commit: 8a9e478b567b41ec475344acf3f9e3f7d18e765a Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Sun Sep 27 09:27:43 2020 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Sun Sep 27 09:27:43 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a9e478b
sci-biology/samri: version bump 0.5 Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian <chr <AT> chymera.eu> sci-biology/samri/samri-0.5.ebuild | 71 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 71 insertions(+) diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild new file mode 100644 index 000000000..24912c9c9 --- /dev/null +++ b/sci-biology/samri/samri-0.5.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_7 ) + +inherit distutils-r1 + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI"; +SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb test" +KEYWORDS="~amd64" + +DEPEND=" + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-atlases ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + sci-libs/pybids[${PYTHON_USEDEP}] + sci-libs/scikits_image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +REQUIRED_USE="test? ( atlases )" + +S="${WORKDIR}/SAMRI-${PV}" + +src_prepare() { + distutils-r1_src_prepare + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) +} + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/[email protected]('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + pytest -vv -k "not longtime" || die +}
