From e4e8743b85ad92926397bb2c8690dfb9d9640d75 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Wed, 22 Jan 2020 17:51:00 +0100 Subject: [PATCH] Deprecated by Gentoo Science --- sci-libs/scikits_learn/ChangeLog | 13 --- sci-libs/scikits_learn/Manifest | 1 - .../scikits_learn-0.14.1-system-cblas.patch | 28 ----- .../scikits_learn-0.17.1-system-cblas.patch | 30 ----- .../scikits_learn-0.18.1-system-cblas.patch | 32 ----- .../scikits_learn-0.20.3-cblas-enum.patch | 42 ------- sci-libs/scikits_learn/metadata.xml | 17 --- .../scikits_learn/scikits_learn-0.20.3.ebuild | 109 ------------------ 8 files changed, 272 deletions(-) delete mode 100644 sci-libs/scikits_learn/ChangeLog delete mode 100644 sci-libs/scikits_learn/Manifest delete mode 100644 sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch delete mode 100644 sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch delete mode 100644 sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch delete mode 100644 sci-libs/scikits_learn/files/scikits_learn-0.20.3-cblas-enum.patch delete mode 100644 sci-libs/scikits_learn/metadata.xml delete mode 100644 sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild diff --git a/sci-libs/scikits_learn/ChangeLog b/sci-libs/scikits_learn/ChangeLog deleted file mode 100644 index 94c5161..0000000 --- a/sci-libs/scikits_learn/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ - 10 Nov 2019; - +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; - +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 diff --git a/sci-libs/scikits_learn/Manifest b/sci-libs/scikits_learn/Manifest deleted file mode 100644 index 7cea361..0000000 --- a/sci-libs/scikits_learn/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scikit-learn-0.20.3.tar.gz 11818490 SHA256 c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41 SHA512 fedc697b123e53badd7d75e2e0fa0749d9270c8ba52906227fda98f08b61bb40db9e0d1ffe71b030c30b64e77d000e7ba72cd9530c9f88c988dfc090c6c2872a WHIRLPOOL c8275fb275e39a183091f7bbbf78a364e4f2c297420b603f1c4a154aba23ae241263fad9ef60060c4334ac1a22bdf8ddfe1bbc4a1709db1cc4940a1e356fb976 diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch deleted file mode 100644 index 96c6cc2..0000000 --- a/sci-libs/scikits_learn/files/scikits_learn-0.14.1-system-cblas.patch +++ /dev/null @@ -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: diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch deleted file mode 100644 index 42657a7..0000000 --- a/sci-libs/scikits_learn/files/scikits_learn-0.17.1-system-cblas.patch +++ /dev/null @@ -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') diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch b/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch deleted file mode 100644 index e60f649..0000000 --- a/sci-libs/scikits_learn/files/scikits_learn-0.18.1-system-cblas.patch +++ /dev/null @@ -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') diff --git a/sci-libs/scikits_learn/files/scikits_learn-0.20.3-cblas-enum.patch b/sci-libs/scikits_learn/files/scikits_learn-0.20.3-cblas-enum.patch deleted file mode 100644 index 1d1de4a..0000000 --- a/sci-libs/scikits_learn/files/scikits_learn-0.20.3-cblas-enum.patch +++ /dev/null @@ -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; diff --git a/sci-libs/scikits_learn/metadata.xml b/sci-libs/scikits_learn/metadata.xml deleted file mode 100644 index 0f62a4a..0000000 --- a/sci-libs/scikits_learn/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ - - - - - sci@gentoo.org - Gentoo Science Project - - - scikits.learn is a python library for machine learning. It aims to - implement classic machine learning algorithms while remaining simple - and efficient. - - - scikit-learn - scikit-learn - - diff --git a/sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild b/sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild deleted file mode 100644 index bf6cd0c..0000000 --- a/sci-libs/scikits_learn/scikits_learn-0.20.3.ebuild +++ /dev/null @@ -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 - -}