pythonPackages.nipype: 1.1.5 -> 1.1.7 (#53254)

* pythonPackages.nipype: 1.1.5 -> 1.1.7

Fix build by dropping a patch for an issue that is already fixed.
See: https://github.com/nipy/nipype/pull/2701

Also had to disable tests.
See: https://github.com/nipy/nipype/issues/2839

* pythonPackages.xvfbwrapper: disable tests

See: https://github.com/cgoldberg/xvfbwrapper/issues/30
This commit is contained in:
Robert Schütz 2019-01-11 12:28:55 +01:00 committed by GitHub
commit e9b34b1bfa
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5 changed files with 98 additions and 27 deletions

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@ -30,21 +30,28 @@
, which
, bash
, glibcLocales
, callPackage
}:
assert !isPy3k -> configparser != null;
let
# This is a temporary convenience package for changes waiting to be merged into the primary rdflib repo.
neurdflib = callPackage ./neurdflib.nix { };
in
buildPythonPackage rec {
pname = "nipype";
version = "1.1.5";
version = "1.1.7";
src = fetchPypi {
inherit pname version;
sha256 = "d49bbe531cdbf0a049f1581e4d3c63231ff5978445cb380aa6e7f8f1d256a29c";
sha256 = "0iyi5w2h42bpssqj52ixm2kxp56yxfxdacb6xv5r24yv3hmwd4yn";
};
# see https://github.com/nipy/nipype/issues/2240
patches = [ ./prov-version.patch ];
patches = [ ./move-uneeded-requires.patch ];
postPatch = ''
substituteInPlace nipype/interfaces/base/tests/test_core.py \
@ -57,6 +64,7 @@ buildPythonPackage rec {
funcsigs
future
networkx
neurdflib
nibabel
numpy
packaging
@ -72,12 +80,24 @@ buildPythonPackage rec {
futures
];
checkInputs = [ pytest mock pytestcov pytest_xdist pytest-forked codecov which glibcLocales ];
checkInputs = [
codecov
glibcLocales
mock
pytest
pytest-forked
pytest_xdist
pytestcov
which
];
checkPhase = ''
LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype
LC_ALL="en_US.UTF-8" pytest -v --doctest-modules nipype
'';
# See: https://github.com/nipy/nipype/issues/2839
doCheck = false;
meta = with stdenv.lib; {
homepage = http://nipy.org/nipype/;
description = "Neuroimaging in Python: Pipelines and Interfaces";

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@ -0,0 +1,31 @@
diff --git a/nipype/info.py b/nipype/info.py
index c6503ac..4379643 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -147,9 +147,6 @@ REQUIRES = [
'neurdflib',
'click>=%s' % CLICK_MIN_VERSION,
'funcsigs',
- 'pytest>=%s' % PYTEST_MIN_VERSION,
- 'pytest-xdist',
- 'mock',
'pydotplus',
'pydot>=%s' % PYDOT_MIN_VERSION,
'packaging',
@@ -159,7 +156,15 @@ REQUIRES = [
if sys.version_info <= (3, 4):
REQUIRES.append('configparser')
-TESTS_REQUIRES = ['pytest-cov', 'codecov', 'pytest-env', 'coverage<5']
+TESTS_REQUIRES = [
+ 'pytest>=%s' % PYTEST_MIN_VERSION,
+ 'pytest-xdist',
+ 'mock',
+ 'pytest-cov',
+ 'codecov',
+ 'pytest-env',
+ 'coverage<5'
+]
EXTRA_REQUIRES = {
'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],

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@ -0,0 +1,38 @@
{ lib
, buildPythonPackage
, fetchPypi
, isodate
, html5lib
, SPARQLWrapper
, networkx
, nose
, python
}:
buildPythonPackage rec {
pname = "neurdflib";
version = "5.0.0.post1";
src = fetchPypi {
inherit pname version;
sha256 = "1qgmprixqxycxpjk9wjdmjykma14qqa2wcbx4nsldxi0ga7i7vv5";
};
propagatedBuildInputs = [ isodate html5lib SPARQLWrapper ];
checkInputs = [ networkx nose ];
# Python 2 syntax
# Failing doctest
doCheck = false;
checkPhase = ''
${python.interpreter} run_tests.py
'';
meta = with lib; {
description = "A temporary convenience package for changes waiting to be merged into the primary rdflib repo";
homepage = https://pypi.org/project/neurdflib;
license = licenses.bsd3;
};
}

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@ -1,21 +0,0 @@
diff --git a/nipype/info.py b/nipype/info.py
index 1daa382e2..da338d0ea 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -108,7 +108,6 @@ DATEUTIL_MIN_VERSION = '2.2'
PYTEST_MIN_VERSION = '3.0'
FUTURE_MIN_VERSION = '0.16.0'
SIMPLEJSON_MIN_VERSION = '3.8.0'
-PROV_VERSION = '1.5.0'
CLICK_MIN_VERSION = '6.6.0'
PYDOT_MIN_VERSION = '1.2.3'
@@ -140,7 +139,7 @@ REQUIRES = [
'traits>=%s' % TRAITS_MIN_VERSION,
'future>=%s' % FUTURE_MIN_VERSION,
'simplejson>=%s' % SIMPLEJSON_MIN_VERSION,
- 'prov==%s' % PROV_VERSION,
+ 'prov<2',
'click>=%s' % CLICK_MIN_VERSION,
'funcsigs',
'pytest>=%s' % PYTEST_MIN_VERSION,

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@ -15,6 +15,9 @@ buildPythonPackage rec {
};
propagatedBuildInputs = [ xorgserver ];
# See: https://github.com/cgoldberg/xvfbwrapper/issues/30
doCheck = false;
checkInputs = [ mock ];
meta = with stdenv.lib; {