Version bump

(Portage version: 2.2.01.21313-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

3 files changed, 115 insertions, 2 deletions

diff --git a/sci-libs/scikits_learn/ChangeLog b/sci-libs/scikits_learn/ChangeLog
index 3a0aa4d8183d..a7a388c326e7 100644
--- a/sci-libs/scikits_learn/ChangeLog
+++ b/sci-libs/scikits_learn/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.13 2012/06/21 19:17:13 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/scikits_learn/ChangeLog,v 1.14 2012/11/30 00:25:42 bicatali Exp $
+
+*scikits_learn-0.12.1 (30 Nov 2012)
+
+  30 Nov 2012; Sébastien Fabbro <bicatali@gentoo.org>
+  +files/0.12.1-linalg.patch, +scikits_learn-0.12.1.ebuild:
+  Version bump
 
   21 Jun 2012; Sébastien Fabbro <bicatali@gentoo.org>
   -scikits_learn-0.10-r1.ebuild, scikits_learn-0.11.ebuild:
@@ -101,4 +107,3 @@
   26 Mar 2010; Sébastien Fabbro <bicatali@gentoo.org>
   +scikits_learn-0.2.ebuild, +metadata.xml:
   Initial import
-
diff --git a/sci-libs/scikits_learn/files/0.12.1-linalg.patch b/sci-libs/scikits_learn/files/0.12.1-linalg.patch
new file mode 100644
index 000000000000..ca113ffe6416
--- /dev/null
+++ b/sci-libs/scikits_learn/files/0.12.1-linalg.patch
@@ -0,0 +1,29 @@
+--- 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-0.12.1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.12.1.ebuild
new file mode 100644
index 000000000000..0e2c3fac912c
--- /dev/null
+++ b/sci-libs/scikits_learn/scikits_learn-0.12.1.ebuild
@@ -0,0 +1,79 @@
+# 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-0.12.1.ebuild,v 1.1 2012/11/30 00:25:42 bicatali Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="2"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="2.7-pypy-*"
+
+inherit distutils 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
+	sci-libs/scipy
+	dev-python/matplotlib"
+DEPEND="
+	dev-python/cython
+	dev-python/setuptools
+	sci-libs/scipy
+	doc? ( dev-python/sphinx dev-python/matplotlib )"
+
+S="${WORKDIR}/${MYPN}-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/0.12.1-linalg.patch
+
+	# 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"
+}
+
+src_compile() {
+	distutils_src_compile ${SCIPY_FCONFIG}
+	if use doc; then
+		cd "${S}/doc"
+		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
+}
+
+src_test() {
+	# doc builds and runs tests
+	use doc && return
+	testing() {
+		"$(PYTHON)" setup.py build_ext --inplace ${SCIPY_FCONFIG} || die
+		PYTHONPATH=. nosetests sklearn --exe || die
+	}
+	python_execute_function testing
+}
+
+src_install() {
+	find "${S}" -name \*LICENSE.txt -delete
+	distutils_src_install ${SCIPY_FCONFIG}
+	insinto /usr/share/doc/${PF}
+	use doc && dohtml -r doc/_build/html
+	use examples && doins -r examples
+}