sci-libs/scikits_learn: non-broken version bump ahead of Gentoo Main

https://github.com/gentoo/gentoo/pull/15065#issuecomment-610712405

Package-Manager: Portage-2.3.96, Repoman-2.3.22
Signed-off-by: Horea Christian <chr@chymera.eu>

sci-libs/scikits_learn/ChangeLog

@@ -0,0 +1,8 @@
+*scikits_learn-0.22.1 (08 Apr 2020)
+
+  08 Apr 2020;  <chymera@gentoo.org>
+  +files/scikits_learn-0.18.1-system-cblas.patch,
+  +files/scikits_learn-0.20.2-fix-cdfast.patch, +metadata.xml,
+  +scikits_learn-0.22.1.ebuild:
+  sci-libs/scikits_learn: non-broken version bump ahead of Gentoo Main
+  https://github.com/gentoo/gentoo/pull/15065#issuecomment-610712405

sci-libs/scikits_learn/Manifest

@@ -0,0 +1 @@
+DIST scikit-learn-0.22.1.tar.gz 6942980 SHA256 51ee25330fc244107588545c70e2f3570cfc4017cff09eed69d6e1d82a212b7d SHA512 14191baf3457a3d216d74be34497a3677dd91bb1d3916db6928a4fa1ce93a62c5c9c9879a99fe5317fe088b85b00556087748470a93d3b9d89dbac850a00bc26 WHIRLPOOL e3db86763f1990198137b9ae8035d907ac3d4477c732fd4447dabae084c0dc03a01f5b8b0fed2700dcfa6c0e6e151b9e2c6b7ea5c4a383d44675d082b59fc370

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/files/scikits_learn-0.20.2-fix-cdfast.patch

@@ -0,0 +1,42 @@
+--- scikit-learn-0.20.3.orig/sklearn/linear_model/cd_fast.c	2019-08-09 03:05:05.351926119 +0500
++++ scikit-learn-0.20.3/sklearn/linear_model/cd_fast.c	2019-08-09 03:05:35.022926006 +0500
+@@ -4889,7 +4889,7 @@
+ 
+ static PyObject *__pyx_pf_7sklearn_12linear_model_7cd_fast_8enet_coordinate_descent(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_w, float __pyx_v_alpha, float __pyx_v_beta, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_y, int __pyx_v_max_iter, float __pyx_v_tol, PyObject *__pyx_v_rng, int __pyx_v_random, int __pyx_v_positive) {
+   PyObject *__pyx_v_dtype = NULL;
+-  void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int);
++  void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int);
+   float (*__pyx_v_dot)(int, float *, int, float *, int);
+   void (*__pyx_v_axpy)(int, float, float *, int, float *, int);
+   float (*__pyx_v_asum)(int, float *, int);
+@@ -6279,7 +6279,7 @@
+ 
+ static PyObject *__pyx_pf_7sklearn_12linear_model_7cd_fast_10enet_coordinate_descent(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_w, double __pyx_v_alpha, double __pyx_v_beta, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_y, int __pyx_v_max_iter, double __pyx_v_tol, PyObject *__pyx_v_rng, int __pyx_v_random, int __pyx_v_positive) {
+   PyObject *__pyx_v_dtype = NULL;
+-  void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int);
++  void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int);
+   double (*__pyx_v_dot)(int, double *, int, double *, int);
+   void (*__pyx_v_axpy)(int, double, double *, int, double *, int);
+   double (*__pyx_v_asum)(int, double *, int);
+@@ -16246,8 +16246,8 @@
+   CYTHON_UNUSED float (*__pyx_v_asum)(int, float *, int);
+   void (*__pyx_v_copy)(int, float *, int, float *, int);
+   void (*__pyx_v_scal)(int, float, float *, int);
+-  void (*__pyx_v_ger)(enum CBLAS_ORDER, int, int, float, float *, int, float *, int, float *, int);
+-  void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int);
++  void (*__pyx_v_ger)(CBLAS_ORDER, int, int, float, float *, int, float *, int, float *, int);
++  void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int);
+   unsigned int __pyx_v_n_samples;
+   unsigned int __pyx_v_n_features;
+   unsigned int __pyx_v_n_tasks;
+@@ -17965,8 +17965,8 @@
+   CYTHON_UNUSED double (*__pyx_v_asum)(int, double *, int);
+   void (*__pyx_v_copy)(int, double *, int, double *, int);
+   void (*__pyx_v_scal)(int, double, double *, int);
+-  void (*__pyx_v_ger)(enum CBLAS_ORDER, int, int, double, double *, int, double *, int, double *, int);
+-  void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int);
++  void (*__pyx_v_ger)(CBLAS_ORDER, int, int, double, double *, int, double *, int, double *, int);
++  void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int);
+   unsigned int __pyx_v_n_samples;
+   unsigned int __pyx_v_n_features;
+   unsigned int __pyx_v_n_tasks;

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-0.22.1.ebuild

@@ -0,0 +1,83 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7} )
+
+inherit distutils-r1 flag-o-matic
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Python modules for machine learning and data mining"
+HOMEPAGE="http://scikit-learn.org"
+SRC_URI="mirror://pypi/${MYPN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-python/joblib[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${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:=
+"
+
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/numpy[lapack,${PYTHON_USEDEP}]
+	sci-libs/scipy[${PYTHON_USEDEP}]
+	test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+	virtual/blas:=
+	virtual/cblas:=
+"
+
+S="${WORKDIR}/${MYP}"
+
+python_prepare_all() {
+	# bug #397605
+	[[ ${CHOST} == *-darwin* ]] &&
+		append-ldflags -bundle "-undefined dynamic_lookup" ||
+		append-ldflags -shared
+
+	# remove bundled cblas
+	rm -rf sklearn/src || die "failed to remove bundled cblas"
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	distutils-r1_python_compile
+}
+
+python_test() {
+	esetup.py install \
+		--root="${T}/test-${EPYTHON}"
+	pushd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die > /dev/null
+	pytest -m "not network" -vv || die
+	popd > /dev/null
+	#distutils_install_for_testing
+	#${EPYTHON} -m pytest -v "${BUILD_DIR}/test/lib/sklearn" || die
+}
+
+python_install() {
+	distutils-r1_python_install
+}
+
+python_install_all() {
+	find "${S}" -name \*LICENSE.txt -delete || die
+	distutils-r1_python_install_all
+	if use examples; then
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+}