diff --git a/sci-visualization/fsleyes/ChangeLog b/sci-visualization/fsleyes/ChangeLog index a461ea9..293a171 100644 --- a/sci-visualization/fsleyes/ChangeLog +++ b/sci-visualization/fsleyes/ChangeLog @@ -1,2 +1,10 @@ +*fsleyes-0.32.0 (24 Jan 2020) + + 24 Jan 2020; +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; fsleyes-0.27.3.ebuild: sci-visualization/fsleyes: diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest index 67f98aa..5258d5e 100644 --- a/sci-visualization/fsleyes/Manifest +++ b/sci-visualization/fsleyes/Manifest @@ -1,2 +1 @@ -DIST fsleyes-0.26.2.tar.gz 82646638 SHA256 d702c8905eaadeb38ac5393a0207074c37639f7a74acc4b1f7e04a84bd17b9f6 SHA512 36bb376726f7cafd2b850686230077f1c4d65692c9d76259a3278e2e1e8bec3df86d0a2439262b56f9ab2d10519fddd89cbbfa5b2fd4c218820b10ecebae59d3 WHIRLPOOL 90737e94f1f7fa9d03f93d5946598a55eb6955170ef6b94e2d7cfb30deb0063daaf30cabf6db052ee9c8a78f5535c2cc003b437d4234d04957c6985d203dc2ad -DIST fsleyes-0.27.3.tar.gz 83243157 SHA256 df7d5c40097962333e182d25179f243920f7f44611a456146ed53b37ade8bdbe SHA512 7a109d656edfa4bd7b4d81867bfdf219169c7066f1bf9c700db092d8b82645b71f334fb790e2893bdc38ea51a3a19ee47fabb57371a01da65e685e886916051c WHIRLPOOL e9a333961a470eb2b4f9ff635d4b8d36dc2087df87f0d14ed5d6c53e0fbff8f9a3affa347e7345d15eb3aee711e3c2d7c7eb3805f6358ec0d7d937fa4db614df +DIST fsleyes-0.32.0.tar.gz 87700064 SHA256 5e728b265608df8cf1a18ddda8694446e44550b0072884a5bb2bf70cb6489862 SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a WHIRLPOOL 1446c04514dbaf07d86b61c231f56d12433d6f49b1dfafb971d444fca067a7bacd9d1593981b19fcb5f4d503ad736ff2f4a9588514a2851180af632108f3b301 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 0000000..089a8d8 --- /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 0000000..8b5f2d6 --- /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 0000000..828252e --- /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-0.26.2.ebuild b/sci-visualization/fsleyes/fsleyes-0.26.2.ebuild deleted file mode 100644 index 9c0d9f5..0000000 --- a/sci-visualization/fsleyes/fsleyes-0.26.2.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) - -inherit distutils-r1 gnome2-utils virtualx - -MY_HASH="bfc2c0919b68583b6237cbdd9492e69a7bed30189b19dd21f7ba59f9f39e" - -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[${PYTHON_USEDEP}] - dev-python/pytest-cov[${PYTHON_USEDEP}] - ) - dev-python/setuptools[${PYTHON_USEDEP}] - " - -RDEPEND=" - dev-python/fslpy[${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" - ) - -src_prepare() { - sed -i -e "s/Pillow>=3.2.0,<5.0/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() { - rm tests/test_addmaskdataseries.py - rm tests/test_embed.py - rm tests/test_overlay_displayprops.py - rm tests/test_overlay_freesurfermesh.py - rm tests/test_overlay_giftimesh.py - rm tests/test_screenshot.py - rm tests/test_state.py - rm tests/test_views.py - virtx pytest -v || die -} diff --git a/sci-visualization/fsleyes/fsleyes-0.27.3.ebuild b/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild similarity index 79% rename from sci-visualization/fsleyes/fsleyes-0.27.3.ebuild rename to sci-visualization/fsleyes/fsleyes-0.32.0.ebuild index 20813a8..ee52eee 100644 --- a/sci-visualization/fsleyes/fsleyes-0.27.3.ebuild +++ b/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild @@ -1,13 +1,11 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -PYTHON_COMPAT=( python{2_7,3_5,3_6} ) +PYTHON_COMPAT=( python3_6 ) -inherit distutils-r1 gnome2-utils virtualx - -MY_HASH="bfc2c0919b68583b6237cbdd9492e69a7bed30189b19dd21f7ba59f9f39e" +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" @@ -26,7 +24,6 @@ DEPEND=" ${RDEPEND} dev-python/mock[${PYTHON_USEDEP}] dev-python/pytest[${PYTHON_USEDEP}] - dev-python/pytest-cov[${PYTHON_USEDEP}] ) dev-python/setuptools[${PYTHON_USEDEP}] " @@ -48,12 +45,11 @@ RDEPEND=" sci-visualization/fsleyes-props[${PYTHON_USEDEP}] " -# Tests fail -# https://github.com/pauldmccarthy/fsleyes/issues/14#issuecomment-477191925 -#RESTRICT="test" - 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() { @@ -79,9 +75,5 @@ pkg_postrm() { } python_test() { - rm tests/test_addmaskdataseries.py - rm tests/test_embed.py - rm tests/test_overlay_displayprops.py - rm tests/test_resample.py virtx pytest -vv || die } diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml index 1e458f8..153c0c6 100644 --- a/sci-visualization/fsleyes/metadata.xml +++ b/sci-visualization/fsleyes/metadata.xml @@ -2,7 +2,7 @@ - horea.christ@gmail.com + chr@chymera.eu Horea Christian