sci-libs/scipy: Backport fix for broken lsqr

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

5 files changed, 285 insertions, 25 deletions

diff --git a/sci-libs/scipy/ChangeLog b/sci-libs/scipy/ChangeLog
index 0471f440b21f..7d3030841f7a 100644
--- a/sci-libs/scipy/ChangeLog
+++ b/sci-libs/scipy/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/scipy
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.117 2014/07/22 17:47:47 zerochaos Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/ChangeLog,v 1.118 2014/11/14 20:34:09 jlec Exp $
+
+*scipy-0.14.0-r1 (14 Nov 2014)
+
+  14 Nov 2014; Justin Lecher <jlec@gentoo.org> +scipy-0.14.0-r1.ebuild,
+  +files/scipy-0.14.0-lsqr-backport.patch, metadata.xml:
+  Backport fix for broken lsqr
 
   22 Jul 2014; Rick Farina <zerochaos@gentoo.org> scipy-0.12.1.ebuild,
   scipy-0.13.2.ebuild, scipy-0.13.3.ebuild, scipy-0.14.0.ebuild:
diff --git a/sci-libs/scipy/Manifest b/sci-libs/scipy/Manifest
index f0d994626270..2482201b553f 100644
--- a/sci-libs/scipy/Manifest
+++ b/sci-libs/scipy/Manifest
@@ -5,6 +5,7 @@ AUX scipy-0.12.0-blitz.patch 731 SHA256 4f487a746aa62a39cdab9381dd4191cef0ccb912
 AUX scipy-0.12.0-cephes-missing-include.patch 394 SHA256 0263ba4e9f13c7be0e7160ae73ce98ea37f698ea7e06c3fc090bc4ff7732bc66 SHA512 a4f9adf9b29743b6ca7f42de0695af23ddf7791330a4a58a2f47cd5599af1361aee3b141a016ea1a81a3bc5b8bfcaa3f0478370a09acd37bcd8e519765701510 WHIRLPOOL 59651015bf540ad2218dd65764d68fb5f2b907116245e3e83d14084579314af6c58c34be3f74300166c2450e00833fa4ae6d6de057392d3e947a979555add1bc
 AUX scipy-0.12.0-gerqf.patch 731 SHA256 1f3c2723f1094cb6834349f26d40d060ed4e09c722eea876e160fc9ce2b3ced2 SHA512 007bf3d85364c824c03532a07c2678e48c90858d82fa7248cb5139a6f74b853bc4a27e6932638a14bb61e72abbbfd95265e10502c4fd2eb363758f3132722a10 WHIRLPOOL c2d7de949048dcc76e1bf72f2165226b7a741212ef0c6cfc3709ddd91f11fd274ecfcdf62dd47fb11d824d73b41c57d468414b3ef9e8169f7841688f67bcf6af
 AUX scipy-0.12.0-restore-sys-argv.patch 483 SHA256 c00daf7d49c042972d2c59bf645c21f3bc437459a745da758e2548a973000170 SHA512 7c439aa7e1e0ccc7444c2c091ef03d3d39f2999a33ef487224c78e74cd3a1b84bd18a9e92d84ab2cd3fc7578644beb3b667fdaacb20a239600cb9b1765eeb7fc WHIRLPOOL f0d4a84e40ee26399b121f0d9159914d480789c83f749cf060bc65f63df315f27718359df7c13c64ae7a04eea00470ea109b110310abeba79944a90b97ebb102
+AUX scipy-0.14.0-lsqr-backport.patch 3764 SHA256 e5db9922b84a51452afebd22d6783eef982f3c7160dcf543388daef4bacfa7e2 SHA512 7fbf7c257c6f68045b14dd1dfc3518c47aaeff9c027441acec9399b3c02bd0c473512cbd9f5c1eed2ac54ed8c53d4416759ebd946516fa776324e5fa88d182cf WHIRLPOOL f2e57e4743ac3d0623057aed4ab225988613d95d09cf38a0db26ecc6e1cb3e7769006a45539d5e8fb1728b910766c0620b09973b609aef5967bf66bd9cff8d95
 DIST scipy-0.12.1-html.zip 15578583 SHA256 07c773c6056e5fc0cb65d7048995d0ff056f48f1e482d610865361870ee07998 SHA512 71308ff306ee5556822a279e8dd21efd6c9174fbb5c100acf9e34308cf828789cd257aac5a447a6dbfa8b464447753ea49d6e5819555fbf8db73b3e51fddc2cb WHIRLPOOL 124b12ace1a297789b4f544a28539da964bc756aae72572b2926c9df81b2bd492fdcc4b39bb8b9d83305d21834c7e225a576225a8a94a316707c517583fa9dca
 DIST scipy-0.12.1-ref.pdf 11193207 SHA256 4a8298fba9c6d62aeb392ee6588ac45cb266ed6cffb59573f6c19d7779bfc18b SHA512 cad60983c74a447a0e3ba898b81bdea3101dbad7603f1ca8030e3ff9f431eeb8c7b2dd207a45af616ef596e85c0c1846944057ecc11482fe9b389869ee49b137 WHIRLPOOL af600c6cb5c59306b2f5a84df421465a97cae9138f0cf024a0748c80bd516d8fe6a2db135fd56d66eab25f36c99acb3c0825d50b7d376e0ed3d9bd0c4c282943
 DIST scipy-0.12.1.tar.gz 9012911 SHA256 15122afe6cb377b010982f9bc46cf41b12af703fd34088aa3971a80276b00e76 SHA512 13dba0b2ff9b69a109403110aaaca892362935262e3999992de96b081eae036fe5dbb3ca209d84ade948377c6ccb4137777c36f76121f8745855dc1d08b86e97 WHIRLPOOL 71467b86b992b14b4bc6c354ac4b4ec138951ab0d17b28c07ac605a81852f4f55bdfe35553ffdecd9611ef0daf2c35012424e28db9c9ff8e2cf6eb3fe0d2583a
@@ -16,23 +17,26 @@ DIST scipy-0.14.0.tar.gz 10212944 SHA256 4b41a3e6bf178df1c7f0ef3bfeabf1f56610329
 EBUILD scipy-0.12.1.ebuild 3805 SHA256 5c4e8b9f496e9f96279b3ba8649c7f66d251e77c86017cf102247f6e2895d2d6 SHA512 972cad2341914448941c31fc616a2b1b64ff79ef3f8fd79d7385b52953c5a44c5b8a1ea319a97a07cbac550e2b5f50968bd80153e16cac0fe2d48142b74eed44 WHIRLPOOL 314685828ae74424acc7669523df53c2678381e7e578d65f628759f1e21aab2f5a62b6bd428592285e1fe041407603854f829d90d3e209a71d7573b11ec7a384
 EBUILD scipy-0.13.2.ebuild 3827 SHA256 2345269991f640d9e859e591e5a5cb338f965b8f44d943f0a545a71324591597 SHA512 5519c7164ffc193d15754162f73fb14d17ec77be1b802e743bd3bd1773e6831285fa92f8918b29be0d9edca6f057264192fe287dc1f910723ffa3f7f21f21060 WHIRLPOOL 48fc7a3a54099816feca539b59cb6267ea59315cc369d6f581b926d34af868b87eeee06f2f783ea4d5d3914473af4d80227d00225f6fd424faffe67f48034483
 EBUILD scipy-0.13.3.ebuild 3914 SHA256 de5293fe8fbbea55dc550af0671aaa93643ec1f051c687d6fdf6168ff06f7516 SHA512 862a5ecaaee18145166cff58bf3865deaabed865e52a6f89750fcfc36a975459ada1824ca6e41676a42b014855aaca5eb3c79a2a9f6d2572cc4f2650febc3ea5 WHIRLPOOL 668b1fb8f9567e5c08c6f6b6dec622876f8ea323f0380370e75c089b4bb462689cee26ff9c187112dbd41afd7f708f3593716858e4a686aed35483fe2b93feb6
+EBUILD scipy-0.14.0-r1.ebuild 3978 SHA256 d4114404359f466a000b0d8cee80ea8f94591dc5302cd81fd952da81c13b5335 SHA512 a61775e3885655be71a370d56c443947139b106af7a6bda3107983afab7161b0d87bccc5bfb75616ddc033c8f997101f0666bfc254ab1f3c425355475d97a425 WHIRLPOOL 7a74309dac105722a1a7123be5702455e1c2618e49735f11151761934918717422198fd457fdd15f3f51731c007e44ed60069d3c312cdacb7bd6af0ed94186c0
 EBUILD scipy-0.14.0.ebuild 3927 SHA256 74f646d70b5be2f62d66637c29a7ec01352e1e9d97b0003c1b982a0ef5e7a14c SHA512 27ee56f813a0abdbe1ca0da8fedeb69622aa063aaaff8bbc383f86b312b294df7742df16a0c3fc0c08cbf84859f9232045e08585456ec5d5e43d0ccba8c2edd1 WHIRLPOOL acabd0ae31e1063fe3e2d80590218ce320d9ba3c96b603145702bcb563d373b721963610b09fbb9d0049c5ffa9cda76ab4302097d6a1b3de04503f28cfc3e5fe
-MISC ChangeLog 21231 SHA256 7150d6b0fc296d0e68e03095f6941a2e1059d184d568a9fe29d5c479613c54f6 SHA512 17bb0336456c290d5d2d87f87df971c006b21e7cc97f5496517d659ff1978d090d76c7b820574127c37e05612e6d7fed3169030443ac01ec7df451b1442b5b6c WHIRLPOOL b160f0d0bd62eccf03a5eb9e8d8e4875fe59bb95af24200c47aa275486901d803050b64f282c461868b0e5643eef5d2aa702951e52119dd974375972311adec0
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+MISC ChangeLog 21419 SHA256 c4fa0c0d11cdd0abff5eaa7902a55a0d061a5689357e481543a9edfd182dad18 SHA512 7d562d4fbdc889a64318ebfdd444d3e4dc34758d2b13b9769b0ee729843a7cd3260ca2ca3b14538aa0d71d4546aa8be727bb41ed6e6713e782095e78888f3f6b WHIRLPOOL 0ed81bb7f186d54cde289e4adb8230c7aa9e08689d615f58a278c799ea37087bc3d5019880e6d8381532205ebbf6647af502963930f9f86d1b1a0a875e8a2c78
+MISC metadata.xml 778 SHA256 c585563656be41d539826dbd6ac5f633a0704b73a39b3603b50ce6092d767e73 SHA512 da239d303a88f7bc4356a27965aed91befd379ee142c529ab5177276eb86ac7976b527a2b1397584754f1cec1c6743c98b9af4a540e6cc503607ac3cf529de06 WHIRLPOOL e04375da88108229b3386ae79ba452705a4d4fcdbff9f38c491a4436846c9037d8c68bd8d5524d5435e351a557bd604211477a28da5661c9cce804fe27a34b2a
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diff --git a/sci-libs/scipy/files/scipy-0.14.0-lsqr-backport.patch b/sci-libs/scipy/files/scipy-0.14.0-lsqr-backport.patch
new file mode 100644
index 000000000000..a754e36ab2cf
--- /dev/null
+++ b/sci-libs/scipy/files/scipy-0.14.0-lsqr-backport.patch
@@ -0,0 +1,107 @@
+From 785e3961a685a351bd9d1e8eec0a62035cc4c6aa Mon Sep 17 00:00:00 2001
+From: Olivier Grisel <olivier.grisel@ensta.org>
+Date: Thu, 13 Nov 2014 13:39:35 +0100
+Subject: [PATCH] BUG: ZeroDivisionError in scipy.sparse.linalg.lsqr
+
+---
+ scipy/sparse/linalg/isolve/lsqr.py            |  6 ++--
+ scipy/sparse/linalg/isolve/tests/test_lsqr.py | 51 +++++++++++++++++++++------
+ 2 files changed, 45 insertions(+), 12 deletions(-)
+
+diff --git a/scipy/sparse/linalg/isolve/lsqr.py b/scipy/sparse/linalg/isolve/lsqr.py
+index c4a6c02..de5a6b9 100644
+--- a/scipy/sparse/linalg/isolve/lsqr.py
++++ b/scipy/sparse/linalg/isolve/lsqr.py
+@@ -57,6 +57,8 @@
+ from math import sqrt
+ from scipy.sparse.linalg.interface import aslinearoperator
+ 
++eps = np.finfo(np.float64).eps
++
+ 
+ def _sym_ortho(a, b):
+     """
+@@ -432,8 +434,8 @@ def lsqr(A, b, damp=0.0, atol=1e-8, btol=1e-8, conlim=1e8,
+         # Now use these norms to estimate certain other quantities,
+         # some of which will be small near a solution.
+         test1 = rnorm / bnorm
+-        test2 = arnorm / (anorm * rnorm)
+-        test3 = 1 / acond
++        test2 = arnorm / (anorm * rnorm + eps)
++        test3 = 1 / (acond + eps)
+         t1 = test1 / (1 + anorm * xnorm / bnorm)
+         rtol = btol + atol * anorm * xnorm / bnorm
+ 
+diff --git a/scipy/sparse/linalg/isolve/tests/test_lsqr.py b/scipy/sparse/linalg/isolve/tests/test_lsqr.py
+index f378cca..626288b 100644
+--- a/scipy/sparse/linalg/isolve/tests/test_lsqr.py
++++ b/scipy/sparse/linalg/isolve/tests/test_lsqr.py
+@@ -1,7 +1,7 @@
+ from __future__ import division, print_function, absolute_import
+ 
+ import numpy as np
+-from numpy.testing import assert_
++from numpy.testing import assert_, assert_equal, assert_array_almost_equal
+ from scipy.lib.six import xrange
+ 
+ import scipy.sparse
+@@ -34,6 +34,46 @@ def test_basic():
+     xo = X[0]
+     assert_(norm(svx - xo) < 1e-5)
+ 
++
++def test_gh_2466():
++    row = np.array([0, 0])
++    col = np.array([0, 1])
++    val = np.array([1, -1])
++    A = scipy.sparse.coo_matrix((val, (row, col)), shape=(1, 2))
++    b = np.asarray([4])
++    lsqr(A, b)
++
++
++def test_well_conditioned_problems():
++    # Test that sparse the lsqr solver returns the right solution
++    # on various problems with different random seeds.
++    # This is a non-regression test for a potential ZeroDivisionError
++    # raised when computing the `test2` & `test3` convergence conditions.
++    n = 10
++    A_sparse = scipy.sparse.eye(n, n)
++    A_dense = A_sparse.toarray()
++
++    with np.errstate(invalid='raise'):
++        for seed in range(30):
++            rng = np.random.RandomState(seed + 10)
++            beta = rng.rand(n)
++            beta[beta == 0] = 0.00001  # ensure that all the betas are not null
++            b = A_sparse * beta[:, np.newaxis]
++            output = lsqr(A_sparse, b, show=show)
++
++            # Check that the termination condition corresponds to an approximate
++            # solution to Ax = b
++            assert_equal(output[1], 1)
++            solution = output[0]
++
++            # Check that we recover the ground truth solution
++            assert_array_almost_equal(solution, beta)
++
++            # Sanity check: compare to the dense array solver
++            reference_solution = np.linalg.solve(A_dense, b).ravel()
++            assert_array_almost_equal(solution, reference_solution)
++
++
+ if __name__ == "__main__":
+     svx = np.linalg.solve(G, b)
+ 
+@@ -64,12 +104,3 @@ def test_basic():
+     print("")
+     print(" || x_{direct} - x_{LSQR}|| %9.4e " % norm(svx-xo))
+     print("")
+-
+-
+-def test_gh_2466():
+-    row = np.array([0, 0])
+-    col = np.array([0, 1])
+-    val = np.array([1, -1])
+-    A = scipy.sparse.coo_matrix((val, (row, col)), shape=(1, 2))
+-    b = np.asarray([4])
+-    lsqr(A, b)
diff --git a/sci-libs/scipy/metadata.xml b/sci-libs/scipy/metadata.xml
index 4ee19593821e..350066e901ec 100644
--- a/sci-libs/scipy/metadata.xml
+++ b/sci-libs/scipy/metadata.xml
@@ -1,8 +1,8 @@
 <?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.
@@ -10,10 +10,10 @@
   integration, special functions, signal and image processing, genetic
   algorithms, ODE solvers, and others.
 </longdescription>
-<use>
-  <flag name="sparse">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="sparse">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-0.14.0-r1.ebuild b/sci-libs/scipy/scipy-0.14.0-r1.ebuild
new file mode 100644
index 000000000000..7e11f66d4227
--- /dev/null
+++ b/sci-libs/scipy/scipy-0.14.0-r1.ebuild
@@ -0,0 +1,143 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scipy/scipy-0.14.0-r1.ebuild,v 1.1 2014/11/14 20:34:09 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} )
+
+DOC_PV=0.13.0
+
+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/${PN}-${DOC_PV}/${PN}-html.zip -> ${PN}-${DOC_PV}-html.zip
+		http://docs.scipy.org/doc/${PN}-${DOC_PV}/${PN}-ref.pdf -> ${PN}-${DOC_PV}-ref.pdf
+	)"
+
+LICENSE="BSD LGPL-2"
+SLOT="0"
+IUSE="doc sparse test"
+KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x86-macos"
+
+CDEPEND="
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	sci-libs/arpack:0=
+	virtual/cblas
+	virtual/lapack
+	sparse? ( sci-libs/umfpack:0= )"
+DEPEND="${CDEPEND}
+	dev-lang/swig
+	>=dev-python/cython-0.19.1[${PYTHON_USEDEP}]
+	virtual/pkgconfig
+	doc? ( app-arch/unzip )
+	test? (	dev-python/nose[${PYTHON_USEDEP}] )
+	"
+
+RDEPEND="${CDEPEND}
+	virtual/python-imaging[${PYTHON_USEDEP}]"
+
+DOCS=( HACKING.rst.txt THANKS.txt )
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+src_unpack() {
+	unpack ${P}.tar.gz
+	if use doc; then
+		unzip -qo "${DISTDIR}"/${PN}-${DOC_PV}-html.zip -d html || die
+	fi
+}
+
+pc_incdir() {
+	$(tc-getPKG_CONFIG) --cflags-only-I $@ | \
+		sed -e 's/^-I//' -e 's/[ ]*-I/:/g' -e 's/[ ]*$//' -e 's|^:||'
+}
+
+pc_libdir() {
+	$(tc-getPKG_CONFIG) --libs-only-L $@ | \
+		sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^:||'
+}
+
+pc_libs() {
+	$(tc-getPKG_CONFIG) --libs-only-l $@ | \
+		sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \
+		-e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \
+		| tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||'
+}
+
+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 = $(pc_libs lapack)
+	EOF
+
+	# Drop hashes to force rebuild of cython based .c code
+	rm cythonize.dat || die
+
+	local PATCHES=(
+		"${FILESDIR}"/${PN}-0.12.0-blitz.patch
+		"${FILESDIR}"/${PN}-0.12.0-restore-sys-argv.patch
+		"${FILESDIR}"/${PN}-0.12.0-cephes-missing-include.patch
+		"${FILESDIR}"/${P}-lsqr-backport.patch
+	)
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	${EPYTHON} tools/cythonize.py || die
+	distutils-r1_python_compile ${SCIPY_FCONFIG}
+}
+
+python_test() {
+	# fails with bdist_egg. should it be fixed in distutils-r1 eclass?
+	distutils_install_for_testing ${SCIPY_FCONFIG}
+	cd "${TEST_DIR}" || die "no ${TEST_DIR} available"
+	"${EPYTHON}" -c "
+import scipy, sys
+r = scipy.test('fast',verbose=2)
+sys.exit(0 if r.wasSuccessful() else 1)" || die "Tests fail with ${EPYTHON}"
+}
+
+python_install_all() {
+	if use doc; then
+		dodoc "${DISTDIR}"/${PN}*pdf
+		docinto html
+		dodoc -r "${WORKDIR}"/html/.
+	fi
+	distutils-r1_python_install_all
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+}
+
+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"
+}