sci-visualization/fsleyes: Superseded by Gentoo Science
This commit is contained in:
Horea Christian
parent
50af288bac
commit
e006dcb24b
@ -1,15 +0,0 @@
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*fsleyes-0.32.3 (25 Mar 2020)
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25 Mar 2020; <chymera@gentoo.org> +fsleyes-0.32.3.ebuild:
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sci-visualization/fsleyes: version bump 0.32.3
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*fsleyes-0.32.0 (24 Jan 2020)
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24 Jan 2020; <chymera@gentoo.org> +files/fsleyes-0.32.0-coverage.patch,
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+files/fsleyes-0.32.0-tests_fail.patch,
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+files/fsleyes-0.32.0-tests_timeout.patch, +fsleyes-0.32.0.ebuild,
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-fsleyes-0.26.2.ebuild, -fsleyes-0.27.3.ebuild, metadata.xml:
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sci-visualization/fsleyes: new package
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15 Apr 2019; <chymera@gentoo.org> fsleyes-0.27.3.ebuild:
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sci-visualization/fsleyes:
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@ -1,2 +0,0 @@
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DIST fsleyes-0.32.0.tar.gz 87700064 SHA256 5e728b265608df8cf1a18ddda8694446e44550b0072884a5bb2bf70cb6489862 SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a WHIRLPOOL 1446c04514dbaf07d86b61c231f56d12433d6f49b1dfafb971d444fca067a7bacd9d1593981b19fcb5f4d503ad736ff2f4a9588514a2851180af632108f3b301
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DIST fsleyes-0.32.3.tar.gz 87756679 SHA256 06df776bcca0e6457817132c86a3140edccc5c6f94ff8cfc2b9f54385ad4d394 SHA512 0027f923deac82d7d5f4916716dd46579c9a824d86415896fbb096bcc94cd3eead2f2d754b55d666764783abc9025d6d6f6313d1cee60bd1035348191475dd0f WHIRLPOOL f64a91ebc0e08094725faa311209f8ffb3e507b96808a17966aaf7664e30be7363a6133e05afcf0b958a6d9f3d0ad96b7a164a15bc65462a2875e4114e2dd37d
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@ -1,14 +0,0 @@
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--- a/fsleyes/main.py 2018-09-24 17:46:07.756686411 +0200
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+++ b/fsleyes/main.py 2018-10-06 14:36:53.328135230 +0200
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@@ -325,11 +325,6 @@
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app.SetTopWindow(frame)
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frame.Show()
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- # Check that $FSLDIR is set, complain
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- # to the user if it isn't
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- if not namespace[0].skipfslcheck:
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- wx.CallAfter(fslDirWarning, frame)
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-
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# Check for updates. Ignore point
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# releases, otherwise users might
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# get swamped with update notifications.
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@ -1,13 +0,0 @@
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diff --git a/setup.cfg b/setup.cfg
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index fcb594a..dccad97 100644
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--- a/setup.cfg
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+++ b/setup.cfg
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@@ -9,7 +9,7 @@ ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504
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[tool:pytest]
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testpaths = tests
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-addopts = -v --cov=fsleyes
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+addopts = -v
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markers =
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overlayclitest: Overlay scene test invoked via FSLeyes command line
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clitest: Test invoked via FSLeyes command line
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@ -1,62 +0,0 @@
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diff --git a/tests/actions/test_copyoverlay.py b/tests/actions/test_copyoverlay.py
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index 3509ba6..371813e 100644
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--- a/tests/actions/test_copyoverlay.py
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+++ b/tests/actions/test_copyoverlay.py
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@@ -19,7 +19,11 @@ import fsleyes.actions.copyoverlay as copyoverlay
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from .. import run_with_orthopanel, realYield
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+import pytest
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_copyImage_3d():
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run_with_orthopanel(_test_copyImage_3d)
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def _test_copyImage_3d(panel, overlayList, displayCtx):
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@@ -103,7 +107,9 @@ def _test_copyImage_3d(panel, overlayList, displayCtx):
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assert np.all(copy[5:25, 5:25, 5:25] == img3d[:, :, :])
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overlayList.remove(copy)
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-
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_copyImage_4d():
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run_with_orthopanel(_test_copyImage_4d)
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def _test_copyImage_4d(panel, overlayList, displayCtx):
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@@ -220,6 +226,9 @@ def make_rgb():
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return fslimage.Image(rgb, xform=np.eye(4))
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_copyImage_multiValued():
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run_with_orthopanel(_test_copyImage_multiValued)
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def _test_copyImage_multiValued(panel, overlayList, displayCtx):
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@@ -281,6 +290,9 @@ def _test_copyImage_multiValued(panel, overlayList, displayCtx):
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overlayList.remove(copy)
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_CopyOverlayAction():
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run_with_orthopanel(_test_CopyOverlayAction)
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def _test_CopyOverlayAction(panel, overlayList, displayCtx):
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diff --git a/tests/actions/test_newimage.py b/tests/actions/test_newimage.py
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index cfd6b5a..e9c2ff8 100644
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--- a/tests/actions/test_newimage.py
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+++ b/tests/actions/test_newimage.py
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@@ -82,6 +82,9 @@ def test_newImage():
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assert img.name == 'whaa'
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_NewImageAction():
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run_with_orthopanel(_test_NewImageAction)
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@ -1,61 +0,0 @@
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diff --git a/tests/actions/test_newimage.py b/tests/actions/test_newimage.py
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index a7d159e4..7bc76fb0 100644
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--- a/tests/actions/test_newimage.py
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+++ b/tests/actions/test_newimage.py
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@@ -16,6 +16,7 @@ import fsl.transform.affine as fslaffine
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import fsleyes.actions.newimage as newimage
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from .. import run_with_fsleyes, run_with_orthopanel, realYield
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+import pytest
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class MockNewImageDialog(object):
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initOverride = False
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@@ -121,7 +122,9 @@ def _test_NewImageAction(panel, overlayList, displayCtx):
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overlayList.clear()
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realYield()
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-
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_NewImageAction_existing():
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run_with_orthopanel(_test_NewImageAction_existing)
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@@ -156,7 +156,9 @@ def _test_NewImageAction_existing(panel, overlayList, displayCtx):
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assert old.sameSpace(new)
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assert new.dtype == np.int32
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-
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_NewImageDialog():
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run_with_fsleyes(_test_NewImageDialog)
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diff --git a/tests/actions/test_resample.py b/tests/actions/test_resample.py
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index e883002c..ae1741cc 100644
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--- a/tests/actions/test_resample.py
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+++ b/tests/actions/test_resample.py
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@@ -25,7 +25,11 @@ from .. import (run_with_fsleyes,
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simtext,
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simclick)
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+import pytest
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_resample():
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run_with_orthopanel(_test_resample)
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@@ -132,6 +136,9 @@ def _test_resample(panel, overlayList, displayCtx):
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+@pytest.mark.skip(reason="Known to fail on Gentoo:"
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+ "https://github.com/pauldmccarthy/fsleyes/issues/38"
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+ )
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def test_ResampleDialog():
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run_with_fsleyes(_test_ResampleDialog)
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@ -1,79 +0,0 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_6 )
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inherit distutils-r1 desktop virtualx
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DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
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HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
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SRC_URI="
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https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz
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https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz
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"
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LICENSE="Apache-2.0"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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DEPEND="
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test? (
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${RDEPEND}
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dev-python/mock[${PYTHON_USEDEP}]
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dev-python/pytest[${PYTHON_USEDEP}]
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)
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dev-python/setuptools[${PYTHON_USEDEP}]
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"
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RDEPEND="
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>=dev-python/fslpy-1.13.2[${PYTHON_USEDEP}]
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=dev-python/jinja-2*[${PYTHON_USEDEP}]
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>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
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>=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
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>=dev-python/pillow-3.4.2[${PYTHON_USEDEP}]
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>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
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>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
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=dev-python/pyparsing-2*[${PYTHON_USEDEP}]
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=dev-python/six-1*[${PYTHON_USEDEP}]
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>=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}]
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>=sci-libs/scipy-0.18[${PYTHON_USEDEP}]
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=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
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sci-visualization/fsleyes-widgets[${PYTHON_USEDEP}]
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sci-visualization/fsleyes-props[${PYTHON_USEDEP}]
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"
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PATCHES=(
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"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
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"${FILESDIR}/${PN}-0.32.0-coverage.patch"
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"${FILESDIR}/${PN}-0.32.0-tests_timeout.patch"
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"${FILESDIR}/${PN}-0.32.0-tests_fail.patch"
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)
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src_prepare() {
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sed -i -e "s/Pillow>=3.2.0,<6.0/Pillow>=3.2.0/g" requirements.txt
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distutils-r1_src_prepare
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}
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python_install_all() {
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distutils-r1_python_install_all
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doicon userdoc/images/fsleyes_icon.png
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local size
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for size in 16 32 128 256 512 ; do
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doicon -s ${size} assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png
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done
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make_desktop_entry fsleyes FSLeyes /usr/share/icons/hicolor/128x128/apps/icon_128x128.png
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}
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pkg_postinst() {
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gnome2_icon_cache_update
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}
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pkg_postrm() {
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gnome2_icon_cache_update
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}
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python_test() {
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virtx pytest -vv || die
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}
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@ -1,80 +0,0 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{6,7} )
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inherit distutils-r1 desktop virtualx
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DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10"
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HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master"
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SRC_URI="
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https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz
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https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz
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"
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LICENSE="Apache-2.0"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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DEPEND="
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test? (
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${RDEPEND}
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dev-python/mock[${PYTHON_USEDEP}]
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dev-python/pytest[${PYTHON_USEDEP}]
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)
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dev-python/setuptools[${PYTHON_USEDEP}]
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"
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RDEPEND="
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>=dev-python/fslpy-1.13.2[${PYTHON_USEDEP}]
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=dev-python/jinja-2*[${PYTHON_USEDEP}]
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>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
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>=dev-python/numpy-1.14.0[${PYTHON_USEDEP}]
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>=dev-python/pillow-3.4.2[${PYTHON_USEDEP}]
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>=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}]
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>=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}]
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=dev-python/pyparsing-2*[${PYTHON_USEDEP}]
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=dev-python/six-1*[${PYTHON_USEDEP}]
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>=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}]
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>=sci-libs/scipy-0.18[${PYTHON_USEDEP}]
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sci-libs/nibabel[${PYTHON_USEDEP}]
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sci-visualization/fsleyes-widgets[${PYTHON_USEDEP}]
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sci-visualization/fsleyes-props[${PYTHON_USEDEP}]
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"
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#=sci-libs/nibabel-2*[${PYTHON_USEDEP}]
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PATCHES=(
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"${FILESDIR}/${PN}-0.26.2-fsldir.patch"
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"${FILESDIR}/${PN}-0.32.0-coverage.patch"
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"${FILESDIR}/${PN}-0.32.0-tests_timeout.patch"
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"${FILESDIR}/${PN}-0.32.0-tests_fail.patch"
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)
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src_prepare() {
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sed -i -e "s/Pillow>=3.2.0,<6.0/Pillow>=3.2.0/g" requirements.txt
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distutils-r1_src_prepare
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}
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python_install_all() {
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distutils-r1_python_install_all
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doicon userdoc/images/fsleyes_icon.png
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local size
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for size in 16 32 128 256 512 ; do
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doicon -s ${size} assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png
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done
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make_desktop_entry fsleyes FSLeyes /usr/share/icons/hicolor/128x128/apps/icon_128x128.png
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}
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pkg_postinst() {
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gnome2_icon_cache_update
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}
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pkg_postrm() {
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gnome2_icon_cache_update
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}
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python_test() {
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virtx pytest -vv || die
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}
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@ -1,18 +0,0 @@
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<?xml version='1.0' encoding='UTF-8'?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>chr@chymera.eu</email>
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<name>Horea Christian</name>
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</maintainer>
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<maintainer type="project">
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<email>sci@gentoo.org</email>
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<name>Gentoo Science Project</name>
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</maintainer>
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<longdescription lang="en">
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FSLeyes is a viewer for 3D and 4D neuroimaging data. It is intended as a
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replacement for the much loved FSLView. FSLeyes offers similar functionality
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to FSLView, and aims to improve and expand upon this functionality in many
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ways.
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</longdescription>
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</pkgmetadata>
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