sty: pep8 and metadata fixes

Author: satra

nipype/interfaces/mrtrix/preprocess.py

@@ -84,24 +84,41 @@ def _gen_outfilename(self):
 class DWI2TensorInputSpec(CommandLineInputSpec):
     in_file = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
                              position=-2, desc='Diffusion-weighted images')
-    out_filename = File(name_template="%s_tensor.mif", name_source="in_file", output_name="tensor",
-                        argstr='%s', posidesc='Output tensor filename', position=-1)
-    encoding_file = File(argstr='-grad %s', position= 2,
+    out_filename = File(name_template="%s_tensor.mif", name_source="in_file",
+                        output_name="tensor", argstr='%s',
+                        desc='Output tensor filename', position=-1)
+    encoding_file = File(argstr='-grad %s', position=2,
                          desc=('Encoding file supplied as a 4xN text file with '
                                'each line is in the format [ X Y Z b ], where '
                                '[ X Y Z ] describe the direction of the applied '
                                'gradient, and b gives the b-value in units '
                                '(1000 s/mm^2). See FSL2MRTrix()'))
     ignore_slice_by_volume = traits.List(traits.Int, argstr='-ignoreslices %s',
-                                         sep=' ', position=2, minlen=2, maxlen=2,
-        desc='Requires two values (i.e. [34 1] for [Slice Volume] Ignores the image slices specified when computing the tensor. Slice here means the z coordinate of the slice to be ignored.')
-    ignore_volumes = traits.List(traits.Int, argstr='-ignorevolumes %s', sep=' ', position=2, minlen=1,
-        desc='Requires two values (i.e. [2 5 6] for [Volumes] Ignores the image volumes specified when computing the tensor.')
-    quiet = traits.Bool(argstr='-quiet', position=1, desc="Do not display information messages or progress status.")
-    debug = traits.Bool(argstr='-debug', position=1, desc="Display debugging messages.")
+                                         sep=' ', position=2, minlen=2,
+                                         maxlen=2,
+                                         desc=('Requires two values (i.e. [34 '
+                                               '1] for [Slice Volume] Ignores '
+                                               'the image slices specified '
+                                               'when computing the tensor. '
+                                               'Slice here means the z '
+                                               'coordinate of the slice to be '
+                                               'ignored.'))
+    ignore_volumes = traits.List(traits.Int, argstr='-ignorevolumes %s',
+                                 sep=' ', position=2, minlen=1,
+                                 desc=('Requires two values (i.e. [2 5 6] for '
+                                       '[Volumes] Ignores the image volumes '
+                                       'specified when computing the tensor.'))
+    quiet = traits.Bool(argstr='-quiet', position=1,
+                        desc=("Do not display information messages or progress "
+                              "status."))
+    debug = traits.Bool(argstr='-debug', position=1,
+                        desc="Display debugging messages.")
+
 
 class DWI2TensorOutputSpec(TraitedSpec):
-    tensor = File(exists=True, desc='path/name of output diffusion tensor image')
+    tensor = File(exists=True,
+                  desc='path/name of output diffusion tensor image')
+
 
 class DWI2Tensor(CommandLine):
     """

nipype/interfaces/utility.py

@@ -150,7 +150,7 @@ class RenameInputSpec(DynamicTraitedSpec):
                                         "template"))
     parse_string = traits.String(desc=("Python regexp parse string to define "
                                        "replacement inputs"))
-    use_fullpath = traits.Bool(False, use_default=True,
+    use_fullpath = traits.Bool(False, usedefault=True,
                                desc="Use full path as input to regex parser")
 
 

tools/checkspecs.py

@@ -179,7 +179,7 @@ def test_specs(self, uri):
                         'copyfile', 'usedefault', 'sep', 'hash_files',
                         'deprecated', 'new_name', 'min_ver', 'max_ver',
                         'name_source', 'name_template', 'keep_extension',
-                        'units']
+                        'units', 'output_name']
         in_built = ['type', 'copy', 'parent', 'instance_handler',
                     'comparison_mode', 'array', 'default', 'editor']
         bad_specs = []