or if it has a scalar (non-void) dtype with no records, + # represent it using the rec.array function. Since rec.array +- # converts dtype to a numpy.record for us, use only dtype.descr, +- # not repr(dtype). ++ # converts dtype to a numpy.record for us, convert back ++ # to non-record before printing ++ plain_dtype = self.dtype ++ if plain_dtype.type is record: ++ plain_dtype = sb.dtype((nt.void, plain_dtype)) + lf = '\n'+' '*len("rec.array(") + return ('rec.array(%s, %sdtype=%s)' % +- (lst, lf, repr(self.dtype.descr))) ++ (lst, lf, plain_dtype)) + else: + # otherwise represent it using np.array plus a view + # This should only happen if the user is playing +diff --git a/numpy/core/tests/test_records.py b/numpy/core/tests/test_records.py +index 7a18f29..290bc4f 100644 +--- a/numpy/core/tests/test_records.py ++++ b/numpy/core/tests/test_records.py +@@ -121,6 +121,23 @@ def test_recarray_views(self): + assert_equal(type(rv), np.recarray) + assert_equal(rv.dtype.type, np.record) + ++ # check that accessing nested structures keep record type, but ++ # not for subarrays, non-void structures, non-structured voids ++ test_dtype = [('a', 'f4,f4'), ('b', 'V8'), ('c', ('f4',2)), ++ ('d', ('i8', 'i4,i4'))] ++ r = np.rec.array([((1,1), b'11111111', [1,1], 1), ++ ((1,1), b'11111111', [1,1], 1)], dtype=test_dtype) ++ assert_equal(r.a.dtype.type, np.record) ++ assert_equal(r.b.dtype.type, np.void) ++ assert_equal(r.c.dtype.type, np.float32) ++ assert_equal(r.d.dtype.type, np.int64) ++ # check the same, but for views ++ r = np.rec.array(np.ones(4, dtype='i4,i4')) ++ assert_equal(r.view('f4,f4').dtype.type, np.record) ++ assert_equal(r.view(('i4',2)).dtype.type, np.int32) ++ assert_equal(r.view('V8').dtype.type, np.void) ++ assert_equal(r.view(('i8', 'i4,i4')).dtype.type, np.int64) ++ + #check that we can undo the view + arrs = [np.ones(4, dtype='f4,i4'), np.ones(4, dtype='f8')] + for arr in arrs: +@@ -135,6 +152,12 @@ def test_recarray_repr(self): + a = np.array(np.ones(4, dtype='f8')) + assert_(repr(np.rec.array(a)).startswith('rec.array')) + ++ # check that the 'np.record' part of the dtype isn't shown ++ a = np.rec.array(np.ones(3, dtype='i4,i4')) ++ assert_equal(repr(a).find('numpy.record'), -1) ++ a = np.rec.array(np.ones(3, dtype='i4')) ++ assert_(repr(a).find('dtype=int32') != -1) ++ + def test_recarray_from_names(self): + ra = np.rec.array([ + (1, 'abc', 3.7000002861022949, 0), diff --git a/dev-python/numpy/files/numpy-1.10.1-backport-2.patch b/dev-python/numpy/files/numpy-1.10.1-backport-2.patch new file mode 100644 index 0000000..9c33704 --- /dev/null +++ b/dev-python/numpy/files/numpy-1.10.1-backport-2.patch @@ -0,0 +1,73 @@ +From 0d25dc4175e00cdaf9545e8b1b1a5b879cf67248 Mon Sep 17 00:00:00 2001 +From: Ethan Kruse <[email protected]> +Date: Mon, 19 Oct 2015 13:29:01 -0700 +Subject: [PATCH 1/2] Potential fix for #6462 + +--- + numpy/lib/function_base.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/numpy/lib/function_base.py b/numpy/lib/function_base.py +index 555d083..fef69df 100644 +--- a/numpy/lib/function_base.py ++++ b/numpy/lib/function_base.py +@@ -3339,7 +3339,7 @@ def _median(a, axis=None, out=None, overwrite_input=False): + indexer[axis] = slice(index-1, index+1) + + # Check if the array contains any nan's +- if np.issubdtype(a.dtype, np.inexact): ++ if np.issubdtype(a.dtype, np.inexact) and sz > 0: + # warn and return nans like mean would + rout = mean(part[indexer], axis=axis, out=out) + part = np.rollaxis(part, axis, part.ndim) + +From 59d859fb2160950ac93267d7461ad952145c8724 Mon Sep 17 00:00:00 2001 +From: Ethan Kruse <[email protected]> +Date: Tue, 20 Oct 2015 11:40:49 -0700 +Subject: [PATCH 2/2] Added tests for median of empty arrays + +--- + numpy/lib/tests/test_function_base.py | 30 ++++++++++++++++++++++++++++++ + 1 file changed, 30 insertions(+) + +diff --git a/numpy/lib/tests/test_function_base.py b/numpy/lib/tests/test_function_base.py +index 4516c92..aa41c1f 100644 +--- a/numpy/lib/tests/test_function_base.py ++++ b/numpy/lib/tests/test_function_base.py +@@ -2597,6 +2597,36 @@ def test_nan_behavior(self): + assert_equal(np.median(a, (0, 2)), b) + assert_equal(len(w), 1) + ++ def test_empty(self): ++ # empty arrays ++ a = np.array([], dtype=float) ++ with warnings.catch_warnings(record=True) as w: ++ warnings.filterwarnings('always', '', RuntimeWarning) ++ assert_equal(np.median(a), np.nan) ++ assert_(w[0].category is RuntimeWarning) ++ ++ # multiple dimensions ++ a = np.array([], dtype=float, ndmin=3) ++ # no axis ++ with warnings.catch_warnings(record=True) as w: ++ warnings.filterwarnings('always', '', RuntimeWarning) ++ assert_equal(np.median(a), np.nan) ++ assert_(w[0].category is RuntimeWarning) ++ ++ # axis 0 and 1 ++ b = np.array([], dtype=float, ndmin=2) ++ with warnings.catch_warnings(record=True) as w: ++ warnings.filterwarnings('always', '', RuntimeWarning) ++ assert_equal(np.median(a, axis=0), b) ++ assert_equal(np.median(a, axis=1), b) ++ ++ # axis 2 ++ b = np.array(np.nan, dtype=float, ndmin=2) ++ with warnings.catch_warnings(record=True) as w: ++ warnings.filterwarnings('always', '', RuntimeWarning) ++ assert_equal(np.median(a, axis=2), b) ++ assert_(w[0].category is RuntimeWarning) ++ + def test_object(self): + o = np.arange(7.) + assert_(type(np.median(o.astype(object))), float) diff --git a/dev-python/numpy/numpy-1.10.1-r1.ebuild b/dev-python/numpy/numpy-1.10.1-r1.ebuild new file mode 100644 index 0000000..91cea12 --- /dev/null +++ b/dev-python/numpy/numpy-1.10.1-r1.ebuild @@ -0,0 +1,154 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4,5} ) + +FORTRAN_NEEDED=lapack + +inherit distutils-r1 eutils flag-o-matic fortran-2 multilib multiprocessing toolchain-funcs versionator + +DOC_PV="1.9.1" +DOC_P="${PN}-${DOC_PV}" + +DESCRIPTION="Fast array and numerical python library" +HOMEPAGE="http://www.numpy.org/"; +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz + doc? ( + http://docs.scipy.org/doc/${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 + )" +# It appears the docs haven't been upgraded, still @ 1.8.1 +LICENSE="BSD" +SLOT="0" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~x86-freebsd ~x86-interix ~amd64-linux ~arm-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" +IUSE="doc lapack test" + +RDEPEND=" + dev-python/setuptools[${PYTHON_USEDEP}] + lapack? ( virtual/cblas virtual/lapack )" +DEPEND="${RDEPEND} + doc? ( app-arch/unzip ) + lapack? ( virtual/pkgconfig ) + test? ( >=dev-python/nose-1.0[${PYTHON_USEDEP}] )" + +# Uses distutils.command.config. +DISTUTILS_IN_SOURCE_BUILD=1 + +PATCHES=( + "${FILESDIR}"/${PN}-1.9.2-no-hardcode-blas.patch + "${FILESDIR}"/${P}-backport-1.patch + "${FILESDIR}"/${P}-backport-2.patch +) + +src_unpack() { + default + if use doc; then + unzip -qo "${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) + # make sure _dotblas.so gets built + sed -i -e '/NO_ATLAS_INFO/,+1d' numpy/core/setup.py || die + cat >> site.cfg <<-EOF + [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 "/f2py_cmd/s:'f2py'.*:'f2py':g" \ + -i numpy/tests/test_scripts.py || die + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile -j $(makeopts_jobs) ${NUMPY_FCONFIG} +} + +python_test() { + distutils_install_for_testing ${NUMPY_FCONFIG} + + cd "${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 ${NUMPY_FCONFIG} +} + +python_install_all() { + distutils-r1_python_install_all + + dodoc COMPATIBILITY DEV_README.txt THANKS.txt + + if use doc; then + dohtml -r "${WORKDIR}"/html/* + dodoc "${DISTDIR}"/${PN}-{user,ref}-${DOC_PV}.pdf + fi + + # absent in 1.9 + #docinto f2py + #dodoc numpy/f2py/docs/*.txt + #doman numpy/f2py/f2py.1 +}
