Unbundled Superlu and Qhull, #357879

Package-Manager: portage-2.2.0_alpha28/cvs/Linux x86_64

7 files changed, 261 insertions, 13 deletions

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index 384cfb5d69cf..ef66f5d422bf 100644
--- a/sci-libs/scipy/ChangeLog
+++ b/sci-libs/scipy/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/scipy
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.64 2011/03/07 20:12:04 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.65 2011/03/26 17:10:43 jlec Exp $
+
+*scipy-0.9.0-r1 (26 Mar 2011)
+
+  26 Mar 2011; Justin Lecher <jlec@gentoo.org> scipy-0.8.0.ebuild,
+  scipy-0.9.0.ebuild, +scipy-0.9.0-r1.ebuild, +files/scipy-0.9.0-qhull.patch,
+  +files/scipy-0.9.0-superlu.patch:
+  Unbundled Superlu and Qhull, #357879
 
 *scipy-0.9.0 (07 Mar 2011)
 
diff --git a/sci-libs/scipy/Manifest b/sci-libs/scipy/Manifest
index 9491c1525572..ddf3bae4fb57 100644
--- a/sci-libs/scipy/Manifest
+++ b/sci-libs/scipy/Manifest
@@ -1,12 +1,25 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX scipy-0.6.0-stsci.patch 2209 RMD160 c7c21a23aef7fff9318f224ef2383f7970c1caf9 SHA1 4b86ad61346660959a61dce24b2b9f20595ea473 SHA256 69cec7cfedbc39a30f54ec12852a84017b5a256e966e60a64b4e891b497fd1be
 AUX scipy-0.8.0-python2.7.patch 826 RMD160 9c4cf8bb36e22dd1602fb14b4af5731692b43f9f SHA1 5b7f8a55c67d28448480a211d62379368c029df4 SHA256 cebe98b2a0f755516a154f43f99297a2a654b06b976d97db877b609d0ff0a346
+AUX scipy-0.9.0-qhull.patch 1672 RMD160 7b1d7ceb4cc330b141c993f4f37b2f52a7ffbb9c SHA1 a5180f6a80ad31585edf9da42dcd0751e0cc3a38 SHA256 adbcb54b569c48838df8500a416febbc1f704643874780e4dcf30a635efe6027
+AUX scipy-0.9.0-superlu.patch 1526 RMD160 e9628e30466502aa9f708a082cca02fdf97e6bab SHA1 c17ff6d2da83b262bd898a4d91fa4db0269c6e02 SHA256 10b58353b0cdd6a8a6713ca7186cdb37c33c0ae4e42014322c5ad94465359e8f
 DIST scipy-0.8-html.zip 6570421 RMD160 718a919f095e619a3669c30b3b77816500687daa SHA1 4d9e8e3bc04a3d5aec54b77c4acf36be46af342a SHA256 fd4f0a268cb0c4ca7f1b03da0036e342c06cb2dacf3eda3b893cb759e6655f7e
 DIST scipy-0.8-ref.pdf 4561020 RMD160 e748733add18a452753d2a6ec1a1084024e87756 SHA1 0ccd530749b05f56ee1372e9461ebe99810d1472 SHA256 0715c01702ac7302487544600e16870ef12027c121af336c3ae9bae03e9fd41b
 DIST scipy-0.8.0.tar.gz 5560625 RMD160 cce915a5760f9bcf4cc39381cb01d1a5726a57f3 SHA1 d7a84e5dc440d05e4d198411a2e0c6b8ec9adfc5 SHA256 b12937bd3a71ace8d7d6b7e19f8f220630969c2822e6248fc0bbc8f2cc18d825
 DIST scipy-0.9-html.zip 8516420 RMD160 01dc795021f2a360ac4713bf35619c8a01a1efb1 SHA1 527712601a68abacbfc6d4a4e104a865618d8219 SHA256 6f3148881502ca2cd2964fef7baf9bfec6fe2329ec3f1832e1e6d864aed0f889
 DIST scipy-0.9-ref.pdf 5299022 RMD160 38b23f2c32b568d89a4bd02061cf95a0db87a1cf SHA1 9d1af3044d7e461f3ecb4fb3c00b3e31d1ea4419 SHA256 ed2641c180eef2f842536a611982fbd91c33c95a7e7e3c279d7ae6f10071be47
 DIST scipy-0.9.0.tar.gz 6084552 RMD160 2aef8c3413ba9c7731d078b27eef1e03419de606 SHA1 a586b10d0613cd61dbfcfd42f3d2609062cd10b8 SHA256 913089de94721be864e0a57fdab52603f3150250a2e0ce4ed6928ca1125f6b23
-EBUILD scipy-0.8.0.ebuild 4116 RMD160 9f344e8a20c0517334e4072d6e24354d2e3cdf8b SHA1 62a1eb216df148397beb7fe25026af44194074d7 SHA256 7837ae6e4a54efd8d7ee0a417af186ff6ca81f3d03c772c17208c3213721d246
-EBUILD scipy-0.9.0.ebuild 4034 RMD160 67606020432bf35465f408ce738cfcc87c378818 SHA1 6945f7b6201db5ef5dc9723e49bd067fc036b7dc SHA256 8466d5bf0dcb46ed2b35fc4fc1c84dafb84d4d6bccd5a2eeb5dd3e21aacef557
-MISC ChangeLog 12933 RMD160 b0d38ba57b7490c933bee585122fda6732d0d32d SHA1 960994879382d85c26d3cc7d9f0c58179f7c5669 SHA256 453500e4e48ed2c8c8d2055e7bef29cafa3e07cfc1645144e947175877c09eea
+EBUILD scipy-0.8.0.ebuild 4116 RMD160 1e3ed2eac7c8625d38d1582e027c895e9b29cd27 SHA1 c8d874e33ae8e997bb4d55ee0cb4197c2f6a839b SHA256 5f31f57cbba672a10541858045d9fd34c0eba3538095f0878279aaec4eb2dc38
+EBUILD scipy-0.9.0-r1.ebuild 4202 RMD160 e261245444ad15a01c5030373c7a673df8fd034f SHA1 2fcb7d38ead9e224108a91bb54171b9ccc58b4a7 SHA256 4b0ce9a9263b883236dce52c911b5ef2591da3a6680ce4318258ed4df7b17ea0
+EBUILD scipy-0.9.0.ebuild 4052 RMD160 952f9cc636cb2f8ec0df431518bc21f12cc89fd6 SHA1 05b4f83109b0978ae246b5af3471589593824ebf SHA256 e117d282157006d2af44d72dddd6da359afc041cd659f8d6438a9271aecf12ff
+MISC ChangeLog 13181 RMD160 4fa3eeef3b9a750f7b868e885286bf6ede938a78 SHA1 c99a3184f8fa58c34e35a8dd667b3175a21c9e94 SHA256 245ef6a3f3ee199c76327e73996d021a6bb93b3dc05374e98b9afe68d9d146c7
 MISC metadata.xml 697 RMD160 05eb973594c8fe27be71e813f2a2294cf9e3f46e SHA1 1dbbb06751c0fc5760618d8998f9d169b3f774ae SHA256 1bfca083b6aa7c4fbd95b638daa2158b2eaa5cb93fe7a99abe9a2bc08b21e48e
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEARECAAYFAk2OHhoACgkQgAnW8HDreRZ3MQCgiBpC0PNKRZBzukWc4ByBZLeN
+wrYAn21a0JonnyLPPgq6bxfg4dAkbelP
+=cbSC
+-----END PGP SIGNATURE-----
diff --git a/sci-libs/scipy/files/scipy-0.9.0-qhull.patch b/sci-libs/scipy/files/scipy-0.9.0-qhull.patch
new file mode 100644
index 000000000000..cb06df4c4734
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.9.0-qhull.patch
@@ -0,0 +1,44 @@
+ scipy/spatial/qhull.c  |    4 ++--
+ scipy/spatial/setup.py |   14 +++++++-------
+ 2 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/scipy/spatial/qhull.c b/scipy/spatial/qhull.c
+index 91e22b3..e433ae9 100644
+--- a/scipy/spatial/qhull.c
++++ b/scipy/spatial/qhull.c
+@@ -202,8 +202,8 @@
+ #include "numpy/arrayobject.h"
+ #include "numpy/ufuncobject.h"
+ #include "math.h"
+-#include "qhull/src/qset.h"
+-#include "qhull/src/qhull.h"
++#include "qhull/qset.h"
++#include "qhull/qhull.h"
+ #include "qhull_blas.h"
+ 
+ 
+diff --git a/scipy/spatial/setup.py b/scipy/spatial/setup.py
+index 7401d55..254c23d 100755
+--- a/scipy/spatial/setup.py
++++ b/scipy/spatial/setup.py
+@@ -16,13 +16,13 @@ def configuration(parent_package = '', top_path = None):
+                  'random.c', 'rboxlib.c', 'stat.c', 'user.c', 'usermem.c',
+                  'userprintf.c']
+ 
+-    config.add_library('qhull',
+-                       sources=[join('qhull', 'src', x) for x in qhull_src],
+-                       include_dirs=[get_python_inc(),
+-                                     get_numpy_include_dirs()],
+-                       # XXX: GCC dependency!
+-                       #extra_compiler_args=['-fno-strict-aliasing'],
+-                       )
++#    config.add_library('qhull',
++#                       sources=[join('qhull', 'src', x) for x in qhull_src],
++#                       include_dirs=[get_python_inc(),
++#                                     get_numpy_include_dirs()],
++#                       # XXX: GCC dependency!
++#                       #extra_compiler_args=['-fno-strict-aliasing'],
++#                       )
+ 
+     lapack = dict(get_info('lapack_opt'))
+     try:
diff --git a/sci-libs/scipy/files/scipy-0.9.0-superlu.patch b/sci-libs/scipy/files/scipy-0.9.0-superlu.patch
new file mode 100644
index 000000000000..88f60be0cbbf
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.9.0-superlu.patch
@@ -0,0 +1,40 @@
+--- scipy/sparse/linalg/dsolve/_superluobject.h.orig	2011-03-24 22:05:15.995923005 +1300
++++ scipy/sparse/linalg/dsolve/_superluobject.h	2011-03-24 22:06:09.638923002 +1300
+@@ -9,11 +9,10 @@
+ #define __SUPERLU_OBJECT
+ 
+ #include "Python.h"
+-#include "SuperLU/SRC/slu_zdefs.h"
++#include "superlu/slu_zdefs.h"
+ #include "numpy/arrayobject.h"
+-#include "SuperLU/SRC/slu_util.h"
+-#include "SuperLU/SRC/slu_dcomplex.h"
+-#include "SuperLU/SRC/slu_scomplex.h"
++#include "superlu/slu_util.h"
++#include "superlu/slu_dcomplex.h"
+ 
+ 
+ #define _CHECK_INTEGER(x) (PyArray_ISINTEGER(x) && (x)->descr->elsize == sizeof(int))
+ 
+--- scipy/sparse/linalg/dsolve/setup.py.orig	2011-02-20 22:58:20.000000000 +1300
++++ scipy/sparse/linalg/dsolve/setup.py	2011-03-25 11:08:02.691267018 +1300
+@@ -25,18 +25,12 @@
+         # when using MSVC + MKL, lsame is already in MKL
+         sources.remove(join(superlu_src, 'lsame.c'))
+ 
+-    config.add_library('superlu_src',
+-                       sources = sources,
+-                       macros = superlu_defs,
+-                       include_dirs=[superlu_src],
+-                       )
+-
+     # Extension
+     config.add_extension('_superlu',
+                          sources = ['_superlumodule.c',
+                                     '_superlu_utils.c',
+                                     '_superluobject.c'],
+-                         libraries = ['superlu_src'],
++                         libraries = ['superlu'],
+                          extra_info = lapack_opt,
+                          )
+ 
diff --git a/sci-libs/scipy/scipy-0.8.0.ebuild b/sci-libs/scipy/scipy-0.8.0.ebuild
index 181f58a03eb4..4aaa0ceb88af 100644
--- a/sci-libs/scipy/scipy-0.8.0.ebuild
+++ b/sci-libs/scipy/scipy-0.8.0.ebuild
@@ -1,8 +1,9 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.8.0.ebuild,v 1.6 2011/01/23 11:50:58 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.8.0.ebuild,v 1.7 2011/03/26 17:10:43 jlec Exp $
 
 EAPI="2"
+
 PYTHON_DEPEND="2"
 SUPPORT_PYTHON_ABIS="1"
 RESTRICT_PYTHON_ABIS="3.* *-jython"
@@ -11,13 +12,13 @@ inherit eutils distutils flag-o-matic toolchain-funcs versionator
 
 SP="${PN}-$(get_version_component_range 1-2)"
 
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
 	doc? (
 		http://docs.scipy.org/doc/${SP}.x/${PN}-html.zip -> ${SP}-html.zip
 		http://docs.scipy.org/doc/${SP}.x/${PN}-ref.pdf -> ${SP}-ref.pdf
 	)"
-DESCRIPTION="Scientific algorithms library for Python"
-HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy"
 
 LICENSE="BSD"
 SLOT="0"
@@ -69,7 +70,8 @@ src_unpack() {
 }
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PN}-0.6.0-stsci.patch \
+	epatch \
+		"${FILESDIR}"/${PN}-0.6.0-stsci.patch \
 		"${FILESDIR}"/${P}-python2.7.patch
 	local libdir="${EPREFIX}"/usr/$(get_libdir)
 	cat > site.cfg <<-EOF
diff --git a/sci-libs/scipy/scipy-0.9.0-r1.ebuild b/sci-libs/scipy/scipy-0.9.0-r1.ebuild
new file mode 100644
index 000000000000..0d76cc7afd8b
--- /dev/null
+++ b/sci-libs/scipy/scipy-0.9.0-r1.ebuild
@@ -0,0 +1,139 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.9.0-r1.ebuild,v 1.1 2011/03/26 17:10:43 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="*-jython"
+
+inherit eutils distutils flag-o-matic toolchain-funcs versionator
+
+SP="${PN}-$(get_version_component_range 1-2)"
+
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
+	doc? (
+		http://docs.scipy.org/doc/${P}/${PN}-html.zip -> ${SP}-html.zip
+		http://docs.scipy.org/doc/${P}/${PN}-ref.pdf -> ${SP}-ref.pdf
+	)"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc umfpack"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+
+CDEPEND="
+	>=dev-python/numpy-1.5
+	media-libs/qhull
+	sci-libs/arpack
+	virtual/cblas
+	virtual/lapack
+	umfpack? ( sci-libs/umfpack )"
+
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig
+	doc? ( app-arch/unzip )
+	umfpack? ( dev-lang/swig )"
+
+RDEPEND="${CDEPEND}
+	dev-python/imaging"
+
+# buggy test suite - still true for 0.9.0
+RESTRICT="test"
+
+DOCS="THANKS.txt LATEST.txt TOCHANGE.txt"
+
+pkg_setup() {
+	# scipy automatically detects libraries by default
+	export {FFTW,FFTW3,UMFPACK}=None
+	use umfpack && 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
+}
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${SP}-html.zip -d html || die
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-superlu.patch \
+		"${FILESDIR}"/${P}-qhull.patch
+	rm -rf ./scipy/sparse/linalg/dsolve/SuperLU ./scipy/spatial/qhull
+	local libdir="${EPREFIX}"/usr/$(get_libdir)
+	cat > site.cfg <<-EOF
+		[atlas]
+		include_dirs = $(pkg-config --cflags-only-I \
+			cblas | sed -e 's/^-I//' -e 's/ -I/:/g')
+		library_dirs = $(pkg-config --libs-only-L \
+			cblas blas lapack| sed -e \
+			's/^-L//' -e 's/ -L/:/g' -e 's/ //g'):${libdir}
+		atlas_libs = $(pkg-config --libs-only-l \
+			cblas blas | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+		lapack_libs = $(pkg-config --libs-only-l \
+			lapack | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+		[blas_opt]
+		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}
+		libraries = $(pkg-config --libs-only-l \
+			cblas blas | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+		[lapack_opt]
+		library_dirs = $(pkg-config --libs-only-L \
+			lapack | sed -e 's/^-L//' -e 's/ -L/:/g' \
+			-e 's/ //g'):${libdir}
+		libraries = $(pkg-config --libs-only-l \
+			lapack | sed -e 's/^-l//' -e 's/ -l/, /g' -e 's/,.pthread//g')
+	EOF
+}
+
+src_compile() {
+	distutils_src_compile ${SCIPY_FCONFIG}
+}
+
+src_test() {
+	testing() {
+		"$(PYTHON)" setup.py build -b "build-${PYTHON_ABI}" install \
+			--home="${S}/test-${PYTHON_ABI}" --no-compile ${SCIPY_FCONFIG} || die "install test failed"
+		pushd "${S}/test-${PYTHON_ABI}/"lib*/python > /dev/null
+		PYTHONPATH=. "$(PYTHON)" -c "import scipy; scipy.test('full')" 2>&1 | tee test.log
+		grep -q ^ERROR test.log && die "test failed"
+		popd > /dev/null
+		rm -fr test-${PYTHON_ABI}
+	}
+	python_execute_function testing
+}
+
+src_install() {
+	distutils_src_install ${SCIPY_FCONFIG}
+	if use doc; then
+		insinto /usr/share/doc/${PF}
+		doins -r "${WORKDIR}"/html || die
+		doins  "${DISTDIR}"/${SP}*pdf || die
+	fi
+}
+
+pkg_postinst() {
+	distutils_pkg_postinst
+
+	elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER"
+	elog "to your prefered image viewer if you don't like the default one. Ex:"
+	elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc"
+}
diff --git a/sci-libs/scipy/scipy-0.9.0.ebuild b/sci-libs/scipy/scipy-0.9.0.ebuild
index d75d7f7a90a0..6efe5139d958 100644
--- a/sci-libs/scipy/scipy-0.9.0.ebuild
+++ b/sci-libs/scipy/scipy-0.9.0.ebuild
@@ -1,8 +1,10 @@
 # Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.9.0.ebuild,v 1.2 2011/03/08 21:08:00 arfrever Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.9.0.ebuild,v 1.3 2011/03/26 17:10:43 jlec Exp $
 
 EAPI="3"
+
+PYTHON_DEPEND="2"
 SUPPORT_PYTHON_ABIS="1"
 RESTRICT_PYTHON_ABIS="*-jython"
 
@@ -11,7 +13,7 @@ inherit eutils distutils flag-o-matic toolchain-funcs versionator
 SP="${PN}-$(get_version_component_range 1-2)"
 
 DESCRIPTION="Scientific algorithms library for Python"
-HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy"
+HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
 	doc? (
 		http://docs.scipy.org/doc/${P}/${PN}-html.zip -> ${SP}-html.zip
@@ -23,11 +25,12 @@ SLOT="0"
 IUSE="doc umfpack"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
 
-CDEPEND=">=dev-python/numpy-1.5
-	virtual/cblas
-	virtual/lapack
+CDEPEND="
+	>=dev-python/numpy-1.5
 	media-libs/qhull
 	sci-libs/arpack
+	virtual/cblas
+	virtual/lapack
 	umfpack? ( sci-libs/umfpack )"
 
 DEPEND="${CDEPEND}