sci-libs/scikits_learn: new package ahead of gentoo main

Package-Manager: Portage-2.3.66, Repoman-2.3.12
Signed-off-by: Horea Christian <horea.christ@yandex.com>

sci-libs/scikits_learn/ChangeLog

@@ -0,0 +1,8 @@
+*scikits_learn-0.20.3 (16 Jun 2019)
+
+  16 Jun 2019;  <chymera@gentoo.org>
+  +files/scikits_learn-0.14.1-system-cblas.patch,
+  +files/scikits_learn-0.17.1-system-cblas.patch,
+  +files/scikits_learn-0.18.1-system-cblas.patch, +metadata.xml,
+  +scikits_learn-0.20.3.ebuild:
+  sci-libs/scikits_learn: new package ahead of gentoo main

sci-libs/scikits_learn/Manifest

@@ -0,0 +1 @@
+DIST scikit-learn-0.20.3.tar.gz 11818490 SHA256 c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41 SHA512 fedc697b123e53badd7d75e2e0fa0749d9270c8ba52906227fda98f08b61bb40db9e0d1ffe71b030c30b64e77d000e7ba72cd9530c9f88c988dfc090c6c2872a WHIRLPOOL c8275fb275e39a183091f7bbbf78a364e4f2c297420b603f1c4a154aba23ae241263fad9ef60060c4334ac1a22bdf8ddfe1bbc4a1709db1cc4940a1e356fb976

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:

sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch

@@ -0,0 +1,30 @@
+diff -Nur scikit-learn-0.17.1.orig/sklearn/_build_utils.py scikit-learn-0.17.1/sklearn/_build_utils.py
+--- scikit-learn-0.17.1.orig/sklearn/_build_utils.py	2016-03-09 00:27:54.756813784 +0000
++++ scikit-learn-0.17.1/sklearn/_build_utils.py	2016-03-09 00:30:09.605118512 +0000
+@@ -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 -Nur scikit-learn-0.17.1.orig/sklearn/setup.py scikit-learn-0.17.1/sklearn/setup.py
+--- scikit-learn-0.17.1.orig/sklearn/setup.py	2016-03-09 00:27:54.806813156 +0000
++++ scikit-learn-0.17.1/sklearn/setup.py	2016-03-09 00:29:28.215638848 +0000
+@@ -58,14 +58,6 @@
+         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')

sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch

@@ -0,0 +1,32 @@
+Index: scikit-learn-0.18.1/sklearn/_build_utils/__init__.py
+===================================================================
+--- scikit-learn-0.18.1.orig/sklearn/_build_utils/__init__.py
++++ scikit-learn-0.18.1/sklearn/_build_utils/__init__.py
+@@ -31,7 +31,7 @@ def get_blas_info():
+         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:
+Index: scikit-learn-0.18.1/sklearn/setup.py
+===================================================================
+--- scikit-learn-0.18.1.orig/sklearn/setup.py
++++ scikit-learn-0.18.1/sklearn/setup.py
+@@ -63,14 +63,6 @@ def configuration(parent_package='', top
+                          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')

sci-libs/scikits_learn/metadata.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <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>
+    <remote-id type="sourceforge">scikit-learn</remote-id>
+  </upstream>
+</pkgmetadata>

sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild

@@ -0,0 +1,106 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
+
+inherit distutils-r1 flag-o-matic
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Python modules for machine learning and data mining"
+HOMEPAGE="https://scikit-learn.org"
+SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples test"
+
+# tried to unbundle virtual/python-funcsigs, funcsigs, odict
+# but it is a large mess to maintain
+
+RDEPEND="
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/nose[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	sci-libs/scikits[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/blas:=
+	virtual/cblas:=
+"
+
+DEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	virtual/blas:=
+	virtual/cblas:=
+"
+
+S="${WORKDIR}/${MYP}"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.18.1-system-cblas.patch )
+
+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"
+
+	# remove bundled cblas
+	rm -r sklearn/src || die
+
+	# commented out, since it is a mess to maintain
+	# use system joblib
+	#rm -r sklearn/externals/joblib || die
+	#sed -i -e '/joblib/d' sklearn/externals/setup.py || die
+	#for f in sklearn/{*/,}*.py; do
+	#	sed -r -e '/^from/s/(sklearn|\.|)\.externals\.joblib/joblib/' \
+	#		-e 's/from (sklearn|\.|)\.externals import/import/' -i $f || die
+	#done
+
+	# use system funcsigs and odict
+	#rm sklearn/externals/funcsigs.py || die
+	#rm sklearn/externals/odict.py || die
+	#for f in sklearn/{utils/fixes.py,gaussian_process/{tests/test_,}kernels.py}; do
+	#	sed -r -e 's/from (sklearn|\.|)\.externals\.funcsigs/from funcsigs/' -i $f || die
+	#done
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile ${SCIPY_FCONFIG}
+}
+
+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 ${SCIPY_FCONFIG}
+	pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null
+	JOBLIB_MULTIPROCESSING=2 SKLEARN_SKIP_NETWORK_TESTS=1 nosetests -v sklearn --exe || die
+	popd > /dev/null
+}
+
+python_install() {
+	distutils-r1_python_install ${SCIPY_FCONFIG}
+}
+
+python_install_all() {
+	find "${S}" -name \*LICENSE.txt -delete
+	distutils-r1_python_install_all
+	if use examples; then
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+}