From e006dcb24b0fc17ae09111ce5a01006dd5425226 Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Thu, 17 Sep 2020 12:25:25 -0400 Subject: [PATCH] sci-visualization/fsleyes: Superseded by Gentoo Science --- sci-visualization/fsleyes/ChangeLog | 15 ---- sci-visualization/fsleyes/Manifest | 2 - .../fsleyes/files/fsleyes-0.26.2-fsldir.patch | 14 ---- .../files/fsleyes-0.32.0-coverage.patch | 13 --- .../files/fsleyes-0.32.0-tests_fail.patch | 62 -------------- .../files/fsleyes-0.32.0-tests_timeout.patch | 61 -------------- .../fsleyes/fsleyes-0.32.0.ebuild | 79 ------------------ .../fsleyes/fsleyes-0.32.3.ebuild | 80 ------------------- sci-visualization/fsleyes/metadata.xml | 18 ----- 9 files changed, 344 deletions(-) delete mode 100644 sci-visualization/fsleyes/ChangeLog delete mode 100644 sci-visualization/fsleyes/Manifest delete mode 100644 sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch delete mode 100644 sci-visualization/fsleyes/files/fsleyes-0.32.0-coverage.patch delete mode 100644 sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_fail.patch delete mode 100644 sci-visualization/fsleyes/files/fsleyes-0.32.0-tests_timeout.patch delete mode 100644 sci-visualization/fsleyes/fsleyes-0.32.0.ebuild delete mode 100644 sci-visualization/fsleyes/fsleyes-0.32.3.ebuild delete mode 100644 sci-visualization/fsleyes/metadata.xml diff --git a/sci-visualization/fsleyes/ChangeLog b/sci-visualization/fsleyes/ChangeLog deleted file mode 100644 index b2b078f..0000000 --- a/sci-visualization/fsleyes/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -*fsleyes-0.32.3 (25 Mar 2020) - - 25 Mar 2020; +fsleyes-0.32.3.ebuild: - sci-visualization/fsleyes: version bump 0.32.3 - -*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 deleted file mode 100644 index 3493a12..0000000 --- a/sci-visualization/fsleyes/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST fsleyes-0.32.0.tar.gz 87700064 SHA256 5e728b265608df8cf1a18ddda8694446e44550b0072884a5bb2bf70cb6489862 SHA512 de501e0527c94faad77bffdc6e9262ae185e661bc1b2ca494d75e7f33d7532b7b786c0b776682a0fa08fc48708e3d090de5319b02d4f9b3c0abb75c7cf1e9d1a WHIRLPOOL 1446c04514dbaf07d86b61c231f56d12433d6f49b1dfafb971d444fca067a7bacd9d1593981b19fcb5f4d503ad736ff2f4a9588514a2851180af632108f3b301 -DIST fsleyes-0.32.3.tar.gz 87756679 SHA256 06df776bcca0e6457817132c86a3140edccc5c6f94ff8cfc2b9f54385ad4d394 SHA512 0027f923deac82d7d5f4916716dd46579c9a824d86415896fbb096bcc94cd3eead2f2d754b55d666764783abc9025d6d6f6313d1cee60bd1035348191475dd0f WHIRLPOOL f64a91ebc0e08094725faa311209f8ffb3e507b96808a17966aaf7664e30be7363a6133e05afcf0b958a6d9f3d0ad96b7a164a15bc65462a2875e4114e2dd37d diff --git a/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch b/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch deleted file mode 100644 index 51392f5..0000000 --- a/sci-visualization/fsleyes/files/fsleyes-0.26.2-fsldir.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- 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 deleted file mode 100644 index 089a8d8..0000000 --- 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 8b5f2d6..0000000 --- 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 828252e..0000000 --- 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-0.32.0.ebuild b/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild deleted file mode 100644 index ee52eee..0000000 --- a/sci-visualization/fsleyes/fsleyes-0.32.0.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# 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 deleted file mode 100644 index fccfbf9..0000000 --- a/sci-visualization/fsleyes/fsleyes-0.32.3.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# 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 deleted file mode 100644 index 153c0c6..0000000 --- a/sci-visualization/fsleyes/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - - - chr@chymera.eu - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - - 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. - -