commit: 7766d151243230173d21865e85dbf7c71853f8ad
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Sep 25 09:26:39 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Sep 25 09:26:39 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7766d151
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 <chr <AT> chymera.eu>
sci-libs/nipype/files/98nipype | 1 +
.../nipype/files/nipype-1.5.0-version_check.patch | 45 ++++++++++++++++++++++
sci-libs/nipype/nipype-1.1.1-r2.ebuild | 2 +-
...{nipype-1.1.1-r1.ebuild => nipype-1.4.2.ebuild} | 21 +++++-----
...{nipype-1.1.1-r1.ebuild => nipype-1.5.0.ebuild} | 44 ++++++++++++++++-----
5 files changed, 92 insertions(+), 21 deletions(-)
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 <c...@chymera.eu>
+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-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}]
${RDEPEND}
)
"
diff --git a/sci-libs/nipype/nipype-1.1.1-r1.ebuild
b/sci-libs/nipype/nipype-1.4.2.ebuild
similarity index 71%
copy from sci-libs/nipype/nipype-1.1.1-r1.ebuild
copy to sci-libs/nipype/nipype-1.4.2.ebuild
index 435268f9c..dd1b5e1f0 100644
--- a/sci-libs/nipype/nipype-1.1.1-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.4.2.ebuild
@@ -18,14 +18,12 @@ KEYWORDS="~amd64 ~x86"
IUSE="test"
DEPEND="
- dev-python/future[${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}]
+ dev-python/pytest[${PYTHON_USEDEP}]
${RDEPEND}
)
"
@@ -34,27 +32,30 @@ DEPEND="
RDEPEND="
>=dev-python/click-6.6[${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[${PYTHON_USEDEP}]
- dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
dev-python/traits[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
"
+#etelemetry and neurdflib
src_prepare() {
- sed -i\
- -e "/'pytest>=%s' % PYTEST_MIN_VERSION,/d"\
- -e "/'pytest-xdist',$/d"\
- nipype/info.py || die
+ 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() {
- pytest -vv\
+ NIPYPE_NO_ET=1 pytest -vv\
|| die
# Upstream test configuration fails
#-c nipype/pytest.ini\
diff --git a/sci-libs/nipype/nipype-1.1.1-r1.ebuild
b/sci-libs/nipype/nipype-1.5.0.ebuild
similarity index 55%
rename from sci-libs/nipype/nipype-1.1.1-r1.ebuild
rename to sci-libs/nipype/nipype-1.5.0.ebuild
index 435268f9c..1c3357c1a 100644
--- a/sci-libs/nipype/nipype-1.1.1-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.5.0.ebuild
@@ -18,14 +18,12 @@ 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[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
${RDEPEND}
)
"
@@ -34,27 +32,45 @@ DEPEND="
RDEPEND="
>=dev-python/click-6.6[${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[${PYTHON_USEDEP}]
- dev-python/pygraphviz[${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[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
"
+PATCHES=(
+ "${FILESDIR}/${P}"-version_check.patch
+)
+
src_prepare() {
- sed -i\
- -e "/'pytest>=%s' % PYTEST_MIN_VERSION,/d"\
- -e "/'pytest-xdist',$/d"\
- nipype/info.py || die
+ # Remove etelemetry
+ sed -i '/"etelemetry/d' nipype/info.py || die
+
+ # Mark failing tests
+ sed -i \
+ -e "/def test_no_et(tmp_path):/i...@pytest.mark.skip('Known to
fail by upstream:
https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+ nipype/tests/test_nipype.py || die
+ sed -i \
+ -e "/def test_fslversion():/i...@pytest.mark.skip('Known to
fail by upstream:
https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+ nipype/interfaces/fsl/tests/test_base.py || die
default
}
+python_install_all() {
+ distutils-r1_python_install_all
+ doenvd "${FILESDIR}/98nipype"
+}
+
python_test() {
- pytest -vv\
+ # 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\
@@ -63,3 +79,11 @@ python_test() {
#--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
+}
