[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/, dev-python/scikit-image/, profiles/updates/

2020-11-09 Thread Benda XU 
commit: 0855a3aee553a2f759d9338eaa5c1eb8714f8ad0
Author: Aisha Tammy  aisha  cc>
AuthorDate: Fri Oct 16 14:29:27 2020 +
Commit: Benda XU  gentoo  org>
CommitDate: Mon Nov  9 14:01:45 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0855a3ae

dev-python/scikit-image: version bump to 0.17.2

remove tests as their build system is horrible and has to download the
test images

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Aisha Tammy  aisha.cc>
Signed-off-by: Benda Xu  gentoo.org>

 .../scikit-image}/Manifest |  1 +
 .../scikit-image}/metadata.xml |  0
 .../scikit-image/scikit-image-0.13.0-r1.ebuild |  0
 dev-python/scikit-image/scikit-image-0.17.2.ebuild | 42 ++
 profiles/updates/4Q-2020   |  1 +
 5 files changed, 44 insertions(+)

diff --git a/sci-libs/scikits_image/Manifest b/dev-python/scikit-image/Manifest
similarity index 50%
rename from sci-libs/scikits_image/Manifest
rename to dev-python/scikit-image/Manifest
index ef33ed7e630..a9303cfafc7 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/dev-python/scikit-image/Manifest
@@ -1 +1,2 @@
 DIST scikit-image-0.13.0.tar.gz 26101533 BLAKE2B 
c28284f64abd58c7bafa8f5f0c781496e8bb28af79c5c730df7cbf2fede958eb88ea420fd7f89e7b8d0d91719a98dd0935af3b2cc50fe501cc8d8d1d0ee56cb9
 SHA512 
923015e373c406ae2fbbfdf83ce8b91e83790bdf7842c4439fdc9fd58cffe46efc0cfc7a1b0b06e1b2d092a909a6f085335640850883e7608dbccd1074046550
+DIST scikit-image-0.17.2.tar.gz 22682646 BLAKE2B 
acfa38caff7aa2e1f724e173f544610e643976a40feb752040d2f20d49d871d19dddb34790bf846476932c771c260ad9bd210781439707d7c5f693c9a8fa021c
 SHA512 
3e57d8bea2fd41270eb17e8489c477f58ed98e56cef0192b0b2d455f27f7a2d705161afd61c7bfd556ec938a9a2bf5663ec1aa7b79609a8e5946806356364e82

diff --git a/sci-libs/scikits_image/metadata.xml 
b/dev-python/scikit-image/metadata.xml
similarity index 100%
rename from sci-libs/scikits_image/metadata.xml
rename to dev-python/scikit-image/metadata.xml

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild 
b/dev-python/scikit-image/scikit-image-0.13.0-r1.ebuild
similarity index 100%
rename from sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
rename to dev-python/scikit-image/scikit-image-0.13.0-r1.ebuild

diff --git a/dev-python/scikit-image/scikit-image-0.17.2.ebuild 
b/dev-python/scikit-image/scikit-image-0.17.2.ebuild
new file mode 100644
index 000..a071cd5c522
--- /dev/null
+++ b/dev-python/scikit-image/scikit-image-0.17.2.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+# 8,9 not on dev-python/pyamg
+PYTHON_COMPAT=( python3_{6..8} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Image processing routines for SciPy"
+HOMEPAGE="https://scikit-image.org/";
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+   dev-python/imageio[${PYTHON_USEDEP}]
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   dev-python/networkx[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pillow[${PYTHON_USEDEP}]
+   dev-python/pywavelets[${PYTHON_USEDEP}]
+   dev-python/scipy[sparse,${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}
+   dev-python/cython[${PYTHON_USEDEP}]
+   dev-python/setuptools[${PYTHON_USEDEP}]
+"
+
+DOCS=( CONTRIBUTORS.txt RELEASE.txt )
+
+pkg_postinst() {
+   optfeature "FITS io capability" dev-python/astropy
+   optfeature "GTK" dev-python/pygtk
+   optfeature "Parallel computation" dev-python/dask
+   optfeature "io plugin providing most standard formats" dev-python/imread
+   # not in portage yet
+   #optfeature "io plugin providing a wide variety of formats, including 
specialized formats using in medical imaging." dev-python/simpleitk
+}

diff --git a/profiles/updates/4Q-2020 b/profiles/updates/4Q-2020
index 8df417391f8..44b73424672 100644
--- a/profiles/updates/4Q-2020
+++ b/profiles/updates/4Q-2020
@@ -3,3 +3,4 @@ move acct-user/openldap acct-user/ldap
 move x11-apps/copyq x11-misc/copyq
 slotmove media-gfx/gimp 2 0
 move sci-libs/scikits_learn dev-python/scikit-learn
+move sci-libs/scikits_image dev-python/scikit-image

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2020-09-07 Thread David Seifert 
commit: 6722e4fe01206bbd2fe1526b0018bad9b16d05bf
Author: David Seifert  gentoo  org>
AuthorDate: Mon Sep  7 08:53:57 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Sep  7 08:53:57 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6722e4fe

sci-libs/scikits_image: Inherit optfeature.eclass

Package-Manager: Portage-3.0.5, Repoman-3.0.1
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild 
b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
index 99a0588f9ff..875c4e86fa4 100644
--- a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
+++ b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{6,7} )
 
-inherit distutils-r1 eutils virtualx
+inherit distutils-r1 optfeature virtualx
 
 MYPN="${PN/scikits_/scikit-}"
 MYP="${MYPN}-${PV}"

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2019-12-29 Thread Andreas Sturmlechner 
commit: 62ded693099a6759cb812d01d4044f5296d255ed
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Dec 28 16:42:05 2019 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Dec 29 13:22:54 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=62ded693

sci-libs/scikits_image: Drop 0.13.0 (r0)

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-libs/scikits_image/scikits_image-0.13.0.ebuild | 58 --
 1 file changed, 58 deletions(-)

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild 
b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
deleted file mode 100644
index 985fd58974d..000
--- a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
+++ /dev/null
@@ -1,58 +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 eutils virtualx
-
-MYPN="${PN/scikits_/scikit-}"
-MYP="${MYPN}-${PV}"
-
-DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="https://scikit-image.org/";
-SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc freeimage pyamg test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-   dev-python/matplotlib[${PYTHON_USEDEP}]
-   dev-python/networkx[${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pillow[${PYTHON_USEDEP}]
-   dev-python/pywavelets[${PYTHON_USEDEP}]
-   dev-python/six[${PYTHON_USEDEP}]
-   sci-libs/scipy[sparse,${PYTHON_USEDEP}]
-   freeimage? ( media-libs/freeimage )
-   pyamg? ( dev-python/pyamg[${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 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
-}
-
-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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2019-12-29 Thread Andreas Sturmlechner 
commit: a7dd5a2f6d1ed621eb09920b1d194bc3b307906e
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Dec 28 16:43:02 2019 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Dec 29 13:22:55 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a7dd5a2f

sci-libs/scikits_image: Drop python2_7

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild 
b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
index 8c4d5a0fd8e..4aaada38a3c 100644
--- a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
+++ b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+PYTHON_COMPAT=( python3_{5,6,7} )
 
 inherit distutils-r1 eutils virtualx

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2019-08-03 Thread Alexey Shvetsov 
commit: 94f22e32c4e5e41597fbb1c8a1c4340638f0c73d
Author: Alexey Shvetsov  gentoo  org>
AuthorDate: Sat Aug  3 20:19:03 2019 +
Commit: Alexey Shvetsov  gentoo  org>
CommitDate: Sat Aug  3 20:19:03 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=94f22e32

sci-libs/scikits_image: Works with py3.7

Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Alexey Shvetsov  gentoo.org>

 .../scikits_image/scikits_image-0.13.0-r1.ebuild   | 57 ++
 1 file changed, 57 insertions(+)

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild 
b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
new file mode 100644
index 000..49f66eaba90
--- /dev/null
+++ b/sci-libs/scikits_image/scikits_image-0.13.0-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1 eutils virtualx
+
+MYPN="${PN/scikits_/scikit-}"
+MYP="${MYPN}-${PV}"
+
+DESCRIPTION="Image processing routines for SciPy"
+HOMEPAGE="https://scikit-image.org/";
+SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc freeimage pyamg test"
+
+RDEPEND="
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   dev-python/networkx[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pillow[${PYTHON_USEDEP}]
+   dev-python/pywavelets[${PYTHON_USEDEP}]
+   dev-python/six[${PYTHON_USEDEP}]
+   sci-libs/scipy[sparse,${PYTHON_USEDEP}]
+   freeimage? ( media-libs/freeimage )
+   pyamg? ( dev-python/pyamg[${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 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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2019-02-26 Thread Aaron Bauman 
commit: 4cb7316442c13a2212a07bedcef29e05676884b9
Author: Michael Mair-Keimberger  gmail  com>
AuthorDate: Sat Feb 23 16:50:57 2019 +
Commit: Aaron Bauman  gentoo  org>
CommitDate: Wed Feb 27 04:21:20 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4cb73164

sci-libs/scikits_image: use HTTPS

Signed-off-by: Michael Mair-Keimberger  gmail.com>
Signed-off-by: Aaron Bauman  gentoo.org>

 sci-libs/scikits_image/scikits_image-0.13.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 fb9abe7e7c7..1863336706d 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 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -11,7 +11,7 @@ MYPN="${PN/scikits_/scikit-}"
 MYP="${MYPN}-${PV}"
 
 DESCRIPTION="Image processing routines for SciPy"
-HOMEPAGE="http://scikit-image.org/";
+HOMEPAGE="https://scikit-image.org/";
 SRC_URI="mirror://pypi/${PN:0:1}/${MYPN}/${MYP}.tar.gz"
 
 LICENSE="BSD"

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2018-01-14 Thread Andreas Sturmlechner 
commit: 1e8f3957c0a197a0127c0c55f953f4e638053996
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sun Jan 14 13:19:30 2018 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Jan 14 13:21:29 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1e8f3957

sci-libs/scikits_image: Drop USE=qt4

Closes: https://bugs.gentoo.org/641938
Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-libs/scikits_image/scikits_image-0.13.0.ebuild | 9 -
 1 file changed, 4 insertions(+), 5 deletions(-)

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 cc09ed813cb..fb9abe7e7c7 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
 }

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/files/, sci-libs/scikits_image/

2018-01-14 Thread Andreas Sturmlechner 
commit: f971c51f2e7ce18f8f1123987aca6bce501ee5c5
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sun Jan 14 13:20:12 2018 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Jan 14 13:21:29 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f971c51f

sci-libs/scikits_image: Drop old

Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-libs/scikits_image/Manifest|  2 -
 .../scikits_image-0.11.3-adapthist-backport.patch  | 82 --
 sci-libs/scikits_image/scikits_image-0.11.3.ebuild | 62 
 sci-libs/scikits_image/scikits_image-0.12.3.ebuild | 57 ---
 4 files changed, 203 deletions(-)

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index e5748441c6c..ef33ed7e630 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,3 +1 @@
-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 
3a2d51f7b826569e5fc2a4502c62b85559ae9fa0240894af1bb8bd2bad1798b786a2070b1f90b4c07339d8186fe5c118a89994503cce920e8e25fc5f3b51
 DIST scikit-image-0.13.0.tar.gz 26101533 BLAKE2B 
c28284f64abd58c7bafa8f5f0c781496e8bb28af79c5c730df7cbf2fede958eb88ea420fd7f89e7b8d0d91719a98dd0935af3b2cc50fe501cc8d8d1d0ee56cb9
 SHA512 
923015e373c406ae2fbbfdf83ce8b91e83790bdf7842c4439fdc9fd58cffe46efc0cfc7a1b0b06e1b2d092a909a6f085335640850883e7608dbccd1074046550

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 0bd96916bfc..000
--- 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 
-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_equa

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2017-06-26 Thread Sebastien Fabbro 
commit: c7d8c60a035d670537f662cf9eea884430017a1c
Author: Sébastien Fabbro  gentoo  org>
AuthorDate: Mon Jun 26 19:30:22 2017 +
Commit: Sebastien Fabbro  gentoo  org>
CommitDate: Tue Jun 27 02:48:47 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c7d8c60a

sci-libs/scikits_image: version bump

Package-Manager: Portage-2.3.6, Repoman-2.3.2

 sci-libs/scikits_image/Manifest|  1 +
 sci-libs/scikits_image/scikits_image-0.13.0.ebuild | 58 ++
 2 files changed, 59 insertions(+)

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 55dff5b0456..bca07fc212e 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,2 +1,3 @@
 DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 
768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 
595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108
 WHIRLPOOL 
43b52943ac3ff40f58863fdfbf588b5f17d6103e2cf2ec09863006da2a288412cc550d47f8c97027904827ccdd5e12a87ec94620d5788273c364276c2f614c6c
 DIST scikit-image-0.12.3.tar.gz 20701373 SHA256 
82da192f0e524701e89c5379c79200bc6dc21373f48bf7778a864c583897d7c7 SHA512 
3a2d51f7b826569e5fc2a4502c62b85559ae9fa0240894af1bb8bd2bad1798b786a2070b1f90b4c07339d8186fe5c118a89994503cce920e8e25fc5f3b51
 WHIRLPOOL 
cfb93cc53612a7b646ec94075a34f501728b18b685968a2f51ea3d00d965c0204f2f567543f1cfa723e54dae90568cda34940cb60790dd4ffc4cac27f718fe23
+DIST scikit-image-0.13.0.tar.gz 26101533 SHA256 
77a636bdc08c7668a15951894548c527f0c8c5c2abc86cb850de17551af51e3e SHA512 
923015e373c406ae2fbbfdf83ce8b91e83790bdf7842c4439fdc9fd58cffe46efc0cfc7a1b0b06e1b2d092a909a6f085335640850883e7608dbccd1074046550
 WHIRLPOOL 
a646b0f6e96d71dac7ae048035ec3ead7b850d8135f23c9222563b1096ccfe281d2d0c733b97709b478d66bb61fad0937c4d6462b43bbdc7798190d1b717422b

diff --git a/sci-libs/scikits_image/scikits_image-0.13.0.ebuild 
b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
new file mode 100644
index 000..cc09ed813cb
--- /dev/null
+++ b/sci-libs/scikits_image/scikits_image-0.13.0.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+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/pywavelets[${PYTHON_USEDEP}]
+   dev-python/six[${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}/${MYP}"
+
+DOCS=( CONTRIBUTORS.txt DEPENDS.txt RELEASE.txt TASKS.txt TODO.txt )
+
+python_test() {
+   distutils_install_for_testing
+   cd "${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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2016-04-10 Thread David Seifert 
commit: caf39f4281602b4f2bcbe385e3eb5282e976d80b
Author: David Seifert  gentoo  org>
AuthorDate: Sun Apr 10 13:11:37 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Apr 10 13:23:22 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=caf39f42

sci-libs/scikits_image: Bump dev-python/cython version dep

Package-Manager: portage-2.2.28

 sci-libs/scikits_image/scikits_image-0.12.3.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild 
b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
index 6f812a2..6b9413a 100644
--- a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
+++ b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
@@ -31,7 +31,7 @@ RDEPEND="
pyamg? ( dev-python/pyamg[${PYTHON_USEDEP}] )
qt4? ( dev-python/PyQt4[${PYTHON_USEDEP}] )"
 DEPEND="${RDEPEND}
-   dev-python/cython[${PYTHON_USEDEP}]
+   >=dev-python/cython-0.23[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]
test? ( dev-python/nose[${PYTHON_USEDEP}] )"

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/files/, sci-libs/scikits_image/

2016-04-06 Thread Sebastien Fabbro 
commit: 31b247eaf817108bb5ad46f455ac59d0dcf45b82
Author: Sébastien Fabbro  gentoo  org>
AuthorDate: Wed Apr  6 23:43:54 2016 +
Commit: Sebastien Fabbro  gentoo  org>
CommitDate: Thu Apr  7 00:33:28 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31b247ea

sci-libs/scikits_image: move heavy dask dependency to optfeature

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=579156

Package-Manager: portage-2.2.28

 sci-libs/scikits_image/Manifest|  3 -
 .../scikits_image-0.11.3-adapthist-backport.patch1 | 73 --
 sci-libs/scikits_image/scikits_image-0.10.0.ebuild | 49 ---
 sci-libs/scikits_image/scikits_image-0.10.1.ebuild | 51 ---
 sci-libs/scikits_image/scikits_image-0.12.3.ebuild |  2 +-
 sci-libs/scikits_image/scikits_image-0.9.3.ebuild  | 48 --
 6 files changed, 1 insertion(+), 225 deletions(-)

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 80e89dd..55dff5b 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,5 +1,2 @@
-DIST scikit-image-0.10.0.tar.gz 9084596 SHA256 
83995570f11654b47d0a0d50ae8b4d11a0de97a44ae195a4c04ba4f10b9dd7f8 SHA512 
be45359fe99499e904b0b0e75870cd301947ca1edc7711ce982d107b1e56c0d15cfd59fe8dcc9eff1bca5b1e4bac5ae23e7adeda028590ea1230db76914b0ab8
 WHIRLPOOL 
adeed1d7f6f7b5a5b01c78672226425d481e9dbb69c36f5927274d91856745f472abd8d055c3ad1f880c348d92d5a1bbca9e4253983e7d3aa01ab2f2dfbe29f1
-DIST scikit-image-0.10.1.tar.gz 16740044 SHA256 
83a1afcc16df75ff27237f84841a95c8f65c4e19ffd64849faa540aab48a5ab7 SHA512 
1fb7c96646775c1015267359ed23916abcc21caa3dd3f31e1d78aedb3994ae56d2cb5b79221e90e2b1997a23dc34679fc6863387bd6bdc9d0e006416c402473a
 WHIRLPOOL 
ddd38401dc29535610d7d9a8014aa36b955e1ba0ae6db6ada4ce2151ca323b25134b3cc5635a9e3f06c86b414311c52dab8dd477665fd6ef266087943da4c6de
 DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 
768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 
595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108
 WHIRLPOOL 
43b52943ac3ff40f58863fdfbf588b5f17d6103e2cf2ec09863006da2a288412cc550d47f8c97027904827ccdd5e12a87ec94620d5788273c364276c2f614c6c
 DIST scikit-image-0.12.3.tar.gz 20701373 SHA256 
82da192f0e524701e89c5379c79200bc6dc21373f48bf7778a864c583897d7c7 SHA512 
3a2d51f7b826569e5fc2a4502c62b85559ae9fa0240894af1bb8bd2bad1798b786a2070b1f90b4c07339d8186fe5c118a89994503cce920e8e25fc5f3b51
 WHIRLPOOL 
cfb93cc53612a7b646ec94075a34f501728b18b685968a2f51ea3d00d965c0204f2f567543f1cfa723e54dae90568cda34940cb60790dd4ffc4cac27f718fe23
-DIST scikit-image-0.9.3.tar.gz 7829788 SHA256 
2c29c65aacdfc056efd0a3b713b5dde666356ffb39e5e2bad3e0d6dbb62524b3 SHA512 
4c34a374c19a54da409a99e610b5de7525a0d738f373f5e9ac172c4f2fb520190b61fb30b56db3efd4f62f56e5bbdea6ed2062041171aca56d5fc5ede900
 WHIRLPOOL 
1f7509a857bfb7cc1f7cd3d2251b90ac128f8acf14dc5174be3b0337a1bfdec6326fe6b46ae674bdd50ecf23e82fa8f56f53322d887a0d4b52c0015b1dd189b5

diff --git 
a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1 
b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1
deleted file mode 100644
index 9d8036c..000
--- 
a/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch1
+++ /dev/null
@@ -1,73 +0,0 @@
- 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 b71916f..e878bfb 100644
 a/skimage/exposure/_adapthist.py
-+++ b/skimage/exposure/_adapthist.py
-@@ -255,12 +255,14 @@ 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 265ce24..83bb551 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,

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/

2016-03-18 Thread Sebastien Fabbro 
commit: c754a2c79c0271bc4c6aa8d9ac01d290fd239c39
Author: Sébastien Fabbro  gentoo  org>
AuthorDate: Fri Mar 18 20:09:23 2016 +
Commit: Sebastien Fabbro  gentoo  org>
CommitDate: Fri Mar 18 20:11:05 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c754a2c7

sci-libs/scikits_image: Version bump

Package-Manager: portage-2.2.28

 sci-libs/scikits_image/Manifest|  1 +
 sci-libs/scikits_image/scikits_image-0.12.3.ebuild | 58 ++
 2 files changed, 59 insertions(+)

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 2f1b123..80e89dd 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,4 +1,5 @@
 DIST scikit-image-0.10.0.tar.gz 9084596 SHA256 
83995570f11654b47d0a0d50ae8b4d11a0de97a44ae195a4c04ba4f10b9dd7f8 SHA512 
be45359fe99499e904b0b0e75870cd301947ca1edc7711ce982d107b1e56c0d15cfd59fe8dcc9eff1bca5b1e4bac5ae23e7adeda028590ea1230db76914b0ab8
 WHIRLPOOL 
adeed1d7f6f7b5a5b01c78672226425d481e9dbb69c36f5927274d91856745f472abd8d055c3ad1f880c348d92d5a1bbca9e4253983e7d3aa01ab2f2dfbe29f1
 DIST scikit-image-0.10.1.tar.gz 16740044 SHA256 
83a1afcc16df75ff27237f84841a95c8f65c4e19ffd64849faa540aab48a5ab7 SHA512 
1fb7c96646775c1015267359ed23916abcc21caa3dd3f31e1d78aedb3994ae56d2cb5b79221e90e2b1997a23dc34679fc6863387bd6bdc9d0e006416c402473a
 WHIRLPOOL 
ddd38401dc29535610d7d9a8014aa36b955e1ba0ae6db6ada4ce2151ca323b25134b3cc5635a9e3f06c86b414311c52dab8dd477665fd6ef266087943da4c6de
 DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 
768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 
595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108
 WHIRLPOOL 
43b52943ac3ff40f58863fdfbf588b5f17d6103e2cf2ec09863006da2a288412cc550d47f8c97027904827ccdd5e12a87ec94620d5788273c364276c2f614c6c
+DIST scikit-image-0.12.3.tar.gz 20701373 SHA256 
82da192f0e524701e89c5379c79200bc6dc21373f48bf7778a864c583897d7c7 SHA512 
3a2d51f7b826569e5fc2a4502c62b85559ae9fa0240894af1bb8bd2bad1798b786a2070b1f90b4c07339d8186fe5c118a89994503cce920e8e25fc5f3b51
 WHIRLPOOL 
cfb93cc53612a7b646ec94075a34f501728b18b685968a2f51ea3d00d965c0204f2f567543f1cfa723e54dae90568cda34940cb60790dd4ffc4cac27f718fe23
 DIST scikit-image-0.9.3.tar.gz 7829788 SHA256 
2c29c65aacdfc056efd0a3b713b5dde666356ffb39e5e2bad3e0d6dbb62524b3 SHA512 
4c34a374c19a54da409a99e610b5de7525a0d738f373f5e9ac172c4f2fb520190b61fb30b56db3efd4f62f56e5bbdea6ed2062041171aca56d5fc5ede900
 WHIRLPOOL 
1f7509a857bfb7cc1f7cd3d2251b90ac128f8acf14dc5174be3b0337a1bfdec6326fe6b46ae674bdd50ecf23e82fa8f56f53322d887a0d4b52c0015b1dd189b5

diff --git a/sci-libs/scikits_image/scikits_image-0.12.3.ebuild 
b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
new file mode 100644
index 000..167652d
--- /dev/null
+++ b/sci-libs/scikits_image/scikits_image-0.12.3.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/dask[${PYTHON_USEDEP}]
+   dev-python/matplotlib[${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[${PYTHON_USEDEP}]
+   dev-python/setuptools[${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
+   # 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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/scikits_image/, sci-libs/scikits_image/files/

2015-11-06 Thread Justin Lecher 
commit: 51fc29a0a8be734001b3c829d4791b018dae08b8
Author: Justin Lecher  gentoo  org>
AuthorDate: Fri Nov  6 16:22:16 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Fri Nov  6 16:22:23 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=51fc29a0

sci-libs/scikits_image: Version Bump

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher  gentoo.org>

 sci-libs/scikits_image/Manifest|  1 +
 .../scikits_image-0.11.3-adapthist-backport.patch  | 82 ++
 .../scikits_image-0.11.3-adapthist-backport.patch1 | 73 +++
 sci-libs/scikits_image/scikits_image-0.11.3.ebuild | 63 +
 4 files changed, 219 insertions(+)

diff --git a/sci-libs/scikits_image/Manifest b/sci-libs/scikits_image/Manifest
index 129ffec..2f1b123 100644
--- a/sci-libs/scikits_image/Manifest
+++ b/sci-libs/scikits_image/Manifest
@@ -1,3 +1,4 @@
 DIST scikit-image-0.10.0.tar.gz 9084596 SHA256 
83995570f11654b47d0a0d50ae8b4d11a0de97a44ae195a4c04ba4f10b9dd7f8 SHA512 
be45359fe99499e904b0b0e75870cd301947ca1edc7711ce982d107b1e56c0d15cfd59fe8dcc9eff1bca5b1e4bac5ae23e7adeda028590ea1230db76914b0ab8
 WHIRLPOOL 
adeed1d7f6f7b5a5b01c78672226425d481e9dbb69c36f5927274d91856745f472abd8d055c3ad1f880c348d92d5a1bbca9e4253983e7d3aa01ab2f2dfbe29f1
 DIST scikit-image-0.10.1.tar.gz 16740044 SHA256 
83a1afcc16df75ff27237f84841a95c8f65c4e19ffd64849faa540aab48a5ab7 SHA512 
1fb7c96646775c1015267359ed23916abcc21caa3dd3f31e1d78aedb3994ae56d2cb5b79221e90e2b1997a23dc34679fc6863387bd6bdc9d0e006416c402473a
 WHIRLPOOL 
ddd38401dc29535610d7d9a8014aa36b955e1ba0ae6db6ada4ce2151ca323b25134b3cc5635a9e3f06c86b414311c52dab8dd477665fd6ef266087943da4c6de
+DIST scikit-image-0.11.3.tar.gz 18589296 SHA256 
768e568f3299966c294b7eb8cd114fc648f7bfaef422ee9cc750dd8d9d09e44b SHA512 
595acb66581ed3ca9679b7f031876e1974000a82ec0eccd14bfd283f829aa3db0fcca10166f4260138698f82b3a772fea83d77761a64fab45bbc35418ade7108
 WHIRLPOOL 
43b52943ac3ff40f58863fdfbf588b5f17d6103e2cf2ec09863006da2a288412cc550d47f8c97027904827ccdd5e12a87ec94620d5788273c364276c2f614c6c
 DIST scikit-image-0.9.3.tar.gz 7829788 SHA256 
2c29c65aacdfc056efd0a3b713b5dde666356ffb39e5e2bad3e0d6dbb62524b3 SHA512 
4c34a374c19a54da409a99e610b5de7525a0d738f373f5e9ac172c4f2fb520190b61fb30b56db3efd4f62f56e5bbdea6ed2062041171aca56d5fc5ede900
 WHIRLPOOL 
1f7509a857bfb7cc1f7cd3d2251b90ac128f8acf14dc5174be3b0337a1bfdec6326fe6b46ae674bdd50ecf23e82fa8f56f53322d887a0d4b52c0015b1dd189b5

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
new file mode 100644
index 000..0bd9691
--- /dev/null
+++ b/sci-libs/scikits_image/files/scikits_image-0.11.3-adapthist-backport.patch
@@ -0,0 +1,82 @@
+From 41159f3fd24e7653c556ddbf6ba93ad2aa8b541f Mon Sep 17 00:00:00 2001
+From: Steven Silvester 
+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():
+