Merge pull request #1866 from satra/fix/bru2

fixing tests and install errors

Author: satra

README.rst

@@ -78,8 +78,8 @@ Support and Communication
 -------------------------
 
 If you have a problem or would like to ask a question about how to do something in Nipype please open an issue to
-`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a 
-platform similar to StackOverflow but dedicated to neuroinformatics. 
+`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a
+platform similar to StackOverflow but dedicated to neuroinformatics.
 
 To participate in the Nipype development related discussions please use the following mailing list::
 

nipype/algorithms/tests/test_auto_CompCor.py

@@ -11,7 +11,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     position=1,
     ),
     doLogJacobian=dict(argstr='%d',
-    mandatory=False,
     position=3,
     ),
     environ=dict(nohash=True,
@@ -35,7 +34,6 @@ def test_CreateJacobianDeterminantImage_inputs():
     terminal_output=dict(nohash=True,
     ),
     useGeometric=dict(argstr='%d',
-    mandatory=False,
     position=4,
     ),
     )

nipype/algorithms/tests/test_auto_ErrorMap.py

@@ -145,9 +145,9 @@ class CreateJacobianDeterminantImageInputSpec(ANTSCommandInputSpec):
     outputImage = File(argstr='%s', mandatory=True,
                          position=2,
                          desc='output filename')
-    doLogJacobian = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+    doLogJacobian = traits.Enum(0, 1, argstr='%d', position=3,
                           desc='return the log jacobian')
-    useGeometric = traits.Enum(0, 1, argstr='%d', mandatory=False, position=4,
+    useGeometric = traits.Enum(0, 1, argstr='%d', position=4,
                           desc='return the geometric jacobian')
 
 class CreateJacobianDeterminantImageOutputSpec(TraitedSpec):

nipype/algorithms/tests/test_auto_Overlap.py

@@ -1844,7 +1844,7 @@ def _filename_from_source(self, name, chain=None):
                 # special treatment for files
                 try:
                     _, base, source_ext = split_filename(source)
-                except AttributeError:
+                except (AttributeError, TypeError):
                     base = source
             else:
                 if name in chain:

nipype/algorithms/tests/test_auto_TSNR.py

@@ -8,7 +8,7 @@
 """
 
 from .base import (FSLCommand, Info, check_fsl, no_fsl, no_fsl_course_data)
-from .preprocess import (FAST, FLIRT, ApplyXfm, ApplyXFM, BET, MCFLIRT, FNIRT,
+from .preprocess import (FAST, FLIRT, ApplyXFM, BET, MCFLIRT, FNIRT,
                          ApplyWarp, SliceTimer, SUSAN, PRELUDE, FUGUE, FIRST)
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,

nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py

@@ -49,7 +49,6 @@ class Level1DesignInputSpec(BaseInterfaceInputSpec):
               "{'dgamma': {'derivs': True}}"))
     orthogonalization = traits.Dict(traits.Int, traits.Dict(traits.Int,
         traits.Either(traits.Bool,traits.Int)),
-        mandatory=False,
         desc=("which regressors to make orthogonal e.g., "
               "{1: {0:0,1:0,2:0}, 2: {0:1,1:1,2:0}} to make the second "
               "regressor in a 2-regressor model orthogonal to the first."),