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From: "Horea Christian" <horea.christ@gmail.com>
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Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" <horea.christ@gmail.com>
Message-ID: <1705934355.1d9d9f6cbf7e933c4fed1f4ec4e3183b1ea0f76c.chymera@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-libs/nipype/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-libs/nipype/nipype-1.5.0.ebuild sci-libs/nipype/nipype-1.8.6.ebuild
X-VCS-Directories: sci-libs/nipype/
X-VCS-Committer: chymera
X-VCS-Committer-Name: Horea Christian
X-VCS-Revision: 1d9d9f6cbf7e933c4fed1f4ec4e3183b1ea0f76c
X-VCS-Branch: master
Date: Mon, 22 Jan 2024 14:42:01 +0000 (UTC)
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commit: 1d9d9f6cbf7e933c4fed1f4ec4e3183b1ea0f76c
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 14:39:15 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 14:39:15 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d9d9f6c
sci-libs/nipype: add 1.8.6, drop 1.5.0
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../{nipype-1.5.0.ebuild => nipype-1.8.6.ebuild} | 25 +++++++++++-----------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild
similarity index 75%
rename from sci-libs/nipype/nipype-1.5.0.ebuild
rename to sci-libs/nipype/nipype-1.8.6.ebuild
index 750c3ba05..88bc23395 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.8.6.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
@@ -16,7 +17,9 @@ LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test"
-RESTRICT="!test? ( test )"
+# Tests fail with numpy import error:
+# https://github.com/nipy/nipype/issues/3626
+RESTRICT="test"
DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
@@ -28,30 +31,28 @@ DEPEND="
${RDEPEND}
)
"
-# Dependency disabled as upstream test configuration which requires it fails
-#dev-python/pytest-xdist[${PYTHON_USEDEP}]
RDEPEND="
- >=dev-python/click-6.6[${PYTHON_USEDEP}]
+ dev-python/click[${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[${PYTHON_USEDEP}]
- dev-python/pydotplus[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
- >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/traits[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${P}"-version_check.patch
- "${FILESDIR}/${P}"-collections.patch
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
)
src_prepare() {
# Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
@@ -69,12 +70,10 @@ python_install_all() {
doenvd "${FILESDIR}/98nipype"
}
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
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() {