diff options
Diffstat (limited to 'sci-visualization')
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 +} |