diff --git a/sci-libs/nipype/ChangeLog b/sci-libs/nipype/ChangeLog deleted file mode 100644 index 9e9915f..0000000 --- a/sci-libs/nipype/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ - 08 Aug 2020; files/nipype-1.5.0-version_check.patch: - sci-libs/nipype: patched version parsing - - 07 Aug 2020; +files/nipype-1.5.0-version_check.patch, - nipype-1.5.0.ebuild: - sci-libs/nipype: patching out autofail on misparsed version check - - 27 Jul 2020; +files/98nipype, nipype-1.5.0.ebuild: - sci-libs/nipype: disabled etelemetry functionality - -*nipype-1.5.0 (17 Jul 2020) - - 17 Jul 2020; +nipype-1.5.0.ebuild: - sci-libs/nipype: version bump 1.5.0 - - 31 Mar 2020; nipype-1.4.2.ebuild: - sci-libs/nipype: fixed test suite - -*nipype-1.4.2 (30 Mar 2020) - - 30 Mar 2020; +nipype-1.4.2.ebuild: - sci-libs/nipype: diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest deleted file mode 100644 index 1006d29..0000000 --- a/sci-libs/nipype/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST nipype-1.4.2.tar.gz 2823870 SHA256 935b660bfd81f773bd5291a90a921cc226f62940950c094be04f080f6c69501d SHA512 f913d1a63105ccb8392adfdba5ec52b3e5ce0c9ad145b062f6e551a811602b77a52f1f6e89d9d5ff366e9b063f0ab965cfbd6ae5f68a79e25e8970e1a864901c WHIRLPOOL 21ab8554f8d5eec5fc7d5d9e137eef24f11443b805c892cb1a3dfbd5f34030a08c39300778337eb5499b011a2049c3c2724988d2210356d0d5525f4758b33fdf -DIST nipype-1.5.0.tar.gz 2735317 SHA256 dbbe74ac99740da749350a6957326bd78d6ba388694b0c09cd92575f111576af SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 WHIRLPOOL ffb44ddcf8d6e6a2d0e4179c89f15d59edc86b5188232e8b170a1352d51aa4b3806313d0a1c6215aced0d916252e27c2d8cc97d5ef94d12ac0418681fae0a40b diff --git a/sci-libs/nipype/files/98nipype b/sci-libs/nipype/files/98nipype deleted file mode 100644 index c848f7c..0000000 --- a/sci-libs/nipype/files/98nipype +++ /dev/null @@ -1 +0,0 @@ -export NIPYPE_NO_ET=1 diff --git a/sci-libs/nipype/files/nipype-1.5.0-version_check.patch b/sci-libs/nipype/files/nipype-1.5.0-version_check.patch deleted file mode 100644 index 8b7f11c..0000000 --- a/sci-libs/nipype/files/nipype-1.5.0-version_check.patch +++ /dev/null @@ -1,45 +0,0 @@ -From b4d57d7ca4359b0990636bbc6091c49706c6ff39 Mon Sep 17 00:00:00 2001 -From: Horea Christian -Date: Fri, 7 Aug 2020 01:12:38 -0400 -Subject: [PATCH] ENH: no more auto-failing on misparsed versions - ---- - nipype/interfaces/base/core.py | 18 ++++++++++++++++++ - 1 file changed, 18 insertions(+) - -diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py -index 82da393a84..1e626fe1b5 100644 ---- a/nipype/interfaces/base/core.py -+++ b/nipype/interfaces/base/core.py -@@ -276,6 +276,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True): - version = LooseVersion(str(self.version)) - for name in names: - min_ver = LooseVersion(str(trait_object.traits()[name].min_ver)) -+ try: -+ min_ver > version -+ except TypeError: -+ iflogger.warning( -+ 'Nipype is having issues parsing the package version ' -+ f'for Trait {name} ({self.__class__.__name__})' -+ f'You may want to check whether {version} is larger than {min_ver}' -+ ) -+ continue - if min_ver > version: - unavailable_traits.append(name) - if not isdefined(getattr(trait_object, name)): -@@ -293,6 +302,15 @@ def _check_version_requirements(self, trait_object, raise_exception=True): - version = LooseVersion(str(self.version)) - for name in names: - max_ver = LooseVersion(str(trait_object.traits()[name].max_ver)) -+ try: -+ max_ver > version -+ except TypeError: -+ iflogger.warning( -+ 'Nipype is having issues parsing the package version ' -+ f'for Trait {name} ({self.__class__.__name__})' -+ f'You may want to check whether {version} is smaller than {max_ver}' -+ ) -+ continue - if max_ver < version: - unavailable_traits.append(name) - if not isdefined(getattr(trait_object, name)): diff --git a/sci-libs/nipype/metadata.xml b/sci-libs/nipype/metadata.xml deleted file mode 100644 index fddca4c..0000000 --- a/sci-libs/nipype/metadata.xml +++ /dev/null @@ -1,28 +0,0 @@ - - - - - horea.christ@gmail.com - Horea Christian - - - sci@gentoo.org - Gentoo Science Project - - -Nipype, an open-source, community-developed initiative under the -umbrella of NiPy, is a Python project that provides a uniform interface -to existing neuroimaging software and facilitates interaction between -these packages within a single workflow. Nipype provides an environment -that encourages interactive exploration of algorithms from different -packages (e.g., SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, Slicer), -eases the design of workflows within and between packages, and reduces -the learning curve necessary to use different packages. Nipype is -creating a collaborative platform for neuroimaging software development -in a high-level language and addressing limitations of existing pipeline systems. - - - nipy/nipype - nipy - - diff --git a/sci-libs/nipype/nipype-1.4.2.ebuild b/sci-libs/nipype/nipype-1.4.2.ebuild deleted file mode 100644 index 3447d67..0000000 --- a/sci-libs/nipype/nipype-1.4.2.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{6,7} ) -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 -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -DEPEND=" - dev-python/numpy[${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[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" -#etelemetry and neurdflib - -src_prepare() { - 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_test() { - NIPYPE_NO_ET=1 pytest -vv\ - || die - # Upstream test configuration fails - #-c nipype/pytest.ini\ - #--doctest-modules nipype\ - #--cov nipype\ - #--cov-config .coveragerc\ - #--cov-report xml:cov.xml\ -} diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.5.0.ebuild deleted file mode 100644 index 0df7333..0000000 --- a/sci-libs/nipype/nipype-1.5.0.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{6,7} ) -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 -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -DEPEND=" - dev-python/numpy[${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/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${P}"-version_check.patch -) - -src_prepare() { - # Remove etelemetry - sed -i '/"etelemetry/d' nipype/info.py || die - - # Mark failing tests - sed -i \ - -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ - nipype/tests/test_nipype.py || die - sed -i \ - -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ - nipype/interfaces/fsl/tests/test_base.py || die - default -} - -python_install_all() { - distutils-r1_python_install_all - doenvd "${FILESDIR}/98nipype" -} - -python_test() { - # Setting environment variable to disable etelemetry version check: - # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 - NIPYPE_NO_ET=1 pytest -vv\ - || die - # 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 -}