From 4225896a33241b6559c2108687c10ce3f65e57ff Mon Sep 17 00:00:00 2001 From: Sebastien Fabbro Date: Mon, 23 Apr 2012 19:49:15 +0000 Subject: 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 (Portage version: 2.1.10.56/cvs/Linux x86_64) --- sci-libs/scikits_learn/ChangeLog | 11 ++- sci-libs/scikits_learn/files/0.10-atlas.patch | 56 ++++++++++++++++ .../scikits_learn/scikits_learn-0.10-r1.ebuild | 77 +++++++++++++++++++++ sci-libs/scikits_learn/scikits_learn-0.10.ebuild | 74 -------------------- sci-libs/scikits_learn/scikits_learn-0.9.ebuild | 78 ---------------------- 5 files changed, 143 insertions(+), 153 deletions(-) create mode 100644 sci-libs/scikits_learn/files/0.10-atlas.patch create mode 100644 sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild delete mode 100644 sci-libs/scikits_learn/scikits_learn-0.10.ebuild delete mode 100644 sci-libs/scikits_learn/scikits_learn-0.9.ebuild (limited to 'sci-libs') 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 +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 scikits_learn-0.10.ebuild, scikits_learn-0.9.ebuild: 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-r1.ebuild b/sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild new file mode 100644 index 000000000000..d54d3ce63cf8 --- /dev/null +++ b/sci-libs/scikits_learn/scikits_learn-0.10-r1.ebuild @@ -0,0 +1,77 @@ +# 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-r1.ebuild,v 1.1 2012/04/23 19:49:14 bicatali Exp $ + +EAPI=4 + +PYTHON_DEPEND="2" +SUPPORT_PYTHON_ABIS="1" +RESTRICT_PYTHON_ABIS="3.*" +DISTUTILS_SRC_TEST="setup.py" + +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" + +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}-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-atlas.patch + # use stock libsvm + cat <<-EOF >> site.cfg + [libsvm] + libraries=svm + library_dirs=${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" + 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_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} + use doc && dohtml -r doc/_build/html + use examples && doins -r examples +} diff --git a/sci-libs/scikits_learn/scikits_learn-0.10.ebuild b/sci-libs/scikits_learn/scikits_learn-0.10.ebuild deleted file mode 100644 index a3515e78b380..000000000000 --- a/sci-libs/scikits_learn/scikits_learn-0.10.ebuild +++ /dev/null @@ -1,74 +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-0.10.ebuild,v 1.2 2012/02/05 01:58:26 floppym 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 - -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 - 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} - use doc && doins "${DISTDIR}"/scikits.learn.pdf && \ - doins -r build/sphinx/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 -} -- cgit v1.2.3-65-gdbad