71 lines
1.9 KiB
Bash
71 lines
1.9 KiB
Bash
# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{5,6} )
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inherit distutils-r1 git-r3
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DESCRIPTION="Small Animal Magnetic Resonance Imaging"
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HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
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SRC_URI=""
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EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
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LICENSE="GPL-3"
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SLOT="0"
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IUSE="labbookdb test"
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KEYWORDS=""
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DEPEND="
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test? (
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dev-python/pytest[${PYTHON_USEDEP}]
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sci-biology/samri_bidsdata
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sci-biology/samri_bindata
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)
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"
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RDEPEND="
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dev-python/argh[${PYTHON_USEDEP}]
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dev-python/joblib[${PYTHON_USEDEP}]
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>=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
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>=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
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dev-python/pandas[${PYTHON_USEDEP}]
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dev-python/scipy[${PYTHON_USEDEP}]
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dev-python/seaborn[${PYTHON_USEDEP}]
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dev-python/statsmodels[${PYTHON_USEDEP}]
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media-gfx/blender
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>=sci-biology/fsl-5.0.9
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sci-biology/bru2nii
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sci-biology/mouse-brain-atlases
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labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
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sci-libs/nibabel[${PYTHON_USEDEP}]
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>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
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>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
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<=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
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sci-libs/scikits_image[${PYTHON_USEDEP}]
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sci-biology/ants
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sci-biology/afni
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sci-biology/nilearn[${PYTHON_USEDEP}]
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"
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#S="${WORKDIR}/SAMRI-${PV}"
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src_prepare() {
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distutils-r1_src_prepare
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sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
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sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
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eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
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}
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python_test() {
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distutils_install_for_testing
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export MPLBACKEND="agg"
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export PATH=${TEST_DIR}/scripts:$PATH
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export PYTHONIOENCODING=utf-8
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./test_scripts.sh || die "Test scripts failed."
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sed -i -e \
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"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
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samri/pipelines/tests/test_repos.py || die
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pytest -vv || die
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}
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