Version bump

(Portage version: 2.2.01.21890-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

7 files changed, 219 insertions, 12 deletions

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index 916c76d3b461..7d6f69f94998 100644
--- a/sci-libs/scipy/ChangeLog
+++ b/sci-libs/scipy/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-libs/scipy
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.89 2013/03/30 13:07:39 floppym Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.90 2013/04/25 16:27:31 bicatali Exp $
+
+*scipy-0.12.0 (25 Apr 2013)
+
+  25 Apr 2013; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/scipy-0.12.0-blitz.patch,
+  +files/scipy-0.12.0-cephes-missing-include.patch,
+  +files/scipy-0.12.0-gerqf.patch, +files/scipy-0.12.0-restore-sys-argv.patch,
+  +scipy-0.12.0.ebuild, metadata.xml:
+  Version bump
 
   30 Mar 2013; Mike Gilbert <floppym@gentoo.org> scipy-0.11.0-r1.ebuild:
   Quote patterns for python_gen_usedep.
diff --git a/sci-libs/scipy/files/scipy-0.12.0-blitz.patch b/sci-libs/scipy/files/scipy-0.12.0-blitz.patch
new file mode 100644
index 000000000000..2817aa39b871
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.12.0-blitz.patch
@@ -0,0 +1,28 @@
+Description: Fixes scipy.weave.inline compalition with g++ 4.3 and upwards
+Author: Sameer Morar <smorar@gmail.com>
+Forwarded: http://projects.scipy.org/scipy/scipy/ticket/739
+Bug-Debian: http://bugs.debian.org/598520
+Bug-Ubuntu: https://launchpad.net/bugs/302649
+
+--- a/scipy/weave/blitz/blitz/blitz.h
++++ b/scipy/weave/blitz/blitz/blitz.h
+@@ -65,6 +65,8 @@
+ 
+ #define BZ_THROW                     // Needed in <blitz/numinquire.h>
+ 
++#include <cstdlib>
++
+ BZ_NAMESPACE(blitz)
+ 
+ #ifdef BZ_HAVE_STD
+--- a/scipy/weave/blitz/blitz/prettyprint.h
++++ b/scipy/weave/blitz/blitz/prettyprint.h
+@@ -22,6 +22,8 @@
+ #ifndef BZ_PRETTYPRINT_H
+ #define BZ_PRETTYPRINT_H
+ 
++#include <cstdlib>
++
+ BZ_NAMESPACE(blitz)
+ 
+ class prettyPrintFormat {
diff --git a/sci-libs/scipy/files/scipy-0.12.0-cephes-missing-include.patch b/sci-libs/scipy/files/scipy-0.12.0-cephes-missing-include.patch
new file mode 100644
index 000000000000..3bd93ad2bc41
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.12.0-cephes-missing-include.patch
@@ -0,0 +1,12 @@
+Missing declarations resulting in insecure code
+bicatali - gentoo - 04/2013
+--- scipy/special/cephes/gels.c.orig	2013-04-25 09:17:00.578809719 -0700
++++ scipy/special/cephes/gels.c	2013-04-25 09:17:18.048916759 -0700
+@@ -63,6 +63,7 @@
+  * C     ..................................................................
+  * C
+  */
++#include <math.h>
+ #include "protos.h"
+ 
+ int gels(A, R, M, EPS, AUX)
diff --git a/sci-libs/scipy/files/scipy-0.12.0-gerqf.patch b/sci-libs/scipy/files/scipy-0.12.0-gerqf.patch
new file mode 100644
index 000000000000..cf93c0ec53f0
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.12.0-gerqf.patch
@@ -0,0 +1,12 @@
+diff -up scipy-0.12.0/scipy/linalg/flapack.pyf.src.gerqf scipy-0.12.0/scipy/linalg/flapack.pyf.src
+--- scipy-0.12.0/scipy/linalg/flapack.pyf.src.gerqf	2013-04-06 10:10:35.000000000 -0600
++++ scipy-0.12.0/scipy/linalg/flapack.pyf.src	2013-04-15 17:03:37.290059000 -0600
+@@ -650,7 +650,7 @@ interface
+      <ftype> dimension(m,n),intent(in,out,copy,out=qr,aligned8) :: a
+      <ftype> dimension(MIN(m,n)),intent(out) :: tau
+ 
+-     integer optional,intent(in),depend(n),check(lwork>=m||lwork==-1) :: lwork=3*m
++     integer optional,intent(in),depend(m),check(lwork>=m||lwork==-1) :: lwork=3*m
+      <ftype> dimension(MAX(lwork,1)),intent(out),depend(lwork) :: work
+      integer intent(out) :: info
+    end subroutine <prefix>gerqf
diff --git a/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch b/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch
new file mode 100644
index 000000000000..3eef739f93a8
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.12.0-restore-sys-argv.patch
@@ -0,0 +1,15 @@
+Description: restore sys.argv in case of exception
+Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=500814
+
+--- a/scipy/weave/build_tools.py
++++ b/scipy/weave/build_tools.py
+@@ -283,6 +283,9 @@ def build_extension(module_path,compiler
+         configure_python_path(build_dir)
+     except SyntaxError: #TypeError:
+         success = 0
++    except Exception, e:
++        restore_sys_argv()
++        raise e
+ 
+     # restore argv after our trick...
+     restore_sys_argv()
diff --git a/sci-libs/scipy/metadata.xml b/sci-libs/scipy/metadata.xml
index 1020ae39f436..3fcc27d2e030 100644
--- a/sci-libs/scipy/metadata.xml
+++ b/sci-libs/scipy/metadata.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci</herd>
-  <longdescription lang="en">
+<herd>sci</herd>
+<longdescription lang="en">
   SciPy is an open source library of scientific tools for Python. SciPy
   supplements the popular numpy module, gathering a variety of high level
   science and engineering modules together as a single package.
-  SciPy includes modules for graphics and plotting, optimization, integration,
-  special functions, signal and image processing, genetic algorithms, ODE
-  solvers, and others.
+  SciPy includes modules for graphics and plotting, optimization,
+  integration, special functions, signal and image processing, genetic
+  algorithms, ODE solvers, and others.
 </longdescription>
-  <use>
-    <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag>
-  </use>
-  <upstream>
-    <remote-id type="pypi">scipy</remote-id>
-  </upstream>
+<use>
+  <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag>
+</use>
+<upstream>
+  <remote-id type="pypi">scipy</remote-id>
+</upstream>
 </pkgmetadata>
diff --git a/sci-libs/scipy/scipy-0.12.0.ebuild b/sci-libs/scipy/scipy-0.12.0.ebuild
new file mode 100644
index 000000000000..aca06103b370
--- /dev/null
+++ b/sci-libs/scipy/scipy-0.12.0.ebuild
@@ -0,0 +1,131 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.12.0.ebuild,v 1.1 2013/04/25 16:27:31 bicatali Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7,3_2,3_3} )
+
+inherit eutils fortran-2 distutils-r1 flag-o-matic multilib toolchain-funcs
+
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="http://www.scipy.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz
+	doc? (
+		http://docs.scipy.org/doc/${PN}/${PN}-html.zip -> ${P}-html.zip
+		http://docs.scipy.org/doc/${PN}/${PN}-ref.pdf -> ${P}-ref.pdf
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+IUSE="doc sparse test"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+
+CDEPEND="
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	sci-libs/arpack
+	virtual/cblas
+	virtual/lapack
+	sparse? ( sci-libs/umfpack )"
+DEPEND="${CDEPEND}
+	dev-lang/swig
+	dev-python/cython[${PYTHON_USEDEP}]
+	virtual/pkgconfig
+	doc? ( app-arch/unzip )
+	test? ( dev-python/nose[${PYTHON_USEDEP}] )"
+
+RDEPEND="${CDEPEND}
+	dev-python/imaging[$(python_gen_usedep 'python2*')]"
+
+DOCS=( HACKING.rst.txt README.txt THANKS.txt LATEST.txt TOCHANGE.txt )
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${P}-html.zip -d html || die
+	fi
+}
+
+pc_incdir() {
+	$(tc-getPKG_CONFIG) --cflags-only-I $@ | \
+		sed -e 's/^-I//' -e 's/[ ]*-I/:/g'
+}
+
+pc_libdir() {
+	$(tc-getPKG_CONFIG) --libs-only-L $@ | \
+		sed -e 's/^-L//' -e 's/[ ]*-L/:/g'
+}
+
+pc_libs() {
+	$(tc-getPKG_CONFIG) --libs-only-l $@ | \
+		sed -e 's/[ ]-l*\(pthread\|m\)[ ]*//g' \
+		-e 's/^-l//' -e 's/[ ]*-l/,/g'
+}
+
+python_prepare_all() {
+	# scipy automatically detects libraries by default
+	export {FFTW,FFTW3,UMFPACK}=None
+	use sparse && 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="${FC}"
+	export SCIPY_FCONFIG="config_fc --noopt --noarch"
+	append-fflags -fPIC
+
+	local libdir="${EPREFIX}"/usr/$(get_libdir)
+	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 = $(pc_libs lapack)
+	EOF
+
+	local PATCHES=(
+		"${FILESDIR}"/${P}-gerqf.patch
+		"${FILESDIR}"/${P}-blitz.patch
+		"${FILESDIR}"/${P}-restore-sys-argv.patch
+		"${FILESDIR}"/${P}-cephes-missing-include.patch
+	)
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile ${SCIPY_FCONFIG}
+}
+
+python_test() {
+	distutils_install_for_testing ${SCIPY_FCONFIG}
+	cd "${TEST_DIR}" || die "no ${TEST_DIR} available"
+	# nasty hack to remove weave tests because it is not python3 compat
+	[[ ${TEST_DIR} =~ python3 ]] && rm -r "${TEST_DIR}"/lib/scipy/weave
+#r = scipy.test('full', verbose=10)
+	"${EPYTHON}" -c "
+import scipy, sys
+r = scipy.test('fast',verbose=2)
+sys.exit(0 if r.wasSuccessful() else 1)" || die "Tests fail with ${EPYTHON}"
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+	if use doc; then
+		dohtml -r "${WORKDIR}"/html/.
+		dodoc "${DISTDIR}"/${P}*pdf
+	fi
+}
+
+pkg_postinst() {
+	elog "You might want to set the variable SCIPY_PIL_IMAGE_VIEWER"
+	elog "to your prefered image viewer. Example:"
+	elog "\t echo \"export SCIPY_PIL_IMAGE_VIEWER=display\" >> ~/.bashrc"
+}