sci-visualization/fsleyes: bump to 1.3.3

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

7 files changed, 66 insertions, 306 deletions

diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest
index 2e3051aae..776a7e0ee 100644
--- a/sci-visualization/fsleyes/Manifest
+++ b/sci-visualization/fsleyes/Manifest
@@ -1,2 +1 @@
-DIST fsleyes-0.32.3.tar.gz 87756679 BLAKE2B 1d094041352ca301fc4574424d73b9dfb49efbf4d7dc69a941a297ba78a267035d62e5f9a384793b52167fb95874ae404103fe0b95f2028e74926286582268ec SHA512 0027f923deac82d7d5f4916716dd46579c9a824d86415896fbb096bcc94cd3eead2f2d754b55d666764783abc9025d6d6f6313d1cee60bd1035348191475dd0f
-DIST fsleyes-0.34.2.tar.gz 88940639 BLAKE2B 33b942f7f0873ebd3749c75a3a1926e4596d85d6c600a66c4fc5878e570315fa003f6e2124b0b9de79637a8298550e37365607867a52cd516ca1d0c301f6945d SHA512 9fdd87e54922a34c5eea71b47abed8cdd69749a94b15cc7d583f9608bdec78021ba08988206545eee9072ad328bbef32b15f6f984a0343fb808553c6b47ea4e4
+DIST fsleyes-1.3.3.tar.gz 91819897 BLAKE2B dde5d4f4831b1fe856c3f6a5eae438cab6570954ab3b11ba6d654fc1ffcbd44bca012c53f4b36bc7fa05a090144b249dea541f5b22147c105c35f01bf14517cf SHA512 a1ce870d88442be3f168e84c3cdc8d468b8a9751a20e2bee33755ef5712f82538e420e94b65ab0a9db3fa2bf91b8630a9868d550c7ee0dad9ff6a8a6c390a122
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch b/sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch
deleted file mode 100644
index 089a8d856..000000000
--- a/sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch
+++ /dev/null
@@ -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
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch b/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch
deleted file mode 100644
index 8b5f2d639..000000000
--- a/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch
+++ /dev/null
@@ -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)
- 
-
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch b/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch
deleted file mode 100644
index 828252ec4..000000000
--- a/sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch
+++ /dev/null
@@ -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)
-
-
diff --git a/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild b/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild
deleted file mode 100644
index 5c98f015d..000000000
--- a/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-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}]
-	>=dev-python/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
-}
diff --git a/sci-visualization/fsleyes/fsleyes-0.34.2.ebuild b/sci-visualization/fsleyes/fsleyes-0.34.2.ebuild
deleted file mode 100644
index 36533c5a8..000000000
--- a/sci-visualization/fsleyes/fsleyes-0.34.2.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-
-inherit xdg 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"
-# hard masked dependency  >=dev-python/fslpy-3.1
-KEYWORDS=""
-
-DEPEND="
-	test? (
-		${RDEPEND}
-		dev-python/mock[${PYTHON_USEDEP}]
-		)
-	"
-
-RDEPEND="
-	>=dev-python/fslpy-3.1[${PYTHON_USEDEP}]
-	=dev-python/jinja-2*[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
-	>=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
-	>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
-	>=dev-python/pyopengl-3.1.0[${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}]
-	>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
-	>=sci-libs/nibabel-2.3[${PYTHON_USEDEP}]
-	>=sci-visualization/fsleyes-widgets-0.8.4[${PYTHON_USEDEP}]
-	>=sci-visualization/fsleyes-props-1.6.7[${PYTHON_USEDEP}]
-	"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
-	"${FILESDIR}/${PN}-0.32.0-tests_timeout.patch"
-	"${FILESDIR}/${PN}-0.32.0-tests_fail.patch"
-	)
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
-	# do not depend on pytest-cov
-	sed -i -e '/addopts/d' setup.cfg || die
-
-	# Fatal Python error: Segmentation fault
-	sed -i -e 's:test_crop:_&:' \
-		tests/test_ortho_cropmode.py || die
-	sed -i -e 's:test_fillSelection:_&:' \
-		tests/test_ortho_editmode.py || die
-
-	# KeyError: 'Unknown atlas ID: harvardoxford-cortical'
-	sed -i -e 's:test_atlaspanel_toggleOverlay:_&:' \
-		tests/test_atlaspanel.py || die
-
-	# This hangs forever
-	sed -i -e 's:test_lightbox:_&:' \
-		tests/test_layouts.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-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
-		newicon -s ${size} assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png "${PN}.png"
-	done
-	make_desktop_entry fsleyes FSLeyes "${PN}"
-}
-
-python_test() {
-	virtx pytest -vv || die
-}
diff --git a/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild b/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild
new file mode 100644
index 000000000..ac86c16fd
--- /dev/null
+++ b/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit xdg 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 -> ${P}.tar.gz
+"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=dev-python/fslpy-3.6[${PYTHON_USEDEP}]
+	>=dev-python/jinja-2[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
+	>=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
+	>=dev-python/pillow-3.2.0[${PYTHON_USEDEP}]
+	>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
+	>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
+	=dev-python/pyparsing-2*[${PYTHON_USEDEP}]
+	>=dev-python/wxpython-4[${PYTHON_USEDEP}]
+	>=dev-python/scipy-0.18[${PYTHON_USEDEP}]
+	>=sci-libs/nibabel-2.3[${PYTHON_USEDEP}]
+	>=sci-visualization/fsleyes-widgets-0.12[${PYTHON_USEDEP}]
+	>=sci-visualization/fsleyes-props-1.7.2[${PYTHON_USEDEP}]
+	"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
+)
+
+distutils_enable_tests pytest
+distutils_enable_sphinx userdoc dev-python/sphinx_rtd_theme
+
+python_prepare_all() {
+	# do not depend on pytest-cov
+	sed -i -e '/addopts/d' setup.cfg || die
+
+	distutils-r1_python_prepare_all
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+	doicon -s 48 fsleyes/assets/linux/hicolor/48x48/apps/*.png
+	domenu fsleyes/assets/linux/*.desktop
+	insinto /usr/share/metainfo
+	doins fsleyes/assets/linux/*.appdata.xml
+	local size
+	for size in 16 32 128 256 512 ; do
+		newicon -s ${size} fsleyes/assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png "${PN}.png"
+	done
+}
+
+python_test() {
+	virtx epytest
+}