commit: decfc6942ba15bf039dec9834a0ef162da0278db Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Wed Mar 25 01:06:58 2020 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Wed Mar 25 01:06:58 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=decfc694
sci-visualization/fsleyes: new package Neuroimaging data viewer Package-Manager: Portage-2.3.95, Repoman-2.3.21 Signed-off-by: Horea Christian <chr <AT> chymera.eu> sci-visualization/fsleyes/ChangeLog | 10 +++ .../fsleyes/files/fsleyes-0.26.2-fsldir.patch | 14 ++++ .../fsleyes/files/fsleyes-0.32.0-coverage.patch | 13 ++++ .../fsleyes/files/fsleyes-0.32.0-tests_fail.patch | 62 +++++++++++++++++ .../files/fsleyes-0.32.0-tests_timeout.patch | 61 +++++++++++++++++ sci-visualization/fsleyes/fsleyes-0.32.0.ebuild | 79 +++++++++++++++++++++ sci-visualization/fsleyes/fsleyes-0.32.3.ebuild | 80 ++++++++++++++++++++++ sci-visualization/fsleyes/metadata.xml | 18 +++++ 8 files changed, 337 insertions(+) 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; <[email protected]> +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; <[email protected]> fsleyes-0.27.3.ebuild: + sci-visualization/fsleyes: 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 + [email protected](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) + +- [email protected](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)) + + [email protected](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) + + [email protected](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' + + [email protected](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() + +- [email protected](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 + +- [email protected](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 + [email protected](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): + + + [email protected](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>[email protected]</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</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>
