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author | Horea Christian <chr@chymera.eu> | 2023-04-06 14:48:08 -0400 |
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committer | Horea Christian <chr@chymera.eu> | 2023-04-06 14:48:08 -0400 |
commit | 1c2d9c184a6d79f1308b5b2ce3b39bca76a8fce9 (patch) | |
tree | db398ae9f5aaac810a62910fb9811542672141ef /sci-libs/nipype/nipype-1.8.4-r1.ebuild | |
parent | sci-mathematics/frama-c: USE flag is deprecated in dependency (diff) | |
download | sci-1c2d9c184a6d79f1308b5b2ce3b39bca76a8fce9.tar.gz sci-1c2d9c184a6d79f1308b5b2ce3b39bca76a8fce9.tar.bz2 sci-1c2d9c184a6d79f1308b5b2ce3b39bca76a8fce9.zip |
sci-libs/nipype: dependency update
Signed-off-by: Horea Christian <chr@chymera.eu>
Diffstat (limited to 'sci-libs/nipype/nipype-1.8.4-r1.ebuild')
-rw-r--r-- | sci-libs/nipype/nipype-1.8.4-r1.ebuild | 93 |
1 files changed, 93 insertions, 0 deletions
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild new file mode 100644 index 000000000..d70509ce1 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +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 -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${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-dependency_compatibility.patch" +) + +src_prepare() { + # Remove etelemetry + 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 +} |