Merge pull request #37952 from Ma27/fix-nipype

pythonPackage.nipype: fix build

pkgs/development/python-modules/nipype/default.nix

@@ -21,8 +21,12 @@
 , simplejson
 , traits
 , xvfbwrapper
+, pytestcov
+, codecov
 # other dependencies
 , which
+, bash
+, glibcLocales
 }:
 
 assert !isPy3k -> configparser != null;
@@ -36,9 +40,14 @@ buildPythonPackage rec {
     sha256 = "47f62fda3d6b9a37aa407a6b78c80e91240aa71e61191ed00da68b02839fe258";
   };
 
-  doCheck = false;  # fails with TypeError: None is not callable
-  checkInputs = [ which ];
-  buildInputs = [ pytest mock ];  # required in installPhase
+  # see https://github.com/nipy/nipype/issues/2240
+  patches = [ ./prov-version.patch ];
+
+  postPatch = ''
+    substituteInPlace nipype/interfaces/base/tests/test_core.py \
+      --replace "/usr/bin/env bash" "${bash}/bin/bash"
+  '';
+
   propagatedBuildInputs = [
     click
     dateutil
@@ -59,6 +68,12 @@ buildPythonPackage rec {
     configparser
   ];
 
+  checkInputs = [ pytest mock pytestcov codecov which glibcLocales ];
+
+  checkPhase = ''
+    LC_ALL="en_US.UTF-8" py.test -v --doctest-modules nipype
+  '';
+
   meta = with stdenv.lib; {
     homepage = http://nipy.org/nipype/;
     description = "Neuroimaging in Python: Pipelines and Interfaces";

pkgs/development/python-modules/nipype/prov-version.patch

@@ -0,0 +1,21 @@
+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,