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@gentoo.org>

3 files changed, 354 insertions, 0 deletions

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 000000000000..77a3c010371f
--- /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 <allan.haldane@gmail.com>
+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 000000000000..9c33704f8e22
--- /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 <eakruse@uw.edu>
+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 <eakruse@uw.edu>
+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 000000000000..91cea129f63c
--- /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
+}