gentoo resync : 14.07.2018

9 files changed, 0 insertions, 349 deletions

diff --git a/dev-python/astroscrappy/Manifest b/dev-python/astroscrappy/Manifest
deleted file mode 100644
index a6c2d656003c..000000000000
--- a/dev-python/astroscrappy/Manifest
+++ /dev/null
@@ -1,10 +0,0 @@
-AUX astroscrappy-1.0.3-dont-install-binary.patch 460 BLAKE2B 6d18dd6fcd8a3353fb1abb4ecdc2e299928c332d0d1dd17b671ec46e28840da3dc8e5aa63feadd211bf66cb1c12a1b56d8233e2a725af9e96c1c45ac1dd89eda SHA512 b18ce0be8e2dc7c4e9c2334ae8987b5e3cfaf51c31de8e5be88a4f49436ddeb2de71caabaffda2441fbd59dc43697386ef0653c3210f8a728d175609d96226d1
-AUX astroscrappy-1.0.3-endian-fix-tests.patch 3941 BLAKE2B b0109cefaa976d6355f6e1fe1416ec9e610a4ab5b4e9412f1e96528314cf8c064cd4773deab7347953a39aad9adcfc3f64e2dbff13d0d3c00191df4ae7c67452 SHA512 0439a414c87428e05c68677248b3bd37a9981aecf89d891c9d7b9c0d96d0f1e62f547cf88e4a8f3f1e71183aca607e407662bdc087bd4cc676bbc075f8653472
-AUX astroscrappy-1.0.3-numpy-fix-tests.patch 933 BLAKE2B cf31eb447908d43e02e0134423ca0ec943243cde31e62ee13c093c221e06666974825f0c327cf6c773174baa7a6e2d9f28a06a527394cf84543b2cd876fe3730 SHA512 1917d7d89550d6303f4faadb498c61669f5590edd836a49a21b4c419b92972244a6a1f90aa73add85e17bc0e336f04b13239948994dee53c57f48ba0a1c6e5a5
-AUX astroscrappy-1.0.3-respect-user-flag.patch 1639 BLAKE2B 41953a090177c8d7ecc5c425d114b41ae19134bfe11674a2f496b369fe981225d8fa5a8b245a16b8a535da93a704f0a32d33dd0348208cfb09ba1e9ce54943c8 SHA512 5d39c2e0dac5647ff624680fdc8f369b92e6b325a3da55ea112d9df31af9534a164cf598a90a369dc0d753782802bfcc6927a8f4e8ca6f347e608a133584a148
-AUX astroscrappy-1.0.5-respect-user-flag.patch 1417 BLAKE2B 11f69ab3cb75ae00ac18553f9096bff9d80273a11232230ce526a9d8e7d680f46e697b99c2051ad499cee55b33d2b4027af335a542f4d6a16e878e94681e69f1 SHA512 9bb2420c761bc11c4add8d058a216ba5995be0c8bcaa11d408b1c8cc51d9e86e70e52744238a760c4cb415248b0a0a7be09207dc2ebe3affd9c26442bb214e91
-DIST astroscrappy-1.0.3.tar.gz 422209 BLAKE2B f0d5a83c6b4718eb6d0a1d60068459da3d886c6ab389be5b65a6b31dfb2bcfff9238e8773d1cfeca8db15289999ccbdcf96ba966f85ca76779077ee6fd0923a6 SHA512 2e96e8e62f81c770802a3c7699ca4455c640bb000aa4bffc22149745eed4e7e33cc4b297649020a601ff7fb242c0545cf9391c19ee2687adab26ac494d37dbb2
-DIST astroscrappy-1.0.5.tar.gz 421910 BLAKE2B 7ca92277e3914b54cce09cb9a5d8e4657dbc2e3aead8904c967be906bdf78d4b73450adff7d7b970ec37e7b4ba5ab275f2c1cdd8b4573b1563daed6ecae14682 SHA512 bad648140abe3032aa76f43b4c61a15bc49b825bb8333d0e2dc6ba244542e5d6b283824336de82c73aefdfd62b952c9089c3237c913faf17874af13725345064
-EBUILD astroscrappy-1.0.3.ebuild 1414 BLAKE2B 28e96012941d13a39c9c0576de35cfd413beb9d0bd4cc2ed98ab720d1070027e4cef746b09b88bd14c002db96912579dd8c64b3508d0a9dccf03ca13614acfef SHA512 21daa270a72eab60d03aa5317429925d0fcf16d9ea96bace1d11fffd2b3c165e7255d324b79387f70c8b57febefee7705c37e5ca9841e13d8559e2a9c05cd8cb
-EBUILD astroscrappy-1.0.5.ebuild 1435 BLAKE2B 037a63dd28be14ce760b458fac1d9462a592f408bd0d8120ba807635d1fcaa1857b2ee6b1f096498d3f02c0394481c771311ca8f7d9deb887ae9abcaeaf30e15 SHA512 0ed29e4ab665f2d71b08b408fb105812b0fd0deab33f215636ad4b8b30d1978d9270de13534515be6ba37029916f01322848ada8324493abd394acfde9156d9c
-MISC metadata.xml 642 BLAKE2B 0fafd3972f80215f48309afe038d5419edb6caedceb873d083aabfa27ab418e5b3128c2031e34280754fe2234e81e276ecd04a41c54acc55d226513b32e5f654 SHA512 803d99c24952fb6bc3e118234c4e2c7c78dcd82717e0240104f042fd305d3e1c675b9b67a7cdedd5a3d0d71967b460b3c32174eaeff6d8b523d6e57dd961d298
diff --git a/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild b/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild
deleted file mode 100644
index fea8b1aceccc..000000000000
--- a/dev-python/astroscrappy/astroscrappy-1.0.3.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} )
-
-inherit distutils-r1 toolchain-funcs flag-o-matic
-
-DESCRIPTION="Optimized cosmic ray annihilation astropy python module"
-HOMEPAGE="https://github.com/astropy/astroscrappy"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc openmp test"
-
-RDEPEND="
-	dev-python/astropy[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-PATCHES=(
-	"${FILESDIR}/${P}-dont-install-binary.patch"
-	"${FILESDIR}/${P}-endian-fix-tests.patch"
-	"${FILESDIR}/${P}-numpy-fix-tests.patch"
-	"${FILESDIR}/${P}-respect-user-flag.patch"
-)
-
-DOCS=( CHANGES.rst )
-
-python_prepare_all() {
-	sed -i -e '/auto_use/s/True/False/' setup.cfg || die
-	use openmp && tc-has-openmp && append-flags -fopenmp
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && esetup.py build_sphinx
-}
-
-python_test() {
-	esetup.py test
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/astroscrappy/astroscrappy-1.0.5.ebuild b/dev-python/astroscrappy/astroscrappy-1.0.5.ebuild
deleted file mode 100644
index 02a537e04e50..000000000000
--- a/dev-python/astroscrappy/astroscrappy-1.0.5.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Optimized cosmic ray annihilation astropy python module"
-HOMEPAGE="https://github.com/astropy/astroscrappy"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc openmp test"
-
-RDEPEND="
-	dev-python/astropy[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-	test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
-
-DOCS=( CHANGES.rst )
-
-PATCHES=(
-	"${FILESDIR}/${PN}-1.0.5-respect-user-flag.patch"
-)
-
-python_prepare_all() {
-	# use astropy-helpers from system
-	sed -i -e '/auto_use/s/True/False/' setup.cfg || die
-	# if the user explicitely does not want openmp, do not forcefully use it
-	if ! use openmp; then
-		sed -e 's/if has_openmp/if False/' \
-			-i astroscrappy/utils/setup_package.py || die
-	fi
-	distutils-r1_python_prepare_all
-}
-
-python_compile_all() {
-	use doc && esetup.py build_sphinx
-}
-
-python_test() {
-	esetup.py test
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch
deleted file mode 100644
index 4c69f00cc88d..000000000000
--- a/dev-python/astroscrappy/files/astroscrappy-1.0.3-dont-install-binary.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Author: Ole Streicher <olebole@debian.org>
-Description: Don't install example/template binary
---- a/setup.py
-+++ b/setup.py
-@@ -80,9 +80,6 @@
- 
- # Define entry points for command-line scripts
- entry_points = {}
--entry_points['console_scripts'] = [
--    'astropy-package-template-example = packagename.example_mod:main',
--]
- 
- # Include all .c files, recursively, including those generated by
- # Cython, since we can not do this in MANIFEST.in with a "dynamic"
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch
deleted file mode 100644
index 7a2bbb6299c6..000000000000
--- a/dev-python/astroscrappy/files/astroscrappy-1.0.3-endian-fix-tests.patch
+++ /dev/null
@@ -1,100 +0,0 @@
-From 5b5ce99c63d03e60b6027f09f72231db11a87bf2 Mon Sep 17 00:00:00 2001
-From: Curtis McCully <cmccully@lcogt.net>
-Date: Thu, 3 Dec 2015 12:02:38 -0800
-Subject: [PATCH] Made tests not endian specific.
---- a/astroscrappy/tests/test_utils.py
-+++ b/astroscrappy/tests/test_utils.py
-@@ -56,7 +56,7 @@
- 
- 
- def test_medfilt5():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed5 = ndimage.filters.median_filter(a, size=(5, 5), mode='nearest')
-     npmed5[:2, :] = a[:2, :]
-     npmed5[-2:, :] = a[-2:, :]
-@@ -68,7 +68,7 @@
- 
- 
- def test_medfilt7():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed7 = ndimage.filters.median_filter(a, size=(7, 7), mode='nearest')
-     npmed7[:3, :] = a[:3, :]
-     npmed7[-3:, :] = a[-3:, :]
-@@ -80,7 +80,7 @@
- 
- 
- def test_sepmedfilt3():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed3 = ndimage.filters.median_filter(a, size=(1, 3), mode='nearest')
-     npmed3[:, :1] = a[:, :1]
-     npmed3[:, -1:] = a[:, -1:]
-@@ -95,7 +95,7 @@
- 
- 
- def test_sepmedfilt5():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed5 = ndimage.filters.median_filter(a, size=(1, 5), mode='nearest')
-     npmed5[:, :2] = a[:, :2]
-     npmed5[:, -2:] = a[:, -2:]
-@@ -110,7 +110,7 @@
- 
- 
- def test_sepmedfilt7():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed7 = ndimage.filters.median_filter(a, size=(1, 7), mode='nearest')
-     npmed7[:, :3] = a[:, :3]
-     npmed7[:, -3:] = a[:, -3:]
-@@ -125,7 +125,7 @@
- 
- 
- def test_sepmedfilt9():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npmed9 = ndimage.filters.median_filter(a, size=(1, 9), mode='nearest')
-     npmed9[:, :4] = a[:, :4]
-     npmed9[:, -4:] = a[:, -4:]
-@@ -174,7 +174,7 @@
- 
- 
- def test_subsample():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     npsubsamp = np.zeros((a.shape[0] * 2, a.shape[1] * 2), dtype=np.float32)
-     for i in range(a.shape[0]):
-         for j in range(a.shape[1]):
-@@ -189,8 +189,8 @@
- 
- def test_rebin():
-     a = np.ascontiguousarray(np.random.random((2002, 2002)), dtype=np.float32)
--    a = a.astype('<f4')
--    nprebin = np.zeros((1001, 1001), dtype=np.float32).astype('<f4')
-+    a = a.astype('f4')
-+    nprebin = np.zeros((1001, 1001), dtype=np.float32).astype('f4')
-     for i in range(1001):
-         for j in range(1001):
-             nprebin[i, j] = (a[2 * i, 2 * j] + a[2 * i + 1, 2 * j] +
-@@ -202,7 +202,7 @@
- 
- 
- def test_laplaceconvolve():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-     k = np.array([[0.0, -1.0, 0.0], [-1.0, 4.0, -1.0], [0.0, -1.0, 0.0]])
-     k = k.astype('<f4')
-     npconv = ndimage.filters.convolve(a, k, mode='constant', cval=0.0)
-@@ -211,8 +211,8 @@
- 
- 
- def test_convolve():
--    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('<f4')
--    k = np.ascontiguousarray(np.random.random((5, 5))).astype('<f4')
-+    a = np.ascontiguousarray(np.random.random((1001, 1001))).astype('f4')
-+    k = np.ascontiguousarray(np.random.random((5, 5))).astype('f4')
-     npconv = ndimage.filters.convolve(a, k, mode='constant', cval=0.0)
-     cconv = convolve(a, k)
-     assert_allclose(cconv, npconv, rtol=0, atol=1e-5)
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch
deleted file mode 100644
index d7a1c93a5740..000000000000
--- a/dev-python/astroscrappy/files/astroscrappy-1.0.3-numpy-fix-tests.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Author: Ole Streicher <olebole@debian.org>
-Description: Cast the numpy arrays in the test to the same data type
-Bug: https://ci.debian.net/data/packages/unstable/amd64/a/astroscrappy/20160112_151253.autopkgtest.log.gz
---- a/astroscrappy/tests/test_astroscrappy.py
-+++ b/astroscrappy/tests/test_astroscrappy.py
-@@ -36,7 +36,7 @@
-     imdata += gaussian(imdata.shape, x, y, brightness, 3.5)
- 
- # Add the poisson noise
--imdata = np.random.poisson(imdata)
-+imdata = np.float32(np.random.poisson(imdata))
- 
- # Add readnoise
- imdata += np.random.normal(0.0, 10.0, size=(1001, 1001))
-@@ -60,4 +60,4 @@
-     # contrast that we can turn our detection threshold up.
-     mask, _clean = detect_cosmics(imdata, readnoise=10., gain=1.0,
-                                   sigclip=6, sigfrac=1.0)
--    assert (mask == expected_crmask).sum() == (1001 * 1001)
-\ No newline at end of file
-+    assert (mask == expected_crmask).sum() == (1001 * 1001)
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch
deleted file mode 100644
index fb7bca64ce7f..000000000000
--- a/dev-python/astroscrappy/files/astroscrappy-1.0.3-respect-user-flag.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- astroscrappy/astroscrappy/utils/setup_package.py.orig	2016-03-09 22:50:34.304043122 +0000
-+++ astroscrappy/astroscrappy/utils/setup_package.py	2016-03-09 22:54:53.560783823 +0000
-@@ -43,30 +43,11 @@
-                     sources=med_sources,
-                     include_dirs=include_dirs,
-                     libraries=libraries,
--                    language="c",
--                    extra_compile_args=['-g', '-O3', '-funroll-loops',
--                                        '-ffast-math'])
-+                    language="c")
-     ext_im = Extension(name=str("astroscrappy.utils.image_utils"),
-                     sources=im_sources,
-                     include_dirs=include_dirs,
-                     libraries=libraries,
--                    language="c",
--                    extra_compile_args=['-g', '-O3', '-funroll-loops',
--                                        '-ffast-math'])
--
--    has_openmp, outputs = check_openmp()
--    if has_openmp:
--        ext_med.extra_compile_args.append('-fopenmp')
--        ext_im.extra_compile_args.append('-fopenmp')
--        ext_med.extra_link_args = ['-g', '-fopenmp']
--        ext_im.extra_link_args = ['-g', '-fopenmp']
--    else:
--        log.warn('OpenMP was not found. '
--                 'astroscrappy will be compiled without OpenMP. '
--                 '(Use the "-v" option of setup.py for more details.)')
--        log.debug(('(Start of OpenMP info)\n'
--                   'compiler stdout:\n{0}\n'
--                   'compiler stderr:\n{1}\n'
--                   '(End of OpenMP info)').format(*outputs))
-+                    language="c")
- 
-     return [ext_med, ext_im]
diff --git a/dev-python/astroscrappy/files/astroscrappy-1.0.5-respect-user-flag.patch b/dev-python/astroscrappy/files/astroscrappy-1.0.5-respect-user-flag.patch
deleted file mode 100644
index b3638e1bffc3..000000000000
--- a/dev-python/astroscrappy/files/astroscrappy-1.0.5-respect-user-flag.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-From f3acf99e65f58e2ee2f409d33f44a3abb1ba90c4 Mon Sep 17 00:00:00 2001
-From: Sébastien Fabbro <bicatali@gentoo.org>
-Date: Wed, 31 Aug 2016 22:19:12 +0000
-Subject: [PATCH] respect user compiling flags Depending on compilers, -O3
- -funroll-loops is not the fastest.
-
----
- astroscrappy/utils/setup_package.py | 8 ++------
- 1 file changed, 2 insertions(+), 6 deletions(-)
-
-diff --git a/astroscrappy/utils/setup_package.py b/astroscrappy/utils/setup_package.py
-index 3e1fba2..c271613 100644
---- a/astroscrappy/utils/setup_package.py
-+++ b/astroscrappy/utils/setup_package.py
-@@ -73,16 +73,12 @@ def get_extensions():
-                     sources=med_sources,
-                     include_dirs=include_dirs,
-                     libraries=libraries,
--                    language="c",
--                    extra_compile_args=['-g', '-O3', '-funroll-loops',
--                                        '-ffast-math'])
-+                    language="c")
-     ext_im = Extension(name=str("astroscrappy.utils.image_utils"),
-                     sources=im_sources,
-                     include_dirs=include_dirs,
-                     libraries=libraries,
--                    language="c",
--                    extra_compile_args=['-g', '-O3', '-funroll-loops',
--                                        '-ffast-math'])
-+                    language="c")
- 
-     has_openmp, outputs = check_openmp()
-     if has_openmp:
--- 
-2.9.3
-
diff --git a/dev-python/astroscrappy/metadata.xml b/dev-python/astroscrappy/metadata.xml
deleted file mode 100644
index 6a303f8428d9..000000000000
--- a/dev-python/astroscrappy/metadata.xml
+++ /dev/null
@@ -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-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-    Astro-SCRAPPY is designed to detect cosmic rays in images (numpy arrays),
-    based on Pieter van Dokkum's L.A.Cosmic algorithm. Parallelization is
-    achieved using OpenMP.
-  </longdescription>
-  <upstream>
-    <remote-id type="pypi">astroscrappy</remote-id>
-    <remote-id type="github">astropy/astroscrappy</remote-id>
-  </upstream>
-</pkgmetadata>