From 7d1a016207c441696ac29201b46c9014012d0b0d Mon Sep 17 00:00:00 2001 From: Sebastien Fabbro Date: Tue, 18 May 2010 17:25:31 +0000 Subject: [PATCH] Applied a patch for the optimize module to work with sage, see bug #320135 Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- sci-libs/scipy/ChangeLog | 8 +- sci-libs/scipy/Manifest | 14 +- .../scipy/files/scipy-0.7.2-optimize.patch | 54 +++++++ sci-libs/scipy/scipy-0.7.2-r1.ebuild | 137 ++++++++++++++++++ 4 files changed, 211 insertions(+), 2 deletions(-) create mode 100644 sci-libs/scipy/files/scipy-0.7.2-optimize.patch create mode 100644 sci-libs/scipy/scipy-0.7.2-r1.ebuild 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 + +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/Manifest b/sci-libs/scipy/Manifest index 3bc8606d0d75..4f02e5d98479 100644 --- a/sci-libs/scipy/Manifest +++ b/sci-libs/scipy/Manifest @@ -1,11 +1,23 @@ +-----BEGIN PGP SIGNED MESSAGE----- +Hash: SHA1 + AUX scipy-0.6.0-stsci.patch 2209 RMD160 c7c21a23aef7fff9318f224ef2383f7970c1caf9 SHA1 4b86ad61346660959a61dce24b2b9f20595ea473 SHA256 69cec7cfedbc39a30f54ec12852a84017b5a256e966e60a64b4e891b497fd1be AUX scipy-0.7.0_beta1-implicit.patch 905 RMD160 a22d5b5c7a67b3a806b63d7708654562fc241300 SHA1 40239fd3a77dc6f8cf9914a266953fd7b4ef41fe SHA256 cbde48ba3e22ef994b4ae0744c6186ef6d3ec608a74b3d0082f22d0be9591b96 AUX 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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" +} -- 2.26.2