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Deprecated by Gentoo Science

This commit is contained in:
Horea Christian 2020-01-22 17:51:00 +01:00
parent 2dd43a1dc2
commit e4e8743b85
8 changed files with 0 additions and 272 deletions
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13
sci-libs/scikits_learn/ChangeLog
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@ -1,13 +0,0 @@
10 Nov 2019; <chymera@gentoo.org>
+files/scikits_learn-0.20.3-cblas-enum.patch, scikits_learn-0.20.3.ebuild:
sci-libs/scikits_learn: fixed CBLAS API usage
https://bugs.gentoo.org/630294#c23
*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

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

28
sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch
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@ -1,28 +0,0 @@
--- 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:

30
sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch
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@ -1,30 +0,0 @@
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')

32
sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch
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@ -1,32 +0,0 @@
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')

42
sci-libs/scikits_learn/files/scikits_learn-0.20.3-cblas-enum.patch
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@ -1,42 +0,0 @@
--- 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;

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sci-libs/scikits_learn/metadata.xml
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@ -1,17 +0,0 @@
<?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>

109
sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild
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@ -1,109 +0,0 @@
# 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}"/${PN}-0.18.1-system-cblas.patch
"${FILESDIR}"/${P}-cblas-enum.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
}