sty: removed white space as a result of check-before-commit

Author: satra

doc/sphinxext/autosummary_generate.py

@@ -54,7 +54,7 @@ def main():
     for name, path in sorted(names.items()):
         if options.output_dir is not None:
             path = options.output_dir
-        
+
         if not os.path.isdir(path):
             os.makedirs(path)
 
@@ -121,7 +121,7 @@ def get_documented_in_docstring(name, module=None, filename=None):
     """
     Find out what items are documented in the given object's docstring.
     See `get_documented_in_lines`.
-    
+
     """
     try:
         obj, real_name = import_by_name(name)
@@ -136,7 +136,7 @@ def get_documented_in_docstring(name, module=None, filename=None):
 def get_documented_in_lines(lines, module=None, filename=None):
     """
     Find out what items are documented in the given lines
-    
+
     Returns
     -------
     documented : dict of list of (filename, title, keyword, toctree)
@@ -153,15 +153,15 @@ def get_documented_in_lines(lines, module=None, filename=None):
     module_re = re.compile(r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
     autosummary_item_re = re.compile(r'^\s+([_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')
     toctree_arg_re = re.compile(r'^\s+:toctree:\s*(.*?)\s*$')
-    
+
     documented = {}
-   
+
     current_title = []
     last_line = None
     toctree = None
     current_module = module
     in_autosummary = False
-    
+
     for line in lines:
         try:
             if in_autosummary:

doc/sphinxext/inheritance_diagram.py

@@ -48,7 +48,7 @@ def my_import(name):
     """Module importer - taken from the python documentation.
 
     This function allows importing names with dots in them."""
-    
+
     mod = __import__(name)
     components = name.split('.')
     for comp in components[1:]:
@@ -103,7 +103,7 @@ def _import_class_or_module(self, name):
             # second call will force the equivalent of 'import a.b' to happen
             # after the top-level import above.
             my_import(fullname)
-            
+
         except ImportError:
             raise ValueError(
                 "Could not import class or module '%s' specified for inheritance diagram" % name)

doc/sphinxext/ipython_console_highlighting.py

@@ -11,7 +11,7 @@
 
 # Third party
 from pygments.lexer import Lexer, do_insertions
-from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer, 
+from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer,
                                    PythonTracebackLexer)
 from pygments.token import Comment, Generic
 
@@ -47,7 +47,7 @@ class IPythonConsoleLexer(Lexer):
 
       - It assumes the default IPython prompts, not customized ones.
     """
-    
+
     name = 'IPython console session'
     aliases = ['ipython']
     mimetypes = ['text/x-ipython-console']

nipype/external/provcopy.py

@@ -328,7 +328,7 @@ def provn_representation(self):
 
     def json_representation(self):
         return {'$': self._uri, 'type': u'xsd:anyURI'}
-    
+
     def rdf_representation(self):
         return URIRef(self.get_uri())
 
@@ -703,7 +703,7 @@ def rdf(self, graph=None, subj=None):
                     obj = RDFLiteral(value)
                 graph.add((subj, pred, obj))
         return graph
-        
+
     def is_asserted(self):
         return self._asserted
 
@@ -718,7 +718,7 @@ def is_relation(self):
 class ProvElement(ProvRecord):
     def is_element(self):
         return True
-    
+
     def rdf(self, graph=None):
         if graph is None:
             graph = Graph()
@@ -1524,15 +1524,15 @@ def rdf(self, graph=None):
             # graph should not None here
             uri = self.get_identifier().rdf_representation()
             graph = Graph(graph.store, uri)
-        
+
         for prefix, namespace in self._namespaces.items():
             graph.bind(prefix, namespace.get_uri())
-        
+
         for record in self._records:
             if record.is_asserted():
                 record.rdf(graph)
         return graph
-    
+
     def get_provjson(self, **kw):
         """Return the `PROV-JSON <http://www.w3.org/Submission/prov-json/>`_ representation for the bundle/document.
 

nipype/interfaces/afni/base.py

@@ -101,7 +101,7 @@ def standard_image(img_name):
 class AFNIBaseCommandInputSpec(CommandLineInputSpec):
     outputtype = traits.Enum('AFNI', Info.ftypes.keys(),
                              desc='AFNI output filetype')
-    
+
 class AFNITraitedSpec(AFNIBaseCommandInputSpec):
     pass
 
@@ -113,12 +113,12 @@ class AFNIBaseCommand(CommandLine):
 
     input_spec = AFNIBaseCommandInputSpec
     _outputtype = None
-    
+
 
     def __init__(self, **inputs):
         super(AFNIBaseCommand, self).__init__(**inputs)
         self.inputs.on_trait_change(self._output_update, 'outputtype')
-        
+
         if self._outputtype is None:
             self._outputtype = Info.outputtype()
 

nipype/interfaces/afni/preprocess.py

@@ -334,9 +334,9 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     mask_only_targets = traits.Bool(desc="use mask only on targets voxels",
                                     argstr="-mask_only_targets",
                                     xor=['mask_source'])
-                                    
-    mask_source = File(exists=True, 
-                        desc="mask for source voxels", 
+
+    mask_source = File(exists=True,
+                        desc="mask for source voxels",
                         argstr="-mask_source %s",
                         xor=['mask_only_targets'])
 

nipype/interfaces/ants/registration.py

@@ -390,7 +390,7 @@ class Registration(ANTSCommand):
     """
     DEF_SAMPLING_STRATEGY = 'Dense'
     """The default sampling stratey argument."""
-    
+
     _cmd = 'antsRegistration'
     input_spec = RegistrationInputSpec
     output_spec = RegistrationOutputSpec
@@ -399,7 +399,7 @@ class Registration(ANTSCommand):
     def _formatMetric(self, index):
         """
         Format the antsRegistration -m metric argument(s).
-        
+
         Parameters
         ----------
         index: the stage index
@@ -427,7 +427,7 @@ def _formatMetric(self, index):
             sampling_percentage = self.inputs.sampling_percentage[index]
             if sampling_percentage:
                 stage_inputs['sampling_percentage'] = sampling_percentage
-        
+
         # Make a list of metric specifications, one per -m command line
         # argument for the current stage.
         # If there are multiple inputs for this stage, then convert the
@@ -442,15 +442,15 @@ def _formatMetric(self, index):
             specs = [dict([(k, v[i]) for k,v in items]) for i in indexes]
         else:
             specs = [stage_inputs]
-        
+
         # Format the --metric command line metric arguments, one per specification.
         return [self._formatMetricArgument(fixed, moving, **spec) for spec in specs]
-    
+
     def _formatMetricArgument(self, fixed, moving, **kwargs):
         retval = '%s[ %s, %s, %g, %d' % (kwargs['metric'],
                                          fixed, moving, kwargs['weight'],
                                          kwargs['radius_or_bins'])
-        
+
         # The optional sampling strategy.
         if kwargs.has_key('sampling_strategy'):
             sampling_strategy = kwargs['sampling_strategy']
@@ -465,9 +465,9 @@ def _formatMetricArgument(self, fixed, moving, **kwargs):
             retval += ', %s' % sampling_strategy
             if kwargs.has_key('sampling_percentage'):
                 retval += ', %g' % kwargs['sampling_percentage']
-        
+
         retval += ' ]'
-        
+
         return retval
 
     def _formatTransform(self, index):

nipype/interfaces/ants/resampling.py

@@ -99,7 +99,7 @@ def _list_outputs(self):
                                                         self.inputs.out_postfix,
                                                         ext)))
         return outputs
-    
+
     def _run_interface(self, runtime):
         runtime = super(WarpTimeSeriesImageMultiTransform, self)._run_interface(runtime, correct_return_codes = [0,1])
         if "100 % complete" not in runtime.stdout:

nipype/interfaces/base.py

@@ -1369,7 +1369,7 @@ class CommandLineInputSpec(BaseInterfaceInputSpec):
                                   desc=('Control terminal output: `stream` - displays'
                                   'to terminal immediately, `allatonce` - waits till '
                                   'command is finished to display output, `file` - writes'
-                                  'output to file, `none` - output is ignored'), 
+                                  'output to file, `none` - output is ignored'),
                                   nohash=True, mandatory=True)
 
 class CommandLine(BaseInterface):
@@ -1692,17 +1692,17 @@ def _gen_outfilename(self):
         raise NotImplementedError
 
 class MpiCommandLineInputSpec(CommandLineInputSpec):
-    use_mpi = traits.Bool(False, 
+    use_mpi = traits.Bool(False,
                           desc="Whether or not to run the command with mpiexec",
                           usedefault=True)
     n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not "
                          "specify if this is managed externally (e.g. through "
                          "SGE)")
-    
+
 
 class MpiCommandLine(CommandLine):
-    '''Implements functionality to interact with command line programs 
-    that can be run with MPI (i.e. using 'mpiexec'). 
+    '''Implements functionality to interact with command line programs
+    that can be run with MPI (i.e. using 'mpiexec').
 
     Examples
     --------
@@ -1711,21 +1711,21 @@ class MpiCommandLine(CommandLine):
     >>> mpi_cli.inputs.args = '-v'
     >>> mpi_cli.cmdline
     'my_mpi_prog -v'
-    
+
     >>> mpi_cli.inputs.use_mpi = True
     >>> mpi_cli.inputs.n_procs = 8
-    >>> mpi_cli.cmdline    
+    >>> mpi_cli.cmdline
     'mpiexec -n 8 my_mpi_prog -v'
     '''
     input_spec = MpiCommandLineInputSpec
-    
+
     @property
     def cmdline(self):
         """Adds 'mpiexec' to begining of command"""
         result = []
         if self.inputs.use_mpi:
             result.append('mpiexec')
-            if self.inputs.n_procs: 
+            if self.inputs.n_procs:
                 result.append('-n %d' % self.inputs.n_procs)
         result.append(super(MpiCommandLine, self).cmdline)
         return ' '.join(result)

nipype/interfaces/c3.py

@@ -29,7 +29,7 @@ class C3dAffineTool(SEMLikeCommandLine):
 
     Example
     =======
-    
+
     >>> from nipype.interfaces.c3 import C3dAffineTool
     >>> c3 = C3dAffineTool()
     >>> c3.inputs.source_file = 'cmatrix.mat'