gentoo resync : 16.01.2018

5 files changed, 5 insertions, 212 deletions

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 23090976310c..ef515e64f22f 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,8 +1,3 @@
-AUX scikits_image-0.11.3-adapthist-backport.patch 3489 BLAKE2B 3f280a69a9a8c462934efdd081963327da84b0a159a5775fd140f1e5462e1d0c0c5d36ce71fce2f2d6bce8e36e446ea6ec64122640d961aca259670bec0e7041 SHA512 5f4e063bc2456f7e78f8485d8a2d68a19e77ab7a171332f758761173cc7608d64c81e69ea785265b71763ab6a0c43c35b17699b954064a38498ebdf0db92e91b
-DIST scikit-image-0.11.3.tar.gz 18589296 BLAKE2B 2b305bc1490050f893035cd727588ad624b66d2dceaceea8935bd2b768cf737d89156fc8b3017f67cdee41d805348ddfcf3e163db3d4f790606457064e618ddb SHA512 595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108
-DIST scikit-image-0.12.3.tar.gz 20701373 BLAKE2B 131c7bed2af0b52a86293f85107f069ca77b71028af22c14a331d8a4563f68470543b5898d534055306db9b7fb58f50cc1b767a168ff9bb780c7446c4888e92f SHA512 3a2d51f7b826569e5fc2a4502c62b85559ae9fa05555240894af1bb8bd2bad1798b786a2070b1f90b4c07339d8186fe5c118a89994503cce920e8e25fc5f3b51
 DIST scikit-image-0.13.0.tar.gz 26101533 BLAKE2B c28284f64abd58c7bafa8f5f0c781496e8bb28af79c5c730df7cbf2fede958eb88ea420fd7f89e7b8d0d91719a98dd0935af3b2cc50fe501cc8d8d1d0ee56cb9 SHA512 923015e373c406ae2fbbfdf83ce8b91e83790bdf7842c4439fdc9fd58cffe46efc0cfc7a1b0b06e1b2d092a909a6f085335640850883e7608dbccd1074046550
-EBUILD scikits_image-0.11.3.ebuild 1907 BLAKE2B 165ea16486fddeed229a9b29e71fe5bd92154e4754d63065a94165cee4d06def8c6653dcbf91ffee577e7fd7a9dfae81d0091d87120bb8d4c141ce044ccdde14 SHA512 449771233b266efe32d64093f0e02ced1c959958788bcce4e5902a0035b053428a17eee2b5aa61facdd2068389d6d5574929dfccfca03d722588d8c7d46e1d4d
-EBUILD scikits_image-0.12.3.ebuild 1826 BLAKE2B c04544ccd2d75ea10d71d008ab8ee4cad0ca54f95c26720265d8de0f22f9d09afac115249aa2f901303c32c6483631b29d830b23f9e5b6d8a0d7b4e39bab646c SHA512 d0788a9af25066908e6b83496619728bed1dbd551ef55a01a720a4a4e444cf1020a87cacaea367c90922bc6a883118b4b663e4bb9e5f9463e88d52b857bfa7b8
-EBUILD scikits_image-0.13.0.ebuild 1852 BLAKE2B 6cac72e3f7b22013bda6f60181c78eda7a0296b673b4014ffe6a6e1fade2a70d35f872b16a2e4ab75b88de3bb83479babb6ebcbf28a38838d2cd858c63f9bb43 SHA512 ecace053bf601c3b2133b2c1f965ac2bb303d12bb7e1e8aabc9997fbeb46876a4d083f8a279a38b96422adb4afafc801d979686188b1cda7e65f74f92f3da57a
+EBUILD scikits_image-0.13.0.ebuild 1804 BLAKE2B f4c2d48daf3d850951e757347420efbe2718a5376c34d07899694b0218ca5c597b79e7e0dc75085b4c62906d1ddbbe29b0fb2be358133315b5338a85642efc56 SHA512 830b93b83a1b595a28d0d24a7e3109dac0109925fee66de25d09e55eb558a1f84668b11b52fa7bede42f0d6b0c54d06775735806a0a3d27347f59f83b0240499
 MISC metadata.xml 834 BLAKE2B d6ed9731e0bfffb39fb127b1ccaa9d449e7cedc4038a5a4a915624fadad131d39df0d1d7123951539074758095d35c1b9730bb4a3da2278b02630903645eb769 SHA512 1c615479bc22c8c66b4f7a2189e38c69f9b8722f051c68473439069ef89598f0505dbd94fe06cbe56a07e41a1a6552f4d8d666703676ef9a165dbcf462e09e40
diff --git a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch
deleted file mode 100644
index 0bd96916bfc1..000000000000
--- a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-From 41159f3fd24e7653c556ddbf6ba93ad2aa8b541f Mon Sep 17 00:00:00 2001
-From: Steven Silvester <steven.silvester@ieee.org>
-Date: Mon, 19 Oct 2015 18:07:32 -0500
-Subject: [PATCH] Fix adapthist mask logic
-
-Use minlength in bincount
-
-Fix mask logic
----
- skimage/exposure/_adapthist.py          |  8 +++++---
- skimage/exposure/tests/test_exposure.py | 14 +++++++-------
- 2 files changed, 12 insertions(+), 10 deletions(-)
-
-diff --git a/skimage/exposure/_adapthist.py b/skimage/exposure/_adapthist.py
-index 343f71b..757daff 100644
---- a/skimage/exposure/_adapthist.py
-+++ b/skimage/exposure/_adapthist.py
-@@ -247,12 +247,14 @@ def clip_histogram(hist, clip_limit):
-     while n_excess > 0:  # Redistribute remaining excess
-         index = 0
-         while n_excess > 0 and index < hist.size:
-+            under_mask = hist < 0
-             step_size = int(hist[hist < clip_limit].size / n_excess)
-             step_size = max(step_size, 1)
-             indices = np.arange(index, hist.size, step_size)
--            under = hist[indices] < clip_limit
--            hist[under] += 1
--            n_excess -= hist[under].size
-+            under_mask[indices] = True
-+            under_mask = (under_mask) & (hist < clip_limit)
-+            hist[under_mask] += 1
-+            n_excess -= under_mask.sum()
-             index += 1
- 
-     return hist
-diff --git a/skimage/exposure/tests/test_exposure.py b/skimage/exposure/tests/test_exposure.py
-index 8fb6d62..1b9c778 100644
---- a/skimage/exposure/tests/test_exposure.py
-+++ b/skimage/exposure/tests/test_exposure.py
-@@ -199,9 +199,9 @@ def test_adapthist_scalar():
-     full_scale = skimage.exposure.rescale_intensity(skimage.img_as_float(img))
- 
-     assert_almost_equal = np.testing.assert_almost_equal
--    assert_almost_equal(peak_snr(full_scale, adapted), 101.2295, 3)
-+    assert_almost_equal(peak_snr(full_scale, adapted), 102.066, 3)
-     assert_almost_equal(norm_brightness_err(full_scale, adapted),
--                        0.041, 3)
-+                        0.038, 3)
-     return img, adapted
- 
- 
-@@ -217,8 +217,8 @@ def test_adapthist_grayscale():
-                                               nbins=128)
-     assert_almost_equal = np.testing.assert_almost_equal
-     assert img.shape == adapted.shape
--    assert_almost_equal(peak_snr(img, adapted), 97.6876, 3)
--    assert_almost_equal(norm_brightness_err(img, adapted), 0.0591, 3)
-+    assert_almost_equal(peak_snr(img, adapted), 102.078, 3)
-+    assert_almost_equal(norm_brightness_err(img, adapted), 0.0529, 3)
-     return data, adapted
- 
- 
-@@ -238,7 +238,7 @@ def test_adapthist_color():
-     assert adapted.max() == 1.0
-     assert img.shape == adapted.shape
-     full_scale = skimage.exposure.rescale_intensity(img)
--    assert_almost_equal(peak_snr(full_scale, adapted), 109.6, 1)
-+    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 1)
-     assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.02, 2)
-     return data, adapted
- 
-@@ -256,8 +256,8 @@ def test_adapthist_alpha():
-     full_scale = skimage.exposure.rescale_intensity(img)
-     assert img.shape == adapted.shape
-     assert_almost_equal = np.testing.assert_almost_equal
--    assert_almost_equal(peak_snr(full_scale, adapted), 109.60, 2)
--    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0235, 3)
-+    assert_almost_equal(peak_snr(full_scale, adapted), 109.393, 2)
-+    assert_almost_equal(norm_brightness_err(full_scale, adapted), 0.0248, 3)
- 
- 
- def peak_snr(img1, img2):
diff --git a/sci-libs/scikits_image/scikits_image-0.11.3.ebuild b/sci-libs/scikits_image/scikits_image-0.11.3.ebuild
deleted file mode 100644
index 99d76385d71a..000000000000
--- a/sci-libs/scikits_image/scikits_image-0.11.3.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_4 )
-
-inherit distutils-r1 eutils virtualx
-
-MYPN="${PN/scikits_/scikit-}"
-MYP="${MYPN}-${PV}"
-
-DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="http://scikit-image.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc freeimage gtk pyamg qt4 test"
-
-RDEPEND="
-	>=dev-python/matplotlib-1.1.0[${PYTHON_USEDEP}]
-	>=dev-python/networkx-1.8[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.6.1[${PYTHON_USEDEP}]
-	>=dev-python/pillow-1.7.8[${PYTHON_USEDEP}]
-	>=dev-python/six-1.3[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.9[sparse,${PYTHON_USEDEP}]
-	freeimage? ( media-libs/freeimage )
-	gtk? ( dev-python/pygtk[$(python_gen_usedep 'python2*')] )
-	pyamg? ( dev-python/pyamg[$(python_gen_usedep 'python2*')] )
-	qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=dev-python/cython-0.21[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (
-		dev-python/nose[${PYTHON_USEDEP}]
-		)"
-
-S="${WORKDIR}/${MYP}"
-
-DOCS=( CONTRIBUTORS.txt CONTRIBUTING.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt )
-
-PATCHES=(
-	"${FILESDIR}"/${P}-adapthist-backport.patch
-)
-
-python_test() {
-	distutils_install_for_testing
-	mkdir for_test && cd for_test || die
-	echo "backend : Agg" > matplotlibrc || die
-	echo "backend.qt4 : PyQt4" >> matplotlibrc || die
-	#echo "backend.qt4 : PySide" >> matplotlibrc || die
-	VIRTUALX_COMMAND=nosetests
-	MPLCONFIGDIR=. virtualmake --exe -v skimage || die
-}
-
-pkg_postinst() {
-	optfeature "FITS io capability" dev-python/astropy
-	#optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
-	#optfeature "io plugin providing most standard formats" dev-python/imread
-}
diff --git a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
deleted file mode 100644
index ed088bd06527..000000000000
--- a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 eutils virtualx
-
-MYPN="${PN/scikits_/scikit-}"
-MYP="${MYPN}-${PV}"
-
-DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="http://scikit-image.org/"
-SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc freeimage pyamg qt4 test"
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pillow[${PYTHON_USEDEP}]
-	dev-python/six[${PYTHON_USEDEP}]
-	sci-libs/scipy[sparse,${PYTHON_USEDEP}]
-	freeimage? ( media-libs/freeimage )
-	pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )
-	qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
-	>=dev-python/cython-0.23[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	test? (	dev-python/nose[${PYTHON_USEDEP}] )"
-
-S="${WORKDIR}/${MYP}"
-
-DOCS=( CONTRIBUTORS.txt CONTRIBUTING.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt )
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die "no ${TEST_DIR} available"
-	echo "backend : Agg" > matplotlibrc || die
-	echo "backend.qt4 : PyQt4" >> matplotlibrc || die
-	#echo "backend.qt4 : PySide" >> matplotlibrc || die
-	MPLCONFIGDIR=. virtx nosetests --exe -v skimage || die
-}
-
-pkg_postinst() {
-	optfeature "FITS io capability" dev-python/astropy
-	optfeature "GTK" dev-python/pygtk
-	optfeature "Parallel computation" dev-python/dask
-	# not in portage yet
-	#optfeature "io plugin providing a wide variety of formats, including specialized formats using in medical imaging." dev-python/simpleitk
-	#optfeature "io plugin providing most standard formats" dev-python/imread
-}
diff --git a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
index cc09ed813cb9..fb9abe7e7c78 100644
--- a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
+++ b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -17,7 +17,7 @@ SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc freeimage pyamg qt4 test"
+IUSE="doc freeimage pyamg test"
 
 RDEPEND="
 	dev-python/matplotlib[${PYTHON_USEDEP}]
@@ -28,8 +28,7 @@ RDEPEND="
 	dev-python/six[${PYTHON_USEDEP}]
 	sci-libs/scipy[sparse,${PYTHON_USEDEP}]
 	freeimage? ( media-libs/freeimage )
-	pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )
-	qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )"
+	pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )"
 DEPEND="${RDEPEND}
 	>=dev-python/cython-0.23[${PYTHON_USEDEP}]
 	dev-python/setuptools[${PYTHON_USEDEP}]
@@ -43,7 +42,7 @@ python_test() {
 	distutils_install_for_testing
 	cd "${TEST_DIR}" || die "no ${TEST_DIR} available"
 	echo "backend : Agg" > matplotlibrc || die
-	echo "backend.qt4 : PyQt4" >> matplotlibrc || die
+	#echo "backend.qt4 : PyQt4" >> matplotlibrc || die
 	#echo "backend.qt4 : PySide" >> matplotlibrc || die
 	MPLCONFIGDIR=. virtx nosetests --exe -v skimage || die
 }