Version bump. Tentative to remove bundled joblib and atlas (which apparently uses only cblas functions)

(Portage version: 2.2.01.22124-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

4 files changed, 75 insertions, 16 deletions

diff --git a/sci-libs/scikits_learn/ChangeLog b/sci-libs/scikits_learn/ChangeLog
index e4f7aeff3509..595d524781e1 100644
--- a/sci-libs/scikits_learn/ChangeLog
+++ b/sci-libs/scikits_learn/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-libs/scikits_learn
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.21 2013/05/15 07:08:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.22 2013/08/08 21:34:41 bicatali Exp $
+
+*scikits_learn-0.14.1 (08 Aug 2013)
+
+  08 Aug 2013; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/scikits_learn-0.14.1-system-cblas.patch, +scikits_learn-0.14.1.ebuild,
+  -scikits_learn-0.13-r1.ebuild, metadata.xml:
+  Version bump. Tentative to remove bundled joblib and atlas (which apparently
+  uses only cblas functions)
 
   15 May 2013; Justin Lecher <jlec@gentoo.org> scikits_learn-0.13.1.ebuild,
   metadata.xml:
diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch
new file mode 100644
index 000000000000..96c6cc2dbde5
--- /dev/null
+++ b/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch
@@ -0,0 +1,28 @@
+--- sklearn/setup.py.orig	2013-08-08 13:54:08.310879167 -0700
++++ sklearn/setup.py	2013-08-08 13:52:59.808456423 -0700
+@@ -68,14 +68,6 @@
+         libraries=libraries,
+     )
+ 
+-    # some libs needs cblas, fortran-compiled BLAS will not be sufficient
+-    blas_info = get_info('blas_opt', 0)
+-    if (not blas_info) or (
+-            ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
+-        config.add_library('cblas',
+-                           sources=[join('src', 'cblas', '*.c')])
+-        warnings.warn(BlasNotFoundError.__doc__)
+-
+     # the following packages depend on cblas, so they have to be build
+     # after the above.
+     config.add_subpackage('linear_model')
+--- sklearn/_build_utils.py.orig	2013-08-08 14:01:35.994589269 -0700
++++ sklearn/_build_utils.py	2013-08-08 12:19:41.875967870 -0700
+@@ -23,7 +23,7 @@
+         return False
+ 
+     blas_info = get_info('blas_opt', 0)
+-    if (not blas_info) or atlas_not_found(blas_info):
++    if (not blas_info):
+         cblas_libs = ['cblas']
+         blas_info.pop('libraries', None)
+     else:
diff --git a/sci-libs/scikits_learn/metadata.xml b/sci-libs/scikits_learn/metadata.xml
index 7b42750bd926..64fe2c7def04 100644
--- a/sci-libs/scikits_learn/metadata.xml
+++ b/sci-libs/scikits_learn/metadata.xml
@@ -1,13 +1,13 @@
 <?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">
   scikits.learn is a python library for machine learning. It aims to
   implement classic machine learning algorithms while remaining simple
   and efficient.
 </longdescription>
-  <upstream>
-    <remote-id type="pypi">scikit-learn</remote-id>
-  </upstream>
+<upstream>
+  <remote-id type="pypi">scikit-learn</remote-id>
+</upstream>
 </pkgmetadata>
diff --git a/sci-libs/scikits_learn/scikits_learn-0.13-r1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.14.1.ebuild
index 6ee74ad153cd..98f449b76640 100644
--- a/sci-libs/scikits_learn/scikits_learn-0.13-r1.ebuild
+++ b/sci-libs/scikits_learn/scikits_learn-0.14.1.ebuild
@@ -1,37 +1,45 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/scikits_learn-0.13-r1.ebuild,v 1.1 2013/02/08 09:16:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/scikits_learn-0.14.1.ebuild,v 1.1 2013/08/08 21:34:41 bicatali Exp $
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
+DISTUTILS_NO_PARALLEL_BUILD=true
 
 inherit distutils-r1 multilib flag-o-matic
 
 MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
 
 DESCRIPTION="Python modules for machine learning and data mining"
 HOMEPAGE="http://scikit-learn.org"
-SRC_URI="mirror://sourceforge/${MYPN}/${MYPN}-${PV}.tar.gz"
+SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
+IUSE="doc examples test"
 
 RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
 	sci-libs/scikits[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
 	sci-libs/scipy[${PYTHON_USEDEP}]
 	dev-python/matplotlib[${PYTHON_USEDEP}]"
 DEPEND="
-	dev-python/cython
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]
 	sci-libs/scipy[${PYTHON_USEDEP}]
 	doc? (
 		dev-python/sphinx[${PYTHON_USEDEP}]
-		dev-python/matplotlib[${PYTHON_USEDEP}] )"
+		dev-python/matplotlib[${PYTHON_USEDEP}] )
+	test? (
+		dev-python/joblib[${PYTHON_USEDEP}]
+		dev-python/nose[${PYTHON_USEDEP}] )"
 
-S="${WORKDIR}/${MYPN}-${PV}"
+S="${WORKDIR}/${MYP}"
 
 python_prepare_all() {
 	# bug #397605
@@ -41,6 +49,19 @@ python_prepare_all() {
 
 	# scikits-learn now uses the horrible numpy.distutils automagic
 	export SCIPY_FCONFIG="config_fc --noopt --noarch"
+
+	# use system joblib
+	rm -r sklearn/externals/joblib/* || die
+	echo "from joblib import *" > sklearn/externals/joblib/__init__.py
+	sed -i -e '/joblib\/test/d' sklearn/externals/setup.py || die
+	sed -i -e 's/..externals.joblib/joblib/g' \
+		sklearn/decomposition/tests/test_sparse_pca.py \
+		sklearn/metrics/pairwise.py || die
+
+	# use gentoo cblas infrastructure
+	epatch "${FILESDIR}"/${P}-system-cblas.patch
+
+	distutils-r1_python_prepare_all
 }
 
 python_compile() {
@@ -64,11 +85,12 @@ python_compile_all() {
 python_test() {
 	# doc builds and runs tests
 	use doc && return
+	distutils_install_for_testing ${SCIPY_FCONFIG}
 	esetup.py \
 		install --root="${T}/test-${EPYTHON}" \
 		--no-compile ${SCIPY_FCONFIG} || die
-	cd "${T}/test-${EPYTHON}/${EPREFIX}$(python_get_sitedir)" || die
-	PYTHONPATH=. nosetests-${EPYTHON} sklearn --exe || die
+	cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
+	PYTHONPATH=. nosetests-${EPYTHON} -v sklearn --exe || die
 }
 
 python_install() {
@@ -77,7 +99,8 @@ python_install() {
 
 python_install_all() {
 	find "${S}" -name \*LICENSE.txt -delete
+	distutils-r1_python_install_all
 	insinto /usr/share/doc/${PF}
-	use doc && dohtml -r doc/_build/html
+	use doc && dohtml -r doc/_build/html/*
 	use examples && doins -r examples
 }