sci-libs/nipype: pushed to Gentoo Science
https://gitweb.gentoo.org/proj/sci.git/commit/?id=7766d151243230173d21865e85dbf7c71853f8ad
This commit is contained in:
Horea Christian
parent
0a1bf51a85
commit
221254f0f9
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08 Aug 2020; <chymera@gentoo.org> files/nipype-1.5.0-version_check.patch:
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sci-libs/nipype: patched version parsing
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07 Aug 2020; <chymera@gentoo.org> +files/nipype-1.5.0-version_check.patch,
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nipype-1.5.0.ebuild:
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sci-libs/nipype: patching out autofail on misparsed version check
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27 Jul 2020; <chymera@gentoo.org> +files/98nipype, nipype-1.5.0.ebuild:
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sci-libs/nipype: disabled etelemetry functionality
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*nipype-1.5.0 (17 Jul 2020)
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17 Jul 2020; <chymera@gentoo.org> +nipype-1.5.0.ebuild:
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sci-libs/nipype: version bump 1.5.0
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31 Mar 2020; <chymera@gentoo.org> nipype-1.4.2.ebuild:
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sci-libs/nipype: fixed test suite
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*nipype-1.4.2 (30 Mar 2020)
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30 Mar 2020; <chymera@gentoo.org> +nipype-1.4.2.ebuild:
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sci-libs/nipype:
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DIST nipype-1.4.2.tar.gz 2823870 SHA256 935b660bfd81f773bd5291a90a921cc226f62940950c094be04f080f6c69501d SHA512 f913d1a63105ccb8392adfdba5ec52b3e5ce0c9ad145b062f6e551a811602b77a52f1f6e89d9d5ff366e9b063f0ab965cfbd6ae5f68a79e25e8970e1a864901c WHIRLPOOL 21ab8554f8d5eec5fc7d5d9e137eef24f11443b805c892cb1a3dfbd5f34030a08c39300778337eb5499b011a2049c3c2724988d2210356d0d5525f4758b33fdf
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DIST nipype-1.5.0.tar.gz 2735317 SHA256 dbbe74ac99740da749350a6957326bd78d6ba388694b0c09cd92575f111576af SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 WHIRLPOOL ffb44ddcf8d6e6a2d0e4179c89f15d59edc86b5188232e8b170a1352d51aa4b3806313d0a1c6215aced0d916252e27c2d8cc97d5ef94d12ac0418681fae0a40b
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export NIPYPE_NO_ET=1
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@ -1,45 +0,0 @@
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From b4d57d7ca4359b0990636bbc6091c49706c6ff39 Mon Sep 17 00:00:00 2001
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From: Horea Christian <chr@chymera.eu>
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Date: Fri, 7 Aug 2020 01:12:38 -0400
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Subject: [PATCH] ENH: no more auto-failing on misparsed versions
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---
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nipype/interfaces/base/core.py | 18 ++++++++++++++++++
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1 file changed, 18 insertions(+)
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diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
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index 82da393a84..1e626fe1b5 100644
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--- a/nipype/interfaces/base/core.py
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+++ b/nipype/interfaces/base/core.py
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@@ -276,6 +276,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
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version = LooseVersion(str(self.version))
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for name in names:
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min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
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+ try:
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+ min_ver > version
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+ except TypeError:
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+ iflogger.warning(
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+ 'Nipype is having issues parsing the package version '
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+ f'for Trait {name} ({self.__class__.__name__})'
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+ f'You may want to check whether {version} is larger than {min_ver}'
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+ )
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+ continue
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if min_ver > version:
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unavailable_traits.append(name)
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if not isdefined(getattr(trait_object, name)):
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@@ -293,6 +302,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
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version = LooseVersion(str(self.version))
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for name in names:
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max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
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+ try:
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+ max_ver > version
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+ except TypeError:
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+ iflogger.warning(
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+ 'Nipype is having issues parsing the package version '
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+ f'for Trait {name} ({self.__class__.__name__})'
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+ f'You may want to check whether {version} is smaller than {max_ver}'
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+ )
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+ continue
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if max_ver < version:
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unavailable_traits.append(name)
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if not isdefined(getattr(trait_object, name)):
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="person">
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<email>horea.christ@gmail.com</email>
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<name>Horea Christian</name>
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</maintainer>
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<maintainer type="project">
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<email>sci@gentoo.org</email>
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<name>Gentoo Science Project</name>
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</maintainer>
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<longdescription lang="en">
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Nipype, an open-source, community-developed initiative under the
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umbrella of NiPy, is a Python project that provides a uniform interface
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to existing neuroimaging software and facilitates interaction between
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these packages within a single workflow. Nipype provides an environment
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that encourages interactive exploration of algorithms from different
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packages (e.g., SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer),
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eases the design of workflows within and between packages, and reduces
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the learning curve necessary to use different packages. Nipype is
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creating a collaborative platform for neuroimaging software development
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in a high-level language and addressing limitations of existing pipeline systems.
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</longdescription>
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<upstream>
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<remote-id type="github">nipy/nipype</remote-id>
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<remote-id type="sourceforge">nipy</remote-id>
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</upstream>
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</pkgmetadata>
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@ -1,66 +0,0 @@
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{6,7} )
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PYTHON_REQ_USE="threads(+),sqlite"
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inherit distutils-r1
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DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
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HOMEPAGE="http://nipy.sourceforge.net/nipype/"
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SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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DEPEND="
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dev-python/numpy[${PYTHON_USEDEP}]
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dev-python/prov[${PYTHON_USEDEP}]
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sci-libs/nibabel[${PYTHON_USEDEP}]
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test? (
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dev-python/mock[${PYTHON_USEDEP}]
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dev-python/pytest[${PYTHON_USEDEP}]
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${RDEPEND}
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)
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"
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# Dependency disabled as upstream test configuration which requires it fails
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#dev-python/pytest-xdist[${PYTHON_USEDEP}]
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RDEPEND="
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>=dev-python/click-6.6[${PYTHON_USEDEP}]
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dev-python/filelock[${PYTHON_USEDEP}]
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dev-python/networkx[${PYTHON_USEDEP}]
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dev-python/packaging[${PYTHON_USEDEP}]
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dev-python/pydot[${PYTHON_USEDEP}]
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dev-python/pydotplus[${PYTHON_USEDEP}]
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dev-python/python-dateutil[${PYTHON_USEDEP}]
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dev-python/simplejson[${PYTHON_USEDEP}]
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dev-python/traits[${PYTHON_USEDEP}]
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sci-libs/scipy[${PYTHON_USEDEP}]
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"
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#etelemetry and neurdflib
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src_prepare() {
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sed -i \
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-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')" \
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nipype/tests/test_nipype.py || die
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sed -i \
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-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
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nipype/interfaces/fsl/tests/test_base.py || die
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default
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}
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python_test() {
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NIPYPE_NO_ET=1 pytest -vv\
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|| die
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# Upstream test configuration fails
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#-c nipype/pytest.ini\
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#--doctest-modules nipype\
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#--cov nipype\
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#--cov-config .coveragerc\
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#--cov-report xml:cov.xml\
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}
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# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{6,7} )
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PYTHON_REQ_USE="threads(+),sqlite"
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inherit distutils-r1
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DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
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HOMEPAGE="http://nipy.sourceforge.net/nipype/"
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SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
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LICENSE="BSD"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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DEPEND="
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dev-python/numpy[${PYTHON_USEDEP}]
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dev-python/prov[${PYTHON_USEDEP}]
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sci-libs/nibabel[${PYTHON_USEDEP}]
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test? (
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dev-python/mock[${PYTHON_USEDEP}]
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dev-python/pytest[${PYTHON_USEDEP}]
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${RDEPEND}
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)
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"
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# Dependency disabled as upstream test configuration which requires it fails
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#dev-python/pytest-xdist[${PYTHON_USEDEP}]
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RDEPEND="
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>=dev-python/click-6.6[${PYTHON_USEDEP}]
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dev-python/filelock[${PYTHON_USEDEP}]
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dev-python/networkx[${PYTHON_USEDEP}]
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dev-python/packaging[${PYTHON_USEDEP}]
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dev-python/pydot[${PYTHON_USEDEP}]
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dev-python/pydotplus[${PYTHON_USEDEP}]
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dev-python/python-dateutil[${PYTHON_USEDEP}]
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>=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
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dev-python/simplejson[${PYTHON_USEDEP}]
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dev-python/traits[${PYTHON_USEDEP}]
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sci-libs/scipy[${PYTHON_USEDEP}]
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"
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PATCHES=(
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"${FILESDIR}/${P}"-version_check.patch
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)
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src_prepare() {
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# Remove etelemetry
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sed -i '/"etelemetry/d' nipype/info.py || die
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# Mark failing tests
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sed -i \
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-e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
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nipype/tests/test_nipype.py || die
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sed -i \
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-e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
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nipype/interfaces/fsl/tests/test_base.py || die
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default
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}
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python_install_all() {
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distutils-r1_python_install_all
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doenvd "${FILESDIR}/98nipype"
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}
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python_test() {
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# Setting environment variable to disable etelemetry version check:
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# https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
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NIPYPE_NO_ET=1 pytest -vv\
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|| die
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# Upstream test configuration fails
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#-c nipype/pytest.ini\
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#--doctest-modules nipype\
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#--cov nipype\
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#--cov-config .coveragerc\
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#--cov-report xml:cov.xml\
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}
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pkg_postinst() {
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echo
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einfo "Please run the following commands if you"
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einfo "intend to use nipype from an existing shell:"
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einfo "source /etc/profile"
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echo
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}
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