sci-visualization/fsleyes: new package

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Horea Christian <chr@chymera.eu>

sci-visualization/fsleyes/ChangeLog

@@ -1,2 +1,10 @@
+*fsleyes-0.32.0 (24 Jan 2020)
+
+  24 Jan 2020;  <chymera@gentoo.org> +files/fsleyes-0.32.0-coverage.patch,
+  +files/fsleyes-0.32.0-tests_fail.patch,
+  +files/fsleyes-0.32.0-tests_timeout.patch, +fsleyes-0.32.0.ebuild,
+  -fsleyes-0.26.2.ebuild, -fsleyes-0.27.3.ebuild, metadata.xml:
+  sci-visualization/fsleyes: new package
+
   15 Apr 2019;  <chymera@gentoo.org> fsleyes-0.27.3.ebuild:
   sci-visualization/fsleyes:

sci-visualization/fsleyes/Manifest

@@ -1,2 +1 @@
-DIST fsleyes-0.26.2.tar.gz 82646638 SHA256 d702c8905eaadeb38ac5393a0207074c37639f7a74acc4b1f7e04a84bd17b9f6 SHA512 36bb376726f7cafd2b850686230077f1c4d65692c9d76259a3278e2e1e8bec3df86d0a2439262b56f9ab2d10519fddd89cbbfa5b2fd4c218820b10ecebae59d3 WHIRLPOOL 90737e94f1f7fa9d03f93d5946598a55eb6955170ef6b94e2d7cfb30deb0063daaf30cabf6db052ee9c8a78f5535c2cc003b437d4234d04957c6985d203dc2ad
+DIST fsleyes-0.32.0.tar.gz 87700064 SHA256 5e728b265608df8cf1a18ddda8694446e44550b0072884a5bb2bf70cb6489862 SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a WHIRLPOOL 1446c04514dbaf07d86b61c231f56d12433d6f49b1dfafb971d444fca067a7bacd9d1593981b19fcb5f4d503ad736ff2f4a9588514a2851180af632108f3b301
-DIST fsleyes-0.27.3.tar.gz 83243157 SHA256 df7d5c40097962333e182d25179f243920f7f44611a456146ed53b37ade8bdbe SHA512 7a109d656edfa4bd7b4d81867bfdf219169c7066f1bf9c700db092d8b82645b71f334fb790e2893bdc38ea51a3a19ee47fabb57371a01da65e685e886916051c WHIRLPOOL e9a333961a470eb2b4f9ff635d4b8d36dc2087df87f0d14ed5d6c53e0fbff8f9a3affa347e7345d15eb3aee711e3c2d7c7eb3805f6358ec0d7d937fa4db614df

sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch

@@ -0,0 +1,13 @@
+diff --git a/setup.cfg b/setup.cfg
+index fcb594a..dccad97 100644
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -9,7 +9,7 @@ ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
+ 
+ [tool:pytest]
+ testpaths = tests
+-addopts   = -v --cov=fsleyes
++addopts   = -v
+ markers   =
+   overlayclitest: Overlay scene test invoked via FSLeyes command line
+   clitest:        Test invoked via FSLeyes command line

sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch

@@ -0,0 +1,62 @@
+diff --git a/tests/actions/test_copyoverlay.py b/tests/actions/test_copyoverlay.py
+index 3509ba6..371813e 100644
+--- a/tests/actions/test_copyoverlay.py
++++ b/tests/actions/test_copyoverlay.py
+@@ -19,7 +19,11 @@ import fsleyes.actions.copyoverlay as copyoverlay
+ 
+ from .. import run_with_orthopanel, realYield
+ 
++import pytest
+ 
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_copyImage_3d():
+     run_with_orthopanel(_test_copyImage_3d)
+ def _test_copyImage_3d(panel, overlayList, displayCtx):
+@@ -103,7 +107,9 @@ def _test_copyImage_3d(panel, overlayList, displayCtx):
+     assert np.all(copy[5:25, 5:25, 5:25] == img3d[:, :, :])
+     overlayList.remove(copy)
+ 
+-
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_copyImage_4d():
+     run_with_orthopanel(_test_copyImage_4d)
+ def _test_copyImage_4d(panel, overlayList, displayCtx):
+@@ -220,6 +226,9 @@ def make_rgb():
+     return fslimage.Image(rgb, xform=np.eye(4))
+ 
+ 
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_copyImage_multiValued():
+     run_with_orthopanel(_test_copyImage_multiValued)
+ def _test_copyImage_multiValued(panel, overlayList, displayCtx):
+@@ -281,6 +290,9 @@ def _test_copyImage_multiValued(panel, overlayList, displayCtx):
+     overlayList.remove(copy)
+ 
+ 
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_CopyOverlayAction():
+     run_with_orthopanel(_test_CopyOverlayAction)
+ def _test_CopyOverlayAction(panel, overlayList, displayCtx):
+diff --git a/tests/actions/test_newimage.py b/tests/actions/test_newimage.py
+index cfd6b5a..e9c2ff8 100644
+--- a/tests/actions/test_newimage.py
++++ b/tests/actions/test_newimage.py
+@@ -82,6 +82,9 @@ def test_newImage():
+     assert        img.name          == 'whaa'
+ 
+ 
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_NewImageAction():
+     run_with_orthopanel(_test_NewImageAction)
+ 
+

sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch

@@ -0,0 +1,61 @@
+diff --git a/tests/actions/test_newimage.py b/tests/actions/test_newimage.py
+index a7d159e4..7bc76fb0 100644
+--- a/tests/actions/test_newimage.py
++++ b/tests/actions/test_newimage.py
+@@ -16,6 +16,7 @@ import fsl.transform.affine as fslaffine
+ import fsleyes.actions.newimage as newimage
+ from .. import run_with_fsleyes, run_with_orthopanel, realYield
+ 
++import pytest
+ 
+ class MockNewImageDialog(object):
+     initOverride = False
+@@ -121,7 +122,9 @@ def _test_NewImageAction(panel, overlayList, displayCtx):
+             overlayList.clear()
+             realYield()
+ 
+-
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_NewImageAction_existing():
+     run_with_orthopanel(_test_NewImageAction_existing)
+
+@@ -156,7 +156,9 @@ def _test_NewImageAction_existing(panel, overlayList, displayCtx):
+         assert old.sameSpace(new)
+         assert new.dtype == np.int32
+
+-
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_NewImageDialog():
+     run_with_fsleyes(_test_NewImageDialog)
+
+diff --git a/tests/actions/test_resample.py b/tests/actions/test_resample.py
+index e883002c..ae1741cc 100644
+--- a/tests/actions/test_resample.py
++++ b/tests/actions/test_resample.py
+@@ -25,7 +25,11 @@ from .. import (run_with_fsleyes,
+                 simtext,
+                 simclick)
+
++import pytest
+
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_resample():
+     run_with_orthopanel(_test_resample)
+
+@@ -132,6 +136,9 @@ def _test_resample(panel, overlayList, displayCtx):
+
+
+
++@pytest.mark.skip(reason="Known to fail on Gentoo:"
++    "https://github.com/pauldmccarthy/fsleyes/issues/38"
++    )
+ def test_ResampleDialog():
+     run_with_fsleyes(_test_ResampleDialog)
+
+

sci-visualization/fsleyes/fsleyes-0.26.2.ebuild

@@ -1,87 +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_5,3_6} )
-
-inherit distutils-r1 gnome2-utils virtualx
-
-MY_HASH="bfc2c0919b68583b6237cbdd9492e69a7bed30189b19dd21f7ba59f9f39e"
-
-DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
-HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
-SRC_URI="
-	https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz
-	https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz
-	"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/mock[${PYTHON_USEDEP}]
-		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-
-RDEPEND="
-	dev-python/fslpy[${PYTHON_USEDEP}]
-	=dev-python/jinja-2*[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
-	>=dev-python/pillow-3.4.2[${PYTHON_USEDEP}]
-	>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
-	>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
-	=dev-python/pyparsing-2*[${PYTHON_USEDEP}]
-	=dev-python/six-1*[${PYTHON_USEDEP}]
-	>=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}]
-	>=sci-libs/scipy-0.18[${PYTHON_USEDEP}]
-	=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
-	sci-visualization/fsleyes-widgets[${PYTHON_USEDEP}]
-	sci-visualization/fsleyes-props[${PYTHON_USEDEP}]
-	"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
-	)
-
-src_prepare() {
-	sed -i -e "s/Pillow>=3.2.0,<5.0/Pillow>=3.2.0/g" requirements.txt
-	distutils-r1_src_prepare
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-	doicon userdoc/images/fsleyes_icon.png
-	local size
-	for size in 16 32 128 256 512 ; do
-		doicon -s ${size} assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png
-	done
-	make_desktop_entry fsleyes FSLeyes /usr/share/icons/hicolor/128x128/apps/icon_128x128.png
-}
-
-pkg_postinst() {
-	gnome2_icon_cache_update
-}
-pkg_postrm() {
-	gnome2_icon_cache_update
-}
-
-python_test() {
-	rm tests/test_addmaskdataseries.py
-	rm tests/test_embed.py
-	rm tests/test_overlay_displayprops.py
-	rm tests/test_overlay_freesurfermesh.py
-	rm tests/test_overlay_giftimesh.py
-	rm tests/test_screenshot.py
-	rm tests/test_state.py
-	rm tests/test_views.py
-	virtx pytest -v || die
-}

sci-visualization/fsleyes/fsleyes-0.32.0.ebuild

@@ -1,13 +1,11 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python{2_7,3_5,3_6} )
+PYTHON_COMPAT=( python3_6 )
 
-inherit distutils-r1 gnome2-utils virtualx
+inherit distutils-r1 desktop virtualx
-
-MY_HASH="bfc2c0919b68583b6237cbdd9492e69a7bed30189b19dd21f7ba59f9f39e"
 
 DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
 HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
@@ -26,7 +24,6 @@ DEPEND="
 		${RDEPEND}
 		dev-python/mock[${PYTHON_USEDEP}]
 		dev-python/pytest[${PYTHON_USEDEP}]
-		dev-python/pytest-cov[${PYTHON_USEDEP}]
 		)
 	dev-python/setuptools[${PYTHON_USEDEP}]
 	"
@@ -48,12 +45,11 @@ RDEPEND="
 	sci-visualization/fsleyes-props[${PYTHON_USEDEP}]
 	"
 
-# Tests fail
-# https://github.com/pauldmccarthy/fsleyes/issues/14#issuecomment-477191925
-#RESTRICT="test"
-
 PATCHES=(
 	"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
+	"${FILESDIR}/${PN}-0.32.0-coverage.patch"
+	"${FILESDIR}/${PN}-0.32.0-tests_timeout.patch"
+	"${FILESDIR}/${PN}-0.32.0-tests_fail.patch"
 	)
 
 src_prepare() {
@@ -79,9 +75,5 @@ pkg_postrm() {
 }
 
 python_test() {
-	rm tests/test_addmaskdataseries.py
-	rm tests/test_embed.py
-	rm tests/test_overlay_displayprops.py
-	rm tests/test_resample.py
 	virtx pytest -vv || die
 }

sci-visualization/fsleyes/metadata.xml

@@ -2,7 +2,7 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 	<maintainer type="person">
-		<email>horea.christ@gmail.com</email>
+		<email>chr@chymera.eu</email>
 		<name>Horea Christian</name>
 	</maintainer>
 	<maintainer type="project">