sci-visualization/fsleyes: Superseded by Gentoo Science

sci-visualization/fsleyes/ChangeLog

@@ -1,15 +0,0 @@
-*fsleyes-0.32.3 (25 Mar 2020)
-
-  25 Mar 2020;  <chymera@gentoo.org> +fsleyes-0.32.3.ebuild:
-  sci-visualization/fsleyes: version bump 0.32.3
-
-*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 +0,0 @@
-DIST fsleyes-0.32.0.tar.gz 87700064 SHA256 5e728b265608df8cf1a18ddda8694446e44550b0072884a5bb2bf70cb6489862 SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a WHIRLPOOL 1446c04514dbaf07d86b61c231f56d12433d6f49b1dfafb971d444fca067a7bacd9d1593981b19fcb5f4d503ad736ff2f4a9588514a2851180af632108f3b301
-DIST fsleyes-0.32.3.tar.gz 87756679 SHA256 06df776bcca0e6457817132c86a3140edccc5c6f94ff8cfc2b9f54385ad4d394 SHA512 0027f923deac82d7d5f4916716dd46579c9a824d86415896fbb096bcc94cd3eead2f2d754b55d666764783abc9025d6d6f6313d1cee60bd1035348191475dd0f WHIRLPOOL f64a91ebc0e08094725faa311209f8ffb3e507b96808a17966aaf7664e30be7363a6133e05afcf0b958a6d9f3d0ad96b7a164a15bc65462a2875e4114e2dd37d

sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch

@@ -1,14 +0,0 @@
---- a/fsleyes/main.py	2018-09-24 17:46:07.756686411 +0200
-+++ b/fsleyes/main.py	2018-10-06 14:36:53.328135230 +0200
-@@ -325,11 +325,6 @@
-         app.SetTopWindow(frame)
-         frame.Show()
- 
--        # Check that $FSLDIR is set, complain
--        # to the user if it isn't
--        if not namespace[0].skipfslcheck:
--            wx.CallAfter(fslDirWarning, frame)
--
-         # Check for updates. Ignore point
-         # releases, otherwise users might
-         # get swamped with update notifications.

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

@@ -1,13 +0,0 @@
-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

@@ -1,62 +0,0 @@
-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

@@ -1,61 +0,0 @@
-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-0.32.0.ebuild

@@ -1,79 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_6 )
-
-inherit distutils-r1 desktop virtualx
-
-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[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-
-RDEPEND="
-	>=dev-python/fslpy-1.13.2[${PYTHON_USEDEP}]
-	=dev-python/jinja-2*[${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"
-	"${FILESDIR}/${PN}-0.32.0-coverage.patch"
-	"${FILESDIR}/${PN}-0.32.0-tests_timeout.patch"
-	"${FILESDIR}/${PN}-0.32.0-tests_fail.patch"
-	)
-
-src_prepare() {
-	sed -i -e "s/Pillow>=3.2.0,<6.0/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() {
-	virtx pytest -vv || die
-}

sci-visualization/fsleyes/fsleyes-0.32.3.ebuild

@@ -1,80 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6,7} )
-
-inherit distutils-r1 desktop virtualx
-
-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[${PYTHON_USEDEP}]
-		)
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	"
-
-RDEPEND="
-	>=dev-python/fslpy-1.13.2[${PYTHON_USEDEP}]
-	=dev-python/jinja-2*[${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[${PYTHON_USEDEP}]
-	sci-libs/nibabel[${PYTHON_USEDEP}]
-	sci-visualization/fsleyes-widgets[${PYTHON_USEDEP}]
-	sci-visualization/fsleyes-props[${PYTHON_USEDEP}]
-	"
-#=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
-
-PATCHES=(
-	"${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() {
-	sed -i -e "s/Pillow>=3.2.0,<6.0/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() {
-	virtx pytest -vv || die
-}

sci-visualization/fsleyes/metadata.xml

@@ -1,18 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>chr@chymera.eu</email>
-		<name>Horea Christian</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		FSLeyes is a viewer for 3D and 4D neuroimaging data. It is intended as a
-		replacement for the much loved FSLView. FSLeyes offers similar functionality
-		to FSLView, and aims to improve and expand upon this functionality in many
-		ways.
-	</longdescription>
-</pkgmetadata>