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# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
DISTUTILS_USE_PEP517=setuptools
inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
if [ "$PV" == "9999" ]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git"
else
SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64"
S="${WORKDIR}/SAMRI-${PV}"
fi
LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb"
REQUIRED_USE="test? ( atlases )"
DEPEND="
test? (
sci-biology/samri_bidsdata
sci-biology/samri_bindata
)
"
RDEPEND="
dev-python/argh[${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[${PYTHON_USEDEP}]
>=media-gfx/blender-2.83.4
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
atlases? ( sci-biology/mouse-brain-templates )
labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
<sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
dev-python/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
"
distutils_enable_tests pytest
distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
src_prepare() {
distutils-r1_src_prepare
sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
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():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
samri/pipelines/tests/test_repos.py || die
epytest -k "not longtime"
}
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