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# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
inherit distutils-r1 git-r3 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI=""
EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
LICENSE="GPL-3"
SLOT="0"
IUSE="+atlases labbookdb test"
KEYWORDS=""
# Numpy dependency to circumvent scikits_learn dependency bug:
# https://bugs.gentoo.org/653052
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/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
>=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[${PYTHON_USEDEP}]
>=sci-libs/nipype-0.14.0_pre20170830[${PYTHON_USEDEP}]
sci-libs/pybids[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
"
REQUIRED_USE="test? ( atlases )"
src_prepare() {
distutils-r1_src_prepare
sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ *`
sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \"/usr/ *`
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:$PATH
export PYTHONIOENCODING=utf-8
./test_scripts.sh || die "Test scripts failed."
sed -i \
-e '1s/^/import pytest \n/' \
-e "/def test_bru2bids():/i@pytest.mark.skip('Skipped by Portage, as this was already tested in test_scripts.sh')" \
samri/pipelines/tests/test_reposit.py || die
cd "${BUILD_DIR}" || die
pytest -vv || die
}
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