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

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index bfc0a9e1514a00d8ec079d246cf1c48d1bda6a64..8f032d7f01ed6597430aeded3a15fbf5a9f44803 100644 (file)
--- 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/Manifest b/sci-libs/scipy/Manifest
index 3bc8606d0d75ca669de059282398875b0765a3ef..4f02e5d98479b54893340b82d8d8554e3ecc1b0c 100644 (file)
--- 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 scipy-0.7.1-weave.patch 413 RMD160 ef71432902d2ae914a9c5fbccf23ee4bb5f77802 SHA1 1f0d07591984be705ec9fb71c9d776e2a4eae25b SHA256 8f9d18c5dbf9cae951ae6d64530650e88f0109fa98d8d2e9e896e0c856a9eaa5
+AUX scipy-0.7.2-optimize.patch 1878 RMD160 59e8da9aa98c803683dd61889c9c93d5a8eaac13 SHA1 33bb4b2df3b21a8ad7211ae6de7f4224264c162e SHA256 8ea93099edd954625a272dd216cd462f5281f9b93ccfa89ec97720ee7b08ce12
 DIST scipy-0.7-html.zip 5723344 RMD160 2629be4420fcad20bd7d9f080e01e4dcf7639c10 SHA1 3db044ef8603578e15754ae890a6e2fddcdadae9 SHA256 35e2e4e4a7aaba8c348175366c120b1a802951abe50af10458c532631e0133bb
 DIST scipy-0.7-ref.pdf 3380649 RMD160 88bda2a06bc20627afbb0354fbe57c1b82dda7eb SHA1 091e1df2d28ee85428c50ee268db56146be96746 SHA256 4acbd75979fabfea9ff9d0cf60e06520c1f4d372f5369add8294f72303d3d0e0
 DIST scipy-0.7.1.tar.gz 4538765 RMD160 b3cb0b40a739cd8b61182f123581d57443b9401a SHA1 ab637e29743cc0c42903a8815043f85d13fb9e42 SHA256 08830d6363a8753ca1376dd22da86d164902711c5feaf0f768b5ee086b3ecd5f
 DIST scipy-0.7.2.tar.gz 4557178 RMD160 456e4ab9d69f9d4056bca6b52474b72bea37b122 SHA1 c3223df023008ee339cf1d3fad74d4566af69c8a SHA256 cae80f12e8b8e72fb2ca2007077e3948af9abc6f2011fe01a68137aea0ef46be
 EBUILD scipy-0.7.1.ebuild 4196 RMD160 ed5ab5975cc20781f3b7c6d6fa3b4b73007cce06 SHA1 bee9535d4ed504cc302af1bd4344a873bc16f43c SHA256 ffc9dd96f44ec13489800a6300a2ea11cf04a29da6aa65bdd2d02d59b6cda1d5
+EBUILD scipy-0.7.2-r1.ebuild 4205 RMD160 72345b56724e2d3ef3bf0175c39c5376f0994a9e SHA1 fc4542149d20215d1ed04281e12235bcc9b09f60 SHA256 fedda703cf8018beb4f8824b6797684a4246ef0b24cd365a005846019f9e7b6d
 EBUILD scipy-0.7.2.ebuild 4153 RMD160 05a24288050135000c3b46700687ba7489bff54c SHA1 419972fa9419be60a419ea59e08bbf1bf39f3a22 SHA256 feea3e88ab00e8be87fd70cbcda274c9426df130a62ef214f7d033c1c4aef876
-MISC ChangeLog 10689 RMD160 65900861d69ad60f3a639fc8fd3175d7db8a93c6 SHA1 f40f811db8ec91201198b60da7e6eb04d07ba9e8 SHA256 ab6b4e6f2e9fa96b89bb29e453e896eb529eefd41ec00b188273014b97c768ab
+MISC ChangeLog 10914 RMD160 9c6cf318e054b78d90be4f0abe7811f57f8db170 SHA1 938955d969fff5cdaa0fccd8f0801f1ac78e7bd4 SHA256 d6b4ceb15cf97bb18fa61231dddd7bcfa85fe088c56a1e79033107afce1fef8c
 MISC metadata.xml 697 RMD160 05eb973594c8fe27be71e813f2a2294cf9e3f46e SHA1 1dbbb06751c0fc5760618d8998f9d169b3f774ae SHA256 1bfca083b6aa7c4fbd95b638daa2158b2eaa5cb93fe7a99abe9a2bc08b21e48e
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkvy1wgACgkQ1ycZbhPLE2BgEwCgsPjCENab8rMSWapjaONKzu3G
++hMAnjSKM9RmkANflSunVdz9d9PKPaKW
+=0Rck
+-----END PGP SIGNATURE-----

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 (file)
index 0000000..4a3bb74
--- /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 (file)
index 0000000..017ccd4
--- /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"
+}