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# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
inherit distutils-r1
DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
HOMEPAGE="https://nipype.readthedocs.io/"
SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test"
# Tests fail with numpy import error:
# https://github.com/nipy/nipype/issues/3626
RESTRICT="test"
DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/prov[${PYTHON_USEDEP}]
sci-libs/nibabel[${PYTHON_USEDEP}]
test? (
dev-python/mock[${PYTHON_USEDEP}]
dev-python/pytest[${PYTHON_USEDEP}]
${RDEPEND}
)
"
RDEPEND="
dev-python/click[${PYTHON_USEDEP}]
dev-python/filelock[${PYTHON_USEDEP}]
dev-python/looseversion[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
<dev-python/traits-6.4.0[${PYTHON_USEDEP}]
"
PATCHES=(
"${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
)
src_prepare() {
# Remove etelemetry
# Doing this separately since the file is affected by another patch.
sed -i '/"etelemetry/d' nipype/info.py requirements.txt || 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"
}
# Reported upstream:
# https://github.com/nipy/nipype/issues/3540
EPYTEST_DESELECT=(
nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
)
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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