Applied a patch for the optimize module to work with sage, see bug #320135

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 198 insertions, 1 deletions

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index bfc0a9e1514a..8f032d7f01ed 100644
--- a/sci-libs/scipy/ChangeLog
+++ b/sci-libs/scipy/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/scipy
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.50 2010/04/22 20:28:27 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.51 2010/05/18 17:25:31 bicatali Exp $
+
+*scipy-0.7.2-r1 (18 May 2010)
+
+  18 May 2010; Sébastien Fabbro <bicatali@gentoo.org>
+  +scipy-0.7.2-r1.ebuild, +files/scipy-0.7.2-optimize.patch:
+  Applied a patch for the optimize module to work with sage, see bug #320135
 
 *scipy-0.7.2 (22 Apr 2010)
 
diff --git a/sci-libs/scipy/files/scipy-0.7.2-optimize.patch b/sci-libs/scipy/files/scipy-0.7.2-optimize.patch
new file mode 100644
index 000000000000..4a3bb74012bd
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.7.2-optimize.patch
@@ -0,0 +1,54 @@
+--- scipy/optimize/optimize.py.orig	2009-07-11 17:56:37.000000000 +1200
++++ scipy/optimize/optimize.py	2010-05-17 21:36:07.605336495 +1200
+@@ -41,6 +41,12 @@
+     m = asarray(m)
+     return numpy.minimum.reduce(m,axis)
+ 
++def is_array_scalar(x):
++    """Test whether `x` is either a scalar or an array scalar.
++
++    """
++    return len(atleast_1d(x) == 1)
++
+ abs = absolute
+ import __builtin__
+ pymin = __builtin__.min
+@@ -1177,13 +1183,12 @@
+ 
+     """
+     # Test bounds are of correct form
+-    x1 = atleast_1d(x1)
+-    x2 = atleast_1d(x2)
+-    if len(x1) != 1 or len(x2) != 1:
+-        raise ValueError, "Optimisation bounds must be scalars" \
+-                " or length 1 arrays"
++
++    if not (is_array_scalar(x1) and is_array_scalar(x2)):
++        raise ValueError("Optimisation bounds must be scalars"
++                         " or array scalars.")
+     if x1 > x2:
+-        raise ValueError, "The lower bound exceeds the upper bound."
++        raise ValueError("The lower bound exceeds the upper bound.")
+ 
+     flag = 0
+     header = ' Func-count     x          f(x)          Procedure'
+--- scipy/optimize/tests/test_optimize.py.orig	2009-07-11 17:56:37.000000000 +1200
++++ scipy/optimize/tests/test_optimize.py	2010-05-18 21:31:39.000000000 +1200
+@@ -159,10 +160,17 @@
+         assert abs(x - 1.5) < 1e-6
+         assert_raises(ValueError,
+                 optimize.fminbound, lambda x: (x - 1.5)**2 - 0.8, 5, 1)
++
++    def test_fminbound_scalar(self):
+         assert_raises(ValueError,
+-                optimize.fminbound, lambda x: (x - 1.5)**2 - 0.8,
++                      optimize.fminbound, lambda x: (x - 1.5)**2 - 0.8,
+                       np.zeros(2), 1)
+ 
++        assert_almost_equal(
++            optimize.fminbound(lambda x: (x - 1.5)**2 - 0.8, 1, np.array(5)),
++            1.5)
++
++
+ class TestTnc(TestCase):
+     """TNC non-linear optimization.
diff --git a/sci-libs/scipy/scipy-0.7.2-r1.ebuild b/sci-libs/scipy/scipy-0.7.2-r1.ebuild
new file mode 100644
index 000000000000..017ccd4765d9
--- /dev/null
+++ b/sci-libs/scipy/scipy-0.7.2-r1.ebuild
@@ -0,0 +1,137 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.7.2-r1.ebuild,v 1.1 2010/05/18 17:25:31 bicatali Exp $
+
+EAPI="2"
+SUPPORT_PYTHON_ABIS="1"
+
+inherit eutils distutils flag-o-matic toolchain-funcs versionator
+
+SP="${PN}-$(get_version_component_range 1-2)"
+
+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 -> ${SP}-ref.pdf
+	)"
+DESCRIPTION="Scientific algorithms library for Python"
+HOMEPAGE="http://www.scipy.org/ http://pypi.python.org/pypi/scipy"
+
+LICENSE="BSD"
+
+SLOT="0"
+IUSE="doc umfpack"
+
+KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+
+CDEPEND=">=dev-python/numpy-1.2
+	virtual/cblas
+	virtual/lapack
+	umfpack? ( sci-libs/umfpack )"
+
+DEPEND="${CDEPEND}
+	dev-util/pkgconfig
+	umfpack? ( dev-lang/swig )
+	doc? ( app-arch/unzip )"
+#	test? ( dev-python/nose )
+
+RDEPEND="${CDEPEND}
+	dev-python/imaging"
+
+RESTRICT_PYTHON_ABIS="3.*"
+
+# buggy tests
+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 SCIPY_FCONFIG="config_fc --noopt --noarch"
+}
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${SP}-html.zip -d html || die
+	fi
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-0.7.0_beta1-implicit.patch
+	epatch "${FILESDIR}"/${PN}-0.6.0-stsci.patch
+	epatch "${FILESDIR}"/${PN}-0.7.1-weave.patch
+	epatch "${FILESDIR}"/${PN}-0.7.2-optimize.patch
+	local libdir="${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() {
+	[[ -n ${FFLAGS} ]] && FFLAGS="${FFLAGS} -fPIC"
+	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"
+}