Fix for missing clapack_* symbols in scipy, #371099

Package-Manager: portage-2.2.0_alpha62/cvs/Linux x86_64

5 files changed, 190 insertions, 6 deletions

diff --git a/dev-python/numpy/ChangeLog b/dev-python/numpy/ChangeLog
index b1d63f8802aa..b26e46ee9b82 100644
--- a/dev-python/numpy/ChangeLog
+++ b/dev-python/numpy/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for dev-python/numpy
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-python/numpy/ChangeLog,v 1.152 2011/08/17 16:46:37 chithanh Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-python/numpy/ChangeLog,v 1.153 2011/10/07 15:36:33 jlec Exp $
+
+*numpy-1.6.1-r1 (07 Oct 2011)
+
+  07 Oct 2011; Justin Lecher <jlec@gentoo.org> +numpy-1.6.1-r1.ebuild,
+  +files/numpy-1.6.1-atlas.patch, metadata.xml:
+  Fix for missing clapack_* symbols in scipy, #371099
 
   17 Aug 2011; Chí-Thanh Christopher Nguyễn <chithanh@gentoo.org>
   numpy-1.6.1.ebuild:
diff --git a/dev-python/numpy/Manifest b/dev-python/numpy/Manifest
index b3f8458c3551..a2df2fe949e5 100644
--- a/dev-python/numpy/Manifest
+++ b/dev-python/numpy/Manifest
@@ -1,7 +1,11 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
 AUX numpy-1.1.0-f2py.patch 1123 RMD160 ff90313cbe8282ac37b0cb98effa0ff6a03760c2 SHA1 5c37ea9be68782e533c7c2d64ca00e8e8ae648ea SHA256 cc67bc8ab7dba2febb91ba15cc51933021743a286c980e0068afd6fabdd065e7
 AUX numpy-1.3.0-fenv-freebsd.patch 1177 RMD160 78a84e18836472bd9c657771c43a44e417ec3e19 SHA1 4dba898255df4784eac9e52633307991c12029de SHA256 2fa3ed9fdeb9dc529d51da4ba8a3a7ea4cc4bb9998fffa66426b1606f2c637b5
 AUX numpy-1.4.0-interix.patch 478 RMD160 9a0290253238e09b824069d0026a5d2f00c90a8f SHA1 261e45c3feb068f033eed9b6468f5115ea418ca5 SHA256 4d6adcc1c66aa1399871c37f57e94ae7138c157ee5575945e83224a36c98c142
 AUX numpy-1.5.1-python-3.2.patch 971 RMD160 7e6ba80d2932279a45340a1d74f89051bbef1f0d SHA1 56fd29f930febd7b4339a821d268470fe41b67a1 SHA256 8add395a3f0a7e381fb96691024d7e2e1e062e2f3a1be8ffccbaf0cc060b4735
+AUX numpy-1.6.1-atlas.patch 712 RMD160 2d13370bebb386b0bc432e344c698309e5e02749 SHA1 dca75ad2e57368b980bcdb4e7fb4da87148f7ae5 SHA256 ceb741ba1383e8c3a05abfbcf67c9fde377d1f53ea93772214e8dfb7c0359705
 DIST numpy-1.5-html.zip 8545276 RMD160 41636f21c2c82ed1d9f15fe595c9d9303f62a2ee SHA1 c4fb912eec5850e5cf20afd47920a0019bfa5535 SHA256 2b71258bc71b623f682eaa791b81e0f81dce43b69546a1bcd3b1a9de830ce057
 DIST numpy-1.5-ref.pdf 7112007 RMD160 35901204b7e4c0ffc08ebb43a8a4dfa5b5a79bf1 SHA1 5e496e87a4f9873759397cb1cf546f6af0533598 SHA256 9ec75950b46e9d086cfb170f6978ba2b146ed7b1dc103af51e3c81ed5b8b5406
 DIST numpy-1.5-user.pdf 562092 RMD160 20d475d9c5a4abbad0ec5f969fdf9a5eef79c4b3 SHA1 6fafde625a81dd4be22a158cd73c010cb219e855 SHA256 afe77bacce8839460330e0c1c8a01508a03dd4a3010c2b8739ab61956d47f69d
@@ -13,6 +17,14 @@ DIST numpy-1.6.0.tar.gz 2633698 RMD160 29bee854e1436e0baad46150606d7a0d2d80ac61
 DIST numpy-1.6.1.tar.gz 2637779 RMD160 e4619fd5860c85a9c00bce0d0cb8dd9bb07a56f5 SHA1 3f73ff9231a1c15e28e6e259ef5cc35a72b34059 SHA256 788b1bc712ee566d4b4d62ef99736c5830fa264cbc56f8651ded1e795c755cdd
 EBUILD numpy-1.5.1.ebuild 5107 RMD160 b86e103a1f358cc172d24655a4836e19efaea7c2 SHA1 20d1865d2edd1b78dc44de8801d167c4ec140eab SHA256 7559513f731ed9ac96ae60de0e35df84ed8ba3f5f6045cabe18efd6250a709a8
 EBUILD numpy-1.6.0.ebuild 4801 RMD160 590604f459ed3f1e4a810e3cb7440401d49c0dac SHA1 846f45b4d4c3492ef50486224af58b1540dbb963 SHA256 fcd824bd3d81b721175c0037922f4752287914b618f01d0c9d6669c5ba5e4c3b
+EBUILD numpy-1.6.1-r1.ebuild 4400 RMD160 baf94c262fca853851073dd34dcf4162e22e9578 SHA1 e3091369982d2179371cfd1d15104b5fa114ea53 SHA256 f88b40428361cb0907d94f7e7b8b6a37daf995bbbbcfe4e15c6a43aa896e2977
 EBUILD numpy-1.6.1.ebuild 4820 RMD160 474904fd117469e8255c3fe708759215ec60ecee SHA1 51649d2c39b688b5a7cee71444b48ef7eed31e2b SHA256 3fc958720f24a600c6e58f1567a2936592e0a8139b033b4705b4fea0c85eb449
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diff --git a/dev-python/numpy/files/numpy-1.6.1-atlas.patch b/dev-python/numpy/files/numpy-1.6.1-atlas.patch
new file mode 100644
index 000000000000..0f0e1ffdaead
--- /dev/null
+++ b/dev-python/numpy/files/numpy-1.6.1-atlas.patch
@@ -0,0 +1,22 @@
+--- numpy/distutils/system_info.py.orig	2011-08-08 11:40:37.514881710 -0500
++++ numpy/distutils/system_info.py	2011-08-08 11:41:36.386872112 -0500
+@@ -1015,9 +1015,6 @@
+             else:
+                 info['language'] = 'f77'
+ 
+-        atlas_version, atlas_extra_info = get_atlas_version(**atlas)
+-        dict_append(info, **atlas_extra_info)
+-
+         self.set_info(**info)
+ 
+ class atlas_blas_info(atlas_info):
+@@ -1042,9 +1039,6 @@
+             dict_append(info,include_dirs=[h])
+         info['language'] = 'c'
+ 
+-        atlas_version, atlas_extra_info = get_atlas_version(**atlas)
+-        dict_append(atlas, **atlas_extra_info)
+-
+         dict_append(info,**atlas)
+ 
+         self.set_info(**info)
diff --git a/dev-python/numpy/metadata.xml b/dev-python/numpy/metadata.xml
index 050cbe6fc61b..067cfe3be15b 100644
--- a/dev-python/numpy/metadata.xml
+++ b/dev-python/numpy/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<herd>python</herd>
-<longdescription lang="en">
+	<herd>sci</herd>
+	<herd>python</herd>
+	<longdescription lang="en">
   NumPy is a general-purpose array-processing Python package designed to
   efficiently manipulate large multi-dimensional arrays of arbitrary
   records without sacrificing too much speed for small multi-dimensional
diff --git a/dev-python/numpy/numpy-1.6.1-r1.ebuild b/dev-python/numpy/numpy-1.6.1-r1.ebuild
new file mode 100644
index 000000000000..440df12bf9db
--- /dev/null
+++ b/dev-python/numpy/numpy-1.6.1-r1.ebuild
@@ -0,0 +1,144 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-python/numpy/numpy-1.6.1-r1.ebuild,v 1.1 2011/10/07 15:36:33 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="*"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="*-jython"
+
+inherit distutils eutils flag-o-matic fortran-2 toolchain-funcs versionator
+
+DOC_P="${PN}-1.6.0"
+
+DESCRIPTION="Fast array and numerical python library"
+HOMEPAGE="http://numpy.scipy.org/ http://pypi.python.org/pypi/numpy"
+SRC_URI="mirror://sourceforge/numpy/${P}.tar.gz
+	doc? (
+		http://docs.scipy.org/doc/${DOC_P}/numpy-html.zip -> ${DOC_P}-html.zip
+		http://docs.scipy.org/doc/${DOC_P}/numpy-ref.pdf -> ${DOC_P}-ref.pdf
+		http://docs.scipy.org/doc/${DOC_P}/numpy-user.pdf -> ${DOC_P}-user.pdf
+	)"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x86-freebsd ~x86-interix ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris"
+IUSE="doc lapack test"
+
+RDEPEND="
+	dev-python/setuptools
+	lapack? ( virtual/cblas virtual/lapack virtual/fortran )"
+DEPEND="${RDEPEND}
+	doc? ( app-arch/unzip )
+	lapack? ( dev-util/pkgconfig )
+	test? ( >=dev-python/nose-0.10 )"
+
+PYTHON_CFLAGS=("* + -fno-strict-aliasing")
+
+# Build system installs f2py${Python_version} scripts.
+PYTHON_NONVERSIONED_EXECUTABLES=("/usr/bin/f2py[[:digit:]]+\.[[:digit:]]+")
+
+DOCS="COMPATIBILITY DEV_README.txt THANKS.txt"
+
+pkg_setup() {
+	use lapack && fortran-2_pkg_setup
+	python_pkg_setup
+
+	# 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
+	if use lapack; then
+		append-fflags -fPIC
+		NUMPY_FCONFIG="config_fc --noopt --noarch"
+		# workaround bug 335908
+		[[ ${FC} == *gfortran* ]] && NUMPY_FCONFIG+=" --fcompiler=gnu95"
+	fi
+}
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${DOC_P}-html.zip -d html || die
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-atlas.patch
+
+	# Gentoo patch for ATLAS library names
+	sed -i \
+		-e "s:'f77blas':'blas':g" \
+		-e "s:'ptf77blas':'blas':g" \
+		-e "s:'ptcblas':'cblas':g" \
+		-e "s:'lapack_atlas':'lapack':g" \
+		numpy/distutils/system_info.py \
+		|| die "sed system_info.py failed"
+
+	if use lapack; then
+		append-ldflags "$(pkg-config --libs-only-other cblas lapack)"
+		sed -i -e '/NO_ATLAS_INFO/,+1d' numpy/core/setup.py || die
+		local libdir="${EPREFIX}"/usr/$(get_libdir)
+		cat >> site.cfg <<-EOF
+			[blas]
+			include_dirs = $(pkg-config --cflags-only-I \
+				cblas | sed -e 's/^-I//' -e 's/ -I/:/g')
+			library_dirs = $(pkg-config --libs-only-L \
+				cblas blas | sed -e 's/^-L//' -e 's/ -L/:/g' -e 's/ //g'):${libdir}
+			blas_libs = $(pkg-config --libs-only-l \
+				cblas blas | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+			[lapack]
+			library_dirs = $(pkg-config --libs-only-L \
+				lapack | sed -e 's/^-L//' -e 's/ -L/:/g' -e 's/ //g'):${libdir}
+			lapack_libs = $(pkg-config --libs-only-l \
+				lapack | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+		EOF
+	else
+		export {ATLAS,PTATLAS,BLAS,LAPACK,MKL}=None
+	fi
+
+	export CC="$(tc-getCC) ${CFLAGS}"
+}
+
+src_compile() {
+	distutils_src_compile ${NUMPY_FCONFIG}
+}
+
+src_test() {
+	testing() {
+		"$(PYTHON)" setup.py ${NUMPY_FCONFIG} build -b "build-${PYTHON_ABI}" install \
+			--home="${S}/test-${PYTHON_ABI}" --no-compile || die "install test failed"
+		pushd "${S}/test-${PYTHON_ABI}/"lib* > /dev/null
+		PYTHONPATH=python "$(PYTHON)" -c "import numpy; numpy.test()" 2>&1 | tee test.log
+		grep -Eq "^(ERROR|FAIL):" test.log && return 1
+		popd > /dev/null
+		rm -fr test-${PYTHON_ABI}
+	}
+	python_execute_function testing
+}
+
+src_install() {
+	distutils_src_install ${NUMPY_FCONFIG}
+
+	delete_txt() {
+		rm -f "${ED}"$(python_get_sitedir)/numpy/*.txt
+	}
+	python_execute_function -q delete_txt
+
+	docinto f2py
+	dodoc numpy/f2py/docs/*.txt || die "dodoc f2py failed"
+	doman numpy/f2py/f2py.1 || die "doman failed"
+
+	if use doc; then
+		insinto /usr/share/doc/${PF}
+		doins -r "${WORKDIR}"/html || die
+		doins  "${DISTDIR}"/${DOC_P}*pdf || die
+	fi
+}