Added a patch which makes sure cblas stock libraries are used instead of bundled ATLAS library. Fixed doc generation with sphinx to link datasets in plot generation

Package-Manager: portage-2.1.10.56/cvs/Linux x86_64

5 files changed, 87 insertions, 98 deletions

diff --git a/sci-libs/scikits_learn/ChangeLog b/sci-libs/scikits_learn/ChangeLog
index 9cd780fa21dc..b6b1e5b69321 100644
--- a/sci-libs/scikits_learn/ChangeLog
+++ b/sci-libs/scikits_learn/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-libs/scikits_learn
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.10 2012/02/05 01:58:26 floppym Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.11 2012/04/23 19:49:14 bicatali Exp $
+
+*scikits_learn-0.10-r1 (23 Apr 2012)
+
+  23 Apr 2012; Sébastien Fabbro <bicatali@gentoo.org> +files/0.10-atlas.patch,
+  -scikits_learn-0.9.ebuild, -scikits_learn-0.10.ebuild,
+  +scikits_learn-0.10-r1.ebuild:
+  Added a patch which makes sure cblas stock libraries are used instead of
+  bundled ATLAS library. Fixed doc generation with sphinx to link datasets in
+  plot generation
 
   05 Feb 2012; Mike Gilbert <floppym@gentoo.org> scikits_learn-0.10.ebuild,
   scikits_learn-0.9.ebuild:
diff --git a/sci-libs/scikits_learn/Manifest b/sci-libs/scikits_learn/Manifest
index 4d534f8da506..b2656c62f90e 100644
--- a/sci-libs/scikits_learn/Manifest
+++ b/sci-libs/scikits_learn/Manifest
@@ -1,16 +1,15 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA1
 
+AUX 0.10-atlas.patch 2524 RMD160 2229ca5e4b2ac26c71481bf216387eae55a64f08 SHA1 c4736cf0ae577010189c71f75e46a2c60bab7e7c SHA256 25f0d89b50c36931ccb52be02676bb2c7f78a0f4f270f01319eea287af132e94
 DIST scikit-learn-0.10.tar.gz 2613175 RMD160 6f09bee8fb3f7f7a6deaae4cb00c7ed5d794a68a SHA1 a26b2616fa23c768ca60fdd50178665d38df5687 SHA256 16ff3ffcd9a0eac7066fc809f03d06c05fea5e2f6d7ea65fb24352700764117b
-DIST scikit-learn-0.9.tar.gz 2275070 RMD160 db73b2b33fe37d737995c878d1ff4733c9d32642 SHA1 25f175de04efef4a999083aebf3b3367cc53fe5f SHA256 5e083180a0eedf8e964c013731da30291afec28190d6be028f1185a283aded0a
-EBUILD scikits_learn-0.10.ebuild 1851 RMD160 b784510d2f6139c64f25c9bda2315c8f9ed83799 SHA1 3a452bdf162450df06682128c98a7b5402c24418 SHA256 d08a5facbf2d07a1863f615a12148e9552c827c44321c1e0f78b24541cf4164e
-EBUILD scikits_learn-0.9.ebuild 1899 RMD160 e77c29c44f80b5ea7c1bb5e6dc9ba7f916b34106 SHA1 37a827486eaeeab28f426df773a1dfeee9303e1c SHA256 6e6711f8917f624ed18fb11c1a50d0ce67c8cfe20656565268a245be18d0dd17
-MISC ChangeLog 2468 RMD160 30a7721d30156ab5392d4a8126f3ff708f56b586 SHA1 94cfa4d8f6d19374d250dfce2b9b3558233cc0bb SHA256 b76b89cb120b80681db037575d3a79e92e4d4ef0452745677f9f1a51bfd35db2
+EBUILD scikits_learn-0.10-r1.ebuild 1972 RMD160 b5f52c70e63b499fa9532801c3969255bd02e189 SHA1 40366d1ca26f6e9f372d07292b3db6d585c1e33a SHA256 f10c2635c94a165db12a7316f0ec6dadbfd93344ba95a6de51043d2fce9d5f60
+MISC ChangeLog 2849 RMD160 884bc192b4ffc61dd031a33ba3fa053c4c5fae7c SHA1 eebd926ec6ccc207922c9a9140798e9e8c24eb8d SHA256 e5a7d2fb5dfffe253e5ddf37aa4c275b9705da4ef723f6681f0b277ce5ac7286
 MISC metadata.xml 360 RMD160 b7e8ec0449f59c0dd0a7e3810b7c86b260d51530 SHA1 a54074283be9e7d2a113220e92a622b6fb4bfe45 SHA256 6d8c6ea79bfa70bc97b21c3b11454f4e47e31c20442a9ff96230d535562e945c
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.17 (GNU/Linux)
+Version: GnuPG v2.0.18 (GNU/Linux)
 
-iF4EAREIAAYFAk8t4kkACgkQC77qH+pIQ6S4qQEApeYzTqAGZuU3ig9kwP1IBitw
-P38sO84h/vwtkA6Z7JkBAJcgRFYmPUVbz9DXtmOQOjBm3rvu7VINBiVuCa+fvK41
-=9cGJ
+iEYEARECAAYFAk+VskMACgkQ1ycZbhPLE2C+wQCfYjUWxRd1ySwCJ81XoT5oVEsG
+6+oAoKGb3LGLKeBu1jkPv7xdFOp/9q+U
+=0u1z
 -----END PGP SIGNATURE-----
diff --git a/sci-libs/scikits_learn/files/0.10-atlas.patch b/sci-libs/scikits_learn/files/0.10-atlas.patch
new file mode 100644
index 000000000000..4d1743dc7a34
--- /dev/null
+++ b/sci-libs/scikits_learn/files/0.10-atlas.patch
@@ -0,0 +1,56 @@
+This patch remove the hardcoding on cblas which was assuming only ATLAS
+provides a cblas implementation.
+bicatali - apr 2012
+
+diff -Nur scikit-learn-0.10.orig/sklearn/cluster/setup.py scikit-learn-0.10/sklearn/cluster/setup.py
+--- scikit-learn-0.10.orig/sklearn/cluster/setup.py	2012-01-11 13:48:21.000000000 +0000
++++ scikit-learn-0.10/sklearn/cluster/setup.py	2012-04-23 19:59:54.000000000 +0100
+@@ -10,8 +10,7 @@
+     from numpy.distutils.system_info import get_info
+ 
+     blas_info = get_info('blas_opt', 0)
+-    if (not blas_info) or (
+-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
++    if (not blas_info):
+         cblas_libs = ['cblas']
+         blas_info.pop('libraries', None)
+     else:
+diff -Nur scikit-learn-0.10.orig/sklearn/linear_model/setup.py scikit-learn-0.10/sklearn/linear_model/setup.py
+--- scikit-learn-0.10.orig/sklearn/linear_model/setup.py	2012-01-11 13:48:21.000000000 +0000
++++ scikit-learn-0.10/sklearn/linear_model/setup.py	2012-04-23 20:00:44.000000000 +0100
+@@ -9,8 +9,7 @@
+ 
+     # cd fast needs CBLAS
+     blas_info = get_info('blas_opt', 0)
+-    if (not blas_info) or (
+-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
++    if (not blas_info):
+         cblas_libs = ['cblas']
+         blas_info.pop('libraries', None)
+     else:
+diff -Nur scikit-learn-0.10.orig/sklearn/setup.py scikit-learn-0.10/sklearn/setup.py
+--- scikit-learn-0.10.orig/sklearn/setup.py	2012-01-11 13:48:21.000000000 +0000
++++ scikit-learn-0.10/sklearn/setup.py	2012-04-23 20:39:34.000000000 +0100
+@@ -44,8 +44,7 @@
+ 
+     # 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', [])):
++    if (not blas_info):
+         config.add_library('cblas',
+                            sources=[join('src', 'cblas', '*.c')])
+         warnings.warn(BlasNotFoundError.__doc__)
+diff -Nur scikit-learn-0.10.orig/sklearn/utils/setup.py scikit-learn-0.10/sklearn/utils/setup.py
+--- scikit-learn-0.10.orig/sklearn/utils/setup.py	2012-01-11 13:48:21.000000000 +0000
++++ scikit-learn-0.10/sklearn/utils/setup.py	2012-04-23 20:02:13.000000000 +0100
+@@ -12,8 +12,7 @@
+ 
+     # cd fast needs CBLAS
+     blas_info = get_info('blas_opt', 0)
+-    if (not blas_info) or (
+-        ('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
++    if (not blas_info):
+         cblas_libs = ['cblas']
+         blas_info.pop('libraries', None)
+     else:
diff --git a/sci-libs/scikits_learn/scikits_learn-0.10.ebuild b/sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild
index a3515e78b380..d54d3ce63cf8 100644
--- a/sci-libs/scikits_learn/scikits_learn-0.10.ebuild
+++ b/sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild
@@ -1,20 +1,19 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/scikits_learn-0.10.ebuild,v 1.2 2012/02/05 01:58:26 floppym Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild,v 1.1 2012/04/23 19:49:14 bicatali Exp $
 
 EAPI=4
-inherit flag-o-matic
 
 PYTHON_DEPEND="2"
 SUPPORT_PYTHON_ABIS="1"
 RESTRICT_PYTHON_ABIS="3.*"
 DISTUTILS_SRC_TEST="setup.py"
 
-inherit distutils multilib
+inherit distutils multilib flag-o-matic
 
 MYPN="${PN/scikits_/scikit-}"
 
-DESCRIPTION="A set of python modules for machine learning and data mining"
+DESCRIPTION="Python modules for machine learning and data mining"
 HOMEPAGE="http://scikit-learn.org"
 SRC_URI="mirror://sourceforge/${MYPN}/${MYPN}-${PV}.tar.gz"
 
@@ -36,6 +35,7 @@ DEPEND="${CDEPEND}
 S="${WORKDIR}/${MYPN}-${PV}"
 
 src_prepare() {
+	epatch "${FILESDIR}"/${PV}-atlas.patch
 	# use stock libsvm
 	cat <<-EOF >> site.cfg
 		[libsvm]
@@ -53,10 +53,14 @@ src_compile() {
 	distutils_src_compile
 	if use doc; then
 		cd "${S}/doc"
-		export VARTEXFONTS="${T}"/fonts
-		MPLCONFIGDIR="${S}/build-$(PYTHON -f --ABI)" \
-			PYTHONPATH=$(ls -d "${S}"/build-$(PYTHON -f --ABI)/lib*) \
-			emake html latex
+		local d=$(ls -d "${S}"/build-$(PYTHON -f --ABI)/lib*)
+		ln -s "${S}"/sklearn/datasets/{data,descr,images} \
+			"${d}"/sklearn/datasets
+		VARTEXFONTS="${T}"/fonts \
+			MPLCONFIGDIR="${S}/build-$(PYTHON -f --ABI)" \
+			PYTHONPATH="${d}" \
+			emake html
+		rm -r "${d}"/sklearn/datasets/{data,desr,images}
 	fi
 }
 
@@ -68,7 +72,6 @@ src_install() {
 	}
 	python_execute_function -q remove_scikits
 	insinto /usr/share/doc/${PF}
-	use doc && doins "${DISTDIR}"/scikits.learn.pdf && \
-		doins -r build/sphinx/html
+	use doc && dohtml -r doc/_build/html
 	use examples && doins -r examples
 }
diff --git a/sci-libs/scikits_learn/scikits_learn-0.9.ebuild b/sci-libs/scikits_learn/scikits_learn-0.9.ebuild
deleted file mode 100644
index c41d9e23968a..000000000000
--- a/sci-libs/scikits_learn/scikits_learn-0.9.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/scikits_learn-0.9.ebuild,v 1.4 2012/02/05 01:58:26 floppym Exp $
-
-EAPI="3"
-inherit flag-o-matic
-
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-RESTRICT_PYTHON_ABIS="3.*"
-DISTUTILS_SRC_TEST="setup.py"
-
-inherit distutils multilib
-
-MYPN="${PN/scikits_/scikit-}"
-
-DESCRIPTION="A set of python modules for machine learning and data mining"
-HOMEPAGE="http://scikit-learn.org"
-SRC_URI="mirror://sourceforge/${MYPN}/${MYPN}-${PV}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc examples"
-
-CDEPEND="sci-libs/scipy
-	>=sci-libs/libsvm-2.91"
-RDEPEND="${CDEPEND}
-	sci-libs/scikits
-	dev-python/matplotlib"
-DEPEND="${CDEPEND}
-	dev-python/cython
-	dev-python/setuptools
-	doc? ( dev-python/sphinx dev-python/matplotlib )"
-
-S="${WORKDIR}/${MYPN}-${PV}"
-
-src_prepare() {
-	# use stock libsvm
-	cat <<-EOF >> site.cfg
-		[libsvm]
-		libraries=svm
-		library_dirs=${EPREFIX}/usr/$(get_libdir)
-		include_dirs=${EPREFIX}/usr/include/
-	EOF
-	# bug #397605
-	[[ ${CHOST} == *-darwin* ]] \
-		&& append-ldflags -bundle "-undefined dynamic_lookup" \
-		|| append-ldflags -shared
-}
-
-src_compile() {
-	distutils_src_compile
-	if use doc; then
-		cd "${S}/doc"
-		export VARTEXFONTS="${T}"/fonts
-		MPLCONFIGDIR="${S}/build-$(PYTHON -f --ABI)" \
-			PYTHONPATH=$(ls -d "${S}"/build-$(PYTHON -f --ABI)/lib*) \
-			emake html latex || die
-	fi
-}
-
-src_install() {
-	find "${S}" -name \*LICENSE.txt -delete
-	distutils_src_install
-	remove_scikits() {
-		rm -f "${ED}"$(python_get_sitedir)/scikits/__init__.py || die
-	}
-	python_execute_function -q remove_scikits
-	insinto /usr/share/doc/${PF}
-	if use doc; then
-		doins "${DISTDIR}"/scikits.learn.pdf || die
-		doins -r build/sphinx/html || die
-	fi
-	if use examples; then
-		doins -r examples || die
-	fi
-}