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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
PYTHON_COMPAT=( python3_{8..10} )
PYTHON_REQ_USE="threads(+),sqlite"
inherit distutils-r1
DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
HOMEPAGE="http://nipy.sourceforge.net/nipype/"
SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test"
RESTRICT="!test? ( test )"
DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/prov[${PYTHON_USEDEP}]
sci-libs/nibabel[${PYTHON_USEDEP}]
test? (
dev-python/mock[${PYTHON_USEDEP}]
dev-python/pytest[${PYTHON_USEDEP}]
${RDEPEND}
)
"
# Dependency disabled as upstream test configuration which requires it fails
#dev-python/pytest-xdist[${PYTHON_USEDEP}]
RDEPEND="
>=dev-python/click-6.6[${PYTHON_USEDEP}]
dev-python/filelock[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]
dev-python/pydotplus[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
>=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
dev-python/traits[${PYTHON_USEDEP}]
"
PATCHES=(
"${FILESDIR}/${P}"-version_check.patch
"${FILESDIR}/${P}"-collections.patch
)
src_prepare() {
# Remove etelemetry
sed -i '/"etelemetry/d' nipype/info.py || die
# Mark failing tests
sed -i \
-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
nipype/tests/test_nipype.py || die
sed -i \
-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
nipype/interfaces/fsl/tests/test_base.py || die
default
}
python_install_all() {
distutils-r1_python_install_all
doenvd "${FILESDIR}/98nipype"
}
EPYTEST_DESELECT=(
nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor
nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor_variance_threshold_and_metadata
nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor
nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help
)
python_test() {
# Setting environment variable to disable etelemetry version check:
# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
NIPYPE_NO_ET=1 epytest
# Upstream test configuration fails
#-c nipype/pytest.ini\
#--doctest-modules nipype\
#--cov nipype\
#--cov-config .coveragerc\
#--cov-report xml:cov.xml\
}
pkg_postinst() {
echo
einfo "Please run the following commands if you"
einfo "intend to use nipype from an existing shell:"
einfo "source /etc/profile"
echo
}
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