Version bump

Package-Manager: portage-2.2.01.21688-prefix/cvs/Linux x86_64
Manifest-Sign-Key: 0x13CB1360

5 files changed, 97 insertions, 92 deletions

diff --git a/sci-libs/scikits_learn/ChangeLog b/sci-libs/scikits_learn/ChangeLog
index 606910f058a7..c4fc24cc146f 100644
--- a/sci-libs/scikits_learn/ChangeLog
+++ b/sci-libs/scikits_learn/ChangeLog
@@ -1,6 +1,13 @@
 # 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 1.18 2013/02/21 00:42:49 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.19 2013/03/03 07:39:23 bicatali Exp $
+
+*scikits_learn-0.13.1 (03 Mar 2013)
+
+  03 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org>
+  +scikits_learn-0.13.1.ebuild, -files/0.10-atlas.patch,
+  -files/0.12.1-linalg.patch:
+  Version bump
 
   21 Feb 2013; Sébastien Fabbro <bicatali@gentoo.org>
   -scikits_learn-0.12.1.ebuild, -scikits_learn-0.13.ebuild, metadata.xml:
diff --git a/sci-libs/scikits_learn/Manifest b/sci-libs/scikits_learn/Manifest
index c2108f262ce3..3048cfa48424 100644
--- a/sci-libs/scikits_learn/Manifest
+++ b/sci-libs/scikits_learn/Manifest
@@ -1,16 +1,16 @@
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 Hash: SHA256
 
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+DIST scikit-learn-0.13.1.tar.gz 3477412 SHA256 a6e4759a779ba792435d096c882a0d66ee29d369755c09209f1a4e50877bdc94 SHA512 945475bf6e5600da63d26217ae6966f8f5e3a8d9c7645363ba9e9d8d4c475e2ebcfa45e75f8988537716b7a9c16980c52df4310b924eec4da9433d1fc98cc34b WHIRLPOOL 0af58429d604eb1fb22f24e155daaa67831d16d49ff414b29a150f03617be1811796d653afb0f7b4eac9f03cf318910dd9544dc3a58543a333fccd8580a59d4b
 DIST scikit-learn-0.13.tar.gz 3464031 SHA256 f89e716fcee123e621ded23d5e1cb25105e48ef17e1fc73b3f439bc745bc913a SHA512 d889cce2dfa46746c9735fa9b7dc44032748895bc39cd734c03804e0a4fda3c95b76114b191130122e9049873519984702283c0a831b0c24ba81d2a5fc8e20fc WHIRLPOOL 4d9891e8c18efa0faad0e452263d7a5ca970d3e593e6be1f32a82c71bb98d728feb3ed24c6b5cf85846f0f5c435173c93427bbd29fb04af8f85ae0ba3222a4d5
 EBUILD scikits_learn-0.13-r1.ebuild 2137 SHA256 92f38c405c548ebcf6ec459d448a3cb49cb74843c663b8823f7069a10b336e6b SHA512 59e272846c80e621c9dd1cde711e95e82dd68b9b00d48faf3266d571bbb218e3d13300d0361bb76af406ddfb29ddf5d66e6eabcbcb6bdad032c72c0e867dd4db WHIRLPOOL 962682a25b9c6ca60aefdeea66ec888636830e13d2255c433baf5a66926a0bf2a56d9093906ec3eb72958c1114615d2431675c4c8b088191bbc6326c7e0985c4
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diff --git a/sci-libs/scikits_learn/files/0.10-atlas.patch b/sci-libs/scikits_learn/files/0.10-atlas.patch
deleted file mode 100644
index 4d1743dc7a34..000000000000
--- a/sci-libs/scikits_learn/files/0.10-atlas.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-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/files/0.12.1-linalg.patch b/sci-libs/scikits_learn/files/0.12.1-linalg.patch
deleted file mode 100644
index ca113ffe6416..000000000000
--- a/sci-libs/scikits_learn/files/0.12.1-linalg.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- a/sklearn/linear_model/least_angle.py
-+++ b/sklearn/linear_model/least_angle.py
-@@ -236,8 +236,8 @@ def lars_path(X, y, Xy=None, Gram=None,
-                 L_.flat[::n_active + 1] += (2 ** i) * eps
-                 least_squares, info = solve_cholesky(L_,
-                                     sign_active[:n_active], lower=True)
--                AA = 1. / np.sqrt(np.sum(least_squares
--                                         * sign_active[:n_active]))
-+                tmp = max(np.sum(least_squares * sign_active[:n_active]), eps)
-+                AA = 1. / np.sqrt(tmp)
-                 i += 1
-         least_squares *= AA
- 
---- a/sklearn/linear_model/tests/test_least_angle.py
-+++ b/sklearn/linear_model/tests/test_least_angle.py
-@@ -101,6 +101,13 @@ def test_collinearity():
-     assert_true(not np.isnan(coef_path_).any())
-     residual = np.dot(X, coef_path_[:, -1]) - y
-     assert_less((residual ** 2).sum(), 1.)  # just make sure it's bounded
-+    
-+    n_samples = 10
-+    X = np.random.rand(n_samples, 5)
-+    y = np.zeros(n_samples)
-+    _, _, coef_path_ = linear_model.lars_path(X, y, Gram='auto', copy_X=False, 
-+         copy_Gram=False, alpha_min=0., method='lasso', verbose=0, max_iter=500)
-+    assert_array_almost_equal(coef_path_, np.zeros_like(coef_path_))
- 
- 
- def test_no_path():
diff --git a/sci-libs/scikits_learn/scikits_learn-0.13.1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.13.1.ebuild
new file mode 100644
index 000000000000..b4acb25d0322
--- /dev/null
+++ b/sci-libs/scikits_learn/scikits_learn-0.13.1.ebuild
@@ -0,0 +1,83 @@
+# 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-0.13.1.ebuild,v 1.1 2013/03/03 07:39:23 bicatali Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 multilib flag-o-matic
+
+MYPN="${PN/scikits_/scikit-}"
+
+DESCRIPTION="Python modules for machine learning and data mining"
+HOMEPAGE="http://scikit-learn.org"
+SRC_URI="mirror://sourceforge/${MYPN}/${MYPN}-${PV}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples"
+
+RDEPEND="
+	sci-libs/scikits[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]"
+DEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	doc? (
+		dev-python/sphinx[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}] )"
+
+S="${WORKDIR}/${MYPN}-${PV}"
+
+python_prepare_all() {
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] \
+		&& append-ldflags -bundle "-undefined dynamic_lookup" \
+		|| append-ldflags -shared
+
+	# scikits-learn now uses the horrible numpy.distutils automagic
+	export SCIPY_FCONFIG="config_fc --noopt --noarch"
+}
+
+python_compile() {
+	distutils-r1_python_compile ${SCIPY_FCONFIG}
+}
+
+python_compile_all() {
+	if use doc; then
+		cd "${S}/doc"
+		local d="${BUILD_DIR}"/lib
+		ln -s "${S}"/sklearn/datasets/{data,descr,images} \
+			"${d}"/sklearn/datasets
+		VARTEXFONTS="${T}"/fonts \
+			MPLCONFIGDIR="${BUILD_DIR}" \
+			PYTHONPATH="${d}" \
+			emake html
+		rm -r "${d}"/sklearn/datasets/{data,desr,images}
+	fi
+}
+
+python_test() {
+	# doc builds and runs tests
+	use doc && return
+	esetup.py \
+		install --root="${T}/test-${EPYTHON}" \
+		--no-compile ${SCIPY_FCONFIG} || die
+	cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die
+	PYTHONPATH=. nosetests-${EPYTHON} sklearn --exe || die
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+}
+
+python_install_all() {
+	find "${S}" -name \*LICENSE.txt -delete
+	insinto /usr/share/doc/${PF}
+	use doc && dohtml -r doc/_build/html
+	use examples && doins -r examples
+}