sci-libs/scipy: Backport fix for broken lsqr

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 265 insertions, 9 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/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"
+}