sci-visualization/fsleyes: new package

Neuroimaging data viewer

Package-Manager: Portage-2.3.95, Repoman-2.3.21
Signed-off-by: Horea Christian <chr@chymera.eu>

9 files changed, 339 insertions, 0 deletions

diff --git a/sci-visualization/fsleyes/ChangeLog b/sci-visualization/fsleyes/ChangeLog
new file mode 100644
index 000000000..293a171cf
--- /dev/null
+++ b/sci-visualization/fsleyes/ChangeLog
@@ -0,0 +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:
diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest
new file mode 100644
index 000000000..451be541a
--- /dev/null
+++ b/sci-visualization/fsleyes/Manifest
@@ -0,0 +1,2 @@
+DIST fsleyes-0.32.0.tar.gz 87700064 BLAKE2B 654905009490eb5d9c1eeecec0b4b2d3965e32e3935895e64a594655588fe60292a9289a3b78545786e9af4d41aa3069180928b8e8218737010068a1b320805f SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a
+DIST fsleyes-0.32.3.tar.gz 87756679 BLAKE2B 1d094041352ca301fc4574424d73b9dfb49efbf4d7dc69a941a297ba78a267035d62e5f9a384793b52167fb95874ae404103fe0b95f2028e74926286582268ec SHA512 0027f923deac82d7d5f4916716dd46579c9a824d86415896fbb096bcc94cd3eead2f2d754b55d666764783abc9025d6d6f6313d1cee60bd1035348191475dd0f
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch b/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch
new file mode 100644
index 000000000..51392f52e
--- /dev/null
+++ b/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch
@@ -0,0 +1,14 @@
+--- 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.
diff --git a/sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch b/sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch
new file mode 100644
index 000000000..089a8d856
--- /dev/null
+++ b/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
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
new file mode 100644
index 000000000..8b5f2d639
--- /dev/null
+++ b/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)
+ 
+
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
new file mode 100644
index 000000000..828252ec4
--- /dev/null
+++ b/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)
+
+
diff --git a/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild b/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild
new file mode 100644
index 000000000..ee52eee60
--- /dev/null
+++ b/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild
@@ -0,0 +1,79 @@
+# 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
+}
diff --git a/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild b/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild
new file mode 100644
index 000000000..fccfbf936
--- /dev/null
+++ b/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild
@@ -0,0 +1,80 @@
+# 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
+}
diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml
new file mode 100644
index 000000000..153c0c611
--- /dev/null
+++ b/sci-visualization/fsleyes/metadata.xml
@@ -0,0 +1,18 @@
+<?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>