From 7766d151243230173d21865e85dbf7c71853f8ad Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Fri, 25 Sep 2020 05:26:39 -0400 Subject: sci-libs/nipype: version bump 1.{4,5}* and old version removal Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian --- sci-libs/nipype/Manifest | 2 + sci-libs/nipype/files/98nipype | 1 + .../nipype/files/nipype-1.5.0-version_check.patch | 45 +++++++++++ sci-libs/nipype/nipype-1.1.1-r1.ebuild | 65 ---------------- sci-libs/nipype/nipype-1.1.1-r2.ebuild | 2 +- sci-libs/nipype/nipype-1.4.2.ebuild | 66 ++++++++++++++++ sci-libs/nipype/nipype-1.5.0.ebuild | 89 ++++++++++++++++++++++ 7 files changed, 204 insertions(+), 66 deletions(-) create mode 100644 sci-libs/nipype/files/98nipype create mode 100644 sci-libs/nipype/files/nipype-1.5.0-version_check.patch delete mode 100644 sci-libs/nipype/nipype-1.1.1-r1.ebuild create mode 100644 sci-libs/nipype/nipype-1.4.2.ebuild create mode 100644 sci-libs/nipype/nipype-1.5.0.ebuild (limited to 'sci-libs') diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest index 8b0a0f7e6..cbf353bd7 100644 --- a/sci-libs/nipype/Manifest +++ b/sci-libs/nipype/Manifest @@ -1 +1,3 @@ DIST nipype-1.1.1.tar.gz 3353518 BLAKE2B 509b6c2b18aab8c8ddfad3ca4ac87401caf0608ee566edecaa20a4329a3bfd9d67dae730ac45342600b4026b66c5043d753d09e5230269d3fc4b946d049ad11e SHA512 dba749ff3b53dfe19992a27f9ad9aedcd360b51b3bf7233bf4b83387ae7181425b27ef43d23747553e9f8eb368b6769d6bec62650e1303ec353dde4de84f1769 +DIST nipype-1.4.2.tar.gz 2823870 BLAKE2B 3af3a5e45fada174908723afd8c747575cba4c8489cd894fdced68a5b10b0638f871c600df921b61a4e809c43ea3b827539410ed713f14829d60f207d5bd8cfd SHA512 f913d1a63105ccb8392adfdba5ec52b3e5ce0c9ad145b062f6e551a811602b77a52f1f6e89d9d5ff366e9b063f0ab965cfbd6ae5f68a79e25e8970e1a864901c +DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 diff --git a/sci-libs/nipype/files/98nipype b/sci-libs/nipype/files/98nipype new file mode 100644 index 000000000..c848f7c2a --- /dev/null +++ b/sci-libs/nipype/files/98nipype @@ -0,0 +1 @@ +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 new file mode 100644 index 000000000..8b7f11c63 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.5.0-version_check.patch @@ -0,0 +1,45 @@ +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/nipype-1.1.1-r1.ebuild b/sci-libs/nipype/nipype-1.1.1-r1.ebuild deleted file mode 100644 index 435268f9c..000000000 --- a/sci-libs/nipype/nipype-1.1.1-r1.ebuild +++ /dev/null @@ -1,65 +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 -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -DEPEND=" - dev-python/future[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/prov[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}] - sci-libs/nibabel[${PYTHON_USEDEP}] - test? ( - dev-python/mock[${PYTHON_USEDEP}] - <=dev-python/pytest-4.6.9[${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[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pydot[${PYTHON_USEDEP}] - dev-python/pydotplus[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -src_prepare() { - sed -i\ - -e "/'pytest>=%s' % PYTEST_MIN_VERSION,/d"\ - -e "/'pytest-xdist',$/d"\ - nipype/info.py || die - default -} - -python_test() { - pytest -vv\ - || die - # Upstream test configuration fails - #-c nipype/pytest.ini\ - #--doctest-modules nipype\ - #--cov nipype\ - #--cov-config .coveragerc\ - #--cov-report xml:cov.xml\ -} diff --git a/sci-libs/nipype/nipype-1.1.1-r2.ebuild b/sci-libs/nipype/nipype-1.1.1-r2.ebuild index 39427865a..528967695 100644 --- a/sci-libs/nipype/nipype-1.1.1-r2.ebuild +++ b/sci-libs/nipype/nipype-1.1.1-r2.ebuild @@ -25,7 +25,7 @@ DEPEND=" sci-libs/nibabel[${PYTHON_USEDEP}] test? ( dev-python/mock[${PYTHON_USEDEP}] - <=dev-python/pytest-4.6.9[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] ${RDEPEND} ) " diff --git a/sci-libs/nipype/nipype-1.4.2.ebuild b/sci-libs/nipype/nipype-1.4.2.ebuild new file mode 100644 index 000000000..dd1b5e1f0 --- /dev/null +++ b/sci-libs/nipype/nipype-1.4.2.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="http://nipy.sourceforge.net/nipype/" +SRC_URI="https://github.com/nipy/nipype/archive/${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[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/traits[${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 new file mode 100644 index 000000000..1c3357c1a --- /dev/null +++ b/sci-libs/nipype/nipype-1.5.0.ebuild @@ -0,0 +1,89 @@ +# 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/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/traits[${PYTHON_USEDEP}] +" + +PATCHES=( + "${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 +} -- cgit v1.2.3-65-gdbad