fixing tests and install errors

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/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.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/interfaces/ants/utils.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/interfaces/base.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/interfaces/fsl/__init__.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/fsl/model.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."),

nipype/interfaces/fsl/preprocess.py

@@ -594,16 +594,6 @@ class ApplyXFM(FLIRT):
     """
     input_spec = ApplyXFMInputSpec
 
-class ApplyXfm(ApplyXFM):
-    """
-    .. deprecated:: 0.12.1
-       Use :py:class:`nipype.interfaces.fsl.ApplyXFM` instead
-    """
-    def __init__(self, **inputs):
-        super(ApplyXfm, self).__init__(**inputs)
-        warn(('This interface has been renamed since 0.12.1, please use '
-              'nipype.interfaces.fsl.ApplyXFM'),
-             UserWarning)
 
 class MCFLIRTInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, position=0, argstr="-in %s", mandatory=True,
@@ -751,7 +741,7 @@ class FNIRTInputSpec(FSLCommandInputSpec):
     inwarp_file = File(exists=True, argstr='--inwarp=%s',
                        desc='name of file containing initial non-linear warps')
     in_intensitymap_file = traits.List(File(exists=True), argstr='--intin=%s',
-                                       copyfiles=False, minlen=1, maxlen=2,
+                                       copyfile=False, minlen=1, maxlen=2,
                                        desc=('name of file/files containing '
                                              'initial intensity mapping '
                                              'usually generated by previous '

nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py

@@ -1,9 +1,9 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from __future__ import unicode_literals
-from ..preprocess import ApplyXfm
+from ..preprocess import ApplyXFM
 
 
-def test_ApplyXfm_inputs():
+def test_ApplyXFM_inputs():
     input_map = dict(angle_rep=dict(argstr='-anglerep %s',
     ),
     apply_isoxfm=dict(argstr='-applyisoxfm %f',
@@ -145,19 +145,19 @@ def test_ApplyXfm_inputs():
     min_ver='5.0.0',
     ),
     )
-    inputs = ApplyXfm.input_spec()
+    inputs = ApplyXFM.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 
 
-def test_ApplyXfm_outputs():
+def test_ApplyXFM_outputs():
     output_map = dict(out_file=dict(),
     out_log=dict(),
     out_matrix_file=dict(),
     )
-    outputs = ApplyXfm.output_spec()
+    outputs = ApplyXFM.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/interfaces/fsl/tests/test_auto_FNIRT.py

@@ -48,7 +48,7 @@ def test_FNIRT_inputs():
     sep=',',
     ),
     in_intensitymap_file=dict(argstr='--intin=%s',
-    copyfiles=False,
+    copyfile=False,
     ),
     inmask_file=dict(argstr='--inmask=%s',
     ),

nipype/interfaces/fsl/tests/test_auto_Level1Design.py

@@ -14,8 +14,7 @@ def test_Level1Design_inputs():
     ),
     model_serial_correlations=dict(mandatory=True,
     ),
-    orthogonalization=dict(mandatory=False,
-    ),
+    orthogonalization=dict(),
     session_info=dict(mandatory=True,
     ),
     )

nipype/interfaces/fsl/tests/test_maths.py

@@ -12,7 +12,7 @@
 from nipype.interfaces.fsl import no_fsl
 
 import pytest
-from nipype.testing.fixtures import create_files_in_directory_plus_output_type 
+from nipype.testing.fixtures import create_files_in_directory_plus_output_type
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")

nipype/interfaces/tests/test_base.py

@@ -209,7 +209,8 @@ class spec2(nib.CommandLineInputSpec):
                        position=2)
         doo = nib.File(exists=True, argstr="%s", position=1)
         goo = traits.Int(argstr="%d", position=4)
-        poo = nib.File(name_source=['goo'], hash_files=False, argstr="%s", position=3)
+        poo = nib.File(name_source=['goo'], hash_files=False, argstr="%s",
+                       position=3)
 
     class TestName(nib.CommandLine):
         _cmd = "mycommand"
@@ -218,6 +219,7 @@ class TestName(nib.CommandLine):
     testobj.inputs.doo = tmp_infile
     testobj.inputs.goo = 99
     assert '%s_generated' % nme in testobj.cmdline
+    assert '%d_generated' % testobj.inputs.goo in testobj.cmdline
     testobj.inputs.moo = "my_%s_template"
     assert 'my_%s_template' % nme in testobj.cmdline