FIX: PEP8 - E124 closing bracket does not match visual indentation

miykael · miykael · commit a0dde7a20e7c · 2015-10-17T17:47:12.000+02:00
diff --git a/examples/dmri_camino_dti.py b/examples/dmri_camino_dti.py
@@ -230,7 +230,7 @@ def get_affine(volume):
 
 tractography.connect([(image2voxel, dtifit,[['voxel_order','in_file']]),
                       (fsl2scheme, dtifit,[['scheme','scheme_file']])
-                     ])
+                      ])
 
 """
 Workflow for applying DT streamline tractogpahy
@@ -302,8 +302,8 @@ def get_affine(volume):
                   (datasource,tractography,[('dwi','inputnode.dwi'),
                                             ('bvals','inputnode.bvals'),
                                             ('bvecs','inputnode.bvecs')
-                                           ])
-                 ])
+                                            ])
+                  ])
 """
 The following functions run the whole workflow and produce a .dot and .png graph of the processing pipeline.
 """
diff --git a/examples/dmri_connectivity.py b/examples/dmri_connectivity.py
@@ -390,7 +390,7 @@ def select_aparc_annot(list_of_files):
                                                 ("bvals", "bval_file")]),
                        (image2voxel, dtifit,[['voxel_order','in_file']]),
                        (fsl2scheme, dtifit,[['scheme','scheme_file']])
-                      ])
+                 ])
 
 """
 Nifti conversions for the parcellated white matter image (used in Camino's conmap),
@@ -483,7 +483,7 @@ def select_aparc_annot(list_of_files):
 mapping.connect([(track, camino2trackvis, [('tracked','in_file')]),
                        (track, vtkstreamlines,[['tracked','in_file']]),
                        (camino2trackvis, trk2camino,[['trackvis','in_file']])
-                      ])
+                 ])
 mapping.connect([(inputnode, camino2trackvis,[(('dwi', get_vox_dims), 'voxel_dims'),
     (('dwi', get_data_dims), 'data_dims')])])
 
@@ -568,7 +568,7 @@ def select_aparc_annot(list_of_files):
                     (datasource,mapping,[('dwi','inputnode.dwi'),
                                                ('bvals','inputnode.bvals'),
                                                ('bvecs','inputnode.bvecs')
-                                               ]),
+                                         ]),
         (infosource,mapping,[('subject_id','inputnode.subject_id')])
                 ])
 
diff --git a/examples/dmri_connectivity_advanced.py b/examples/dmri_connectivity_advanced.py
@@ -425,7 +425,7 @@
 mapping.connect([(dwi2tensor, tensor2vector,[['tensor','in_file']]),
                        (dwi2tensor, tensor2adc,[['tensor','in_file']]),
                        (dwi2tensor, tensor2fa,[['tensor','in_file']]),
-                      ])
+                 ])
 mapping.connect([(tensor2fa, MRmult_merge,[("FA","in1")])])
 mapping.connect([(tensor2fa, MRconvert_fa,[("FA","in_file")])])
 
@@ -582,7 +582,7 @@
                     (datasource,mapping,[('dwi','inputnode.dwi'),
                                                ('bvals','inputnode.bvals'),
                                                ('bvecs','inputnode.bvecs')
-                                               ]),
+                                         ]),
         (infosource,mapping,[('subject_id','inputnode.subject_id')])
                 ])
 
diff --git a/examples/dmri_dtk_odf.py b/examples/dmri_dtk_odf.py
@@ -198,7 +198,7 @@
                     (compute_ODF,tractography,[('bet.mask_file','odf_tracker.mask1_file'),
                                                  ('odf_recon.ODF','odf_tracker.ODF'),
                                                  ('odf_recon.max','odf_tracker.max')
-                                                 ])
+                                               ])
                 ])
 
 dwiproc.inputs.compute_ODF.hardi_mat.oblique_correction = True
diff --git a/examples/dmri_fsl_dti.py b/examples/dmri_fsl_dti.py
@@ -229,7 +229,7 @@
                                             ]),
                       (probtrackx,findthebiggest,[('targets','in_files')]),
                       (flirt, probtrackx, [('out_matrix_file','xfm')])
-                     ])
+                      ])
 
 
 """
diff --git a/examples/dmri_mrtrix_dti.py b/examples/dmri_mrtrix_dti.py
@@ -184,7 +184,7 @@
 tractography.connect([(dwi2tensor, tensor2vector,[['tensor','in_file']]),
                                            (dwi2tensor, tensor2adc,[['tensor','in_file']]),
                                            (dwi2tensor, tensor2fa,[['tensor','in_file']]),
-                                          ])
+                      ])
 tractography.connect([(tensor2fa, MRmult_merge,[("FA","in1")])])
 
 """
@@ -253,7 +253,7 @@
                     (datasource,tractography,[('dwi','inputnode.dwi'),
                                                ('bvals','inputnode.bvals'),
                                                ('bvecs','inputnode.bvecs')
-                                               ])
+                                              ])
                 ])
 
 if __name__ == '__main__':
diff --git a/examples/dmri_tbss_nki.py b/examples/dmri_tbss_nki.py
@@ -120,7 +120,7 @@
                                         'inputnode.distance_map')]),
                   (tbss_source, tbss_MD, [('md_list',
                                            'inputnode.file_list')]),
-            ])
+                  ])
 
 if __name__ == '__main__':
     tbssproc.write_graph()
diff --git a/examples/fmri_ants_openfmri.py b/examples/fmri_ants_openfmri.py
@@ -997,12 +997,12 @@ def get_subs(subject_id, conds, run_id, model_id, task_id):
                                   ('varcopes', 'varcopes'),
                                   ('zstats', 'zstats'),
                                   ('tstats', 'tstats')])
-                                 ])
+                ])
     wf.connect([(modelfit.get_node('modelgen'), datasink,
                                  [('design_cov', 'qa.model'),
                                   ('design_image', 'qa.model.@matrix_image'),
                                   ('design_file', 'qa.model.@matrix'),
-                                 ])])
+                                  ])])
     wf.connect([(preproc, datasink, [('outputspec.motion_parameters',
                                       'qa.motion'),
                                      ('outputspec.motion_plots',
diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py
@@ -362,7 +362,7 @@
                     (volanalysis, volnorm, [('contrastestimate.con_images',
                                              'convertimg2nii.in_file'),
                                             ])
-                  ])
+                    ])
 
 
 """
diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py
@@ -79,7 +79,7 @@
                          (art, modelspec, [('outlier_files', 'outlier_files')]),
                          (modelspec, modelfit, [('session_info', 'inputspec.session_info')]),
                          (preproc, modelfit, [('outputspec.highpassed_files', 'inputspec.functional_data')])
-                        ])
+                         ])
 
 
 """
@@ -240,7 +240,7 @@ def subjectinfo(subject_id):
                          (infosource, modelspec, [(('subject_id', subjectinfo),
                                                    'subject_info')]),
                          (datasource, preproc, [('func', 'inputspec.func')]),
-                    ])
+                         ])
 
 """
 Execute the pipeline
diff --git a/examples/fmri_openfmri.py b/examples/fmri_openfmri.py
@@ -303,7 +303,7 @@ def num_copes(files):
                                         'inputspec.varcopes'),
                                        (('outputspec.copes', num_copes),
                                         'l2model.num_copes'),
-                                       ])
+                                      ])
                 ])
 
     wf.connect(preproc, 'outputspec.mean', registration, 'inputspec.mean_image')
@@ -398,7 +398,7 @@ def get_subs(subject_id, conds, model_id, task_id):
                                   ('varcopes', 'varcopes'),
                                   ('zstats', 'zstats'),
                                   ('tstats', 'tstats')])
-                                 ])
+                ])
     wf.connect([(splitfunc, datasink,
                  [('copes', 'copes.mni'),
                   ('varcopes', 'varcopes.mni'),
diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py
@@ -207,7 +207,7 @@
                                             'level1design.mask_image'),
                                            ('normalize_struct.normalized_files',
                                             'overlaystats.background_image')]),
-                  ])
+                    ])
 
 
 """
diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py
@@ -213,7 +213,7 @@
                                             'level1design.mask_image'),
                                            ('normalize.normalized_source',
                                             'overlaystats.background_image')]),
-                  ])
+                    ])
 
 
 """
diff --git a/examples/howto_caching_example.py b/examples/howto_caching_example.py
@@ -36,7 +36,7 @@
 # Merge all these files along the time dimension
 out_merge = mem.cache(fsl.Merge)(dimension="t",
                             in_files=[t.outputs.out_file for t in threshold],
-                        )
+                                 )
 # And finally compute the mean
 out_mean = mem.cache(fsl.MeanImage)(in_file=out_merge.outputs.merged_file)
 
diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py
@@ -514,13 +514,13 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
                        'min': np.min(mc_in, axis=0).tolist(),
                        'max': np.max(mc_in, axis=0).tolist(),
                        'std': np.std(mc_in, axis=0).tolist()},
-                      ]},
+                     ]},
          {'intensity': [{'using differences': self.inputs.use_differences[1]},
                          {'mean': np.mean(gz, axis=0).tolist(),
                           'min': np.min(gz, axis=0).tolist(),
                           'max': np.max(gz, axis=0).tolist(),
                           'std': np.std(gz, axis=0).tolist()},
-                         ]},
+                        ]},
                  ]
         if self.inputs.use_norm:
             stats.insert(3, {'motion_norm':
diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py
@@ -309,7 +309,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
           'stages linear transform; this allows multiple linear stages to be run where '
           'each stage directly updates the estimated linear transform from the previous '
           'stage. (e.g. Translation -> Rigid -> Affine). '
-          ))
+              ))
     # NOTE: Even though only 0=False and 1=True are allowed, ants uses integer
     # values instead of booleans
     float = traits.Bool(
diff --git a/nipype/interfaces/ants/visualization.py b/nipype/interfaces/ants/visualization.py
@@ -29,7 +29,7 @@ class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec):
             desc=('Possible colormaps: grey, red, green, '
                 'blue, copper, jet, hsv, spring, summer, '
                 'autumn, winter, hot, cool, overunder, custom '
-                ), mandatory = True, position = 4)
+                  ), mandatory = True, position = 4)
     custom_color_map_file=traits.Str('none', argstr='%s', usedefault=True,
             desc = 'custom color map file', position = 5)
     minimum_input = traits.Int(argstr='%d', desc='minimum input',
@@ -110,14 +110,14 @@ class CreateTiledMosaicInputSpec(ANTSCommandInputSpec):
           'value (default = 0). If a mask is specified, the user can use '
           'the mask to define the region, by using the keyword "mask"'
           ' plus an offset, e.g. "-p mask+3".'
-        )
+                             )
     slices = traits.Str(argstr='-s %s',
         desc = ('Number of slices to increment Slice1xSlice2xSlice3'
         '[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]'))
     flip_slice = traits.Str(argstr = '-f %s',
         desc = ('flipXxflipY'))
     permute_axes = traits.Bool(argstr = '-g', desc = 'doPermute'
-        )
+                               )
 
 
 class CreateTiledMosaicOutputSpec(TraitedSpec):
diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py
@@ -209,7 +209,7 @@ class LookupMetaInputSpec(TraitedSpec):
                               desc=("List of meta data keys to lookup, or a "
                               "dict where keys specify the meta data keys to "
                               "lookup and the values specify the output names")
-                             )
+                              )
 
 
 class LookupMeta(BaseInterface):
@@ -299,12 +299,12 @@ def _run_interface(self, runtime):
             classes = [cls
                        for cls in classes
                        if cls in self.inputs.include_classes
-                      ]
+                       ]
         if self.inputs.exclude_classes:
             classes = [cls
                        for cls in classes
                        if not cls in self.inputs.exclude_classes
-                      ]
+                       ]
 
         for cls in classes:
             src_dict = src.meta_ext.get_class_dict(cls)
@@ -359,10 +359,10 @@ class MergeNifti(NiftiGeneratorBase):
     def _run_interface(self, runtime):
         niis = [nb.load(fn)
                 for fn in self.inputs.in_files
-               ]
+                ]
         nws = [NiftiWrapper(nii, make_empty=True)
                for nii in niis
-              ]
+               ]
         if self.inputs.sort_order:
             sort_order = self.inputs.sort_order
             if isinstance(sort_order, string_types):
diff --git a/nipype/interfaces/fsl/tests/test_FILMGLS.py b/nipype/interfaces/fsl/tests/test_FILMGLS.py
@@ -21,7 +21,7 @@ def test_filmgls():
                     threshold = dict(argstr='%f',),
                     tukey_window = dict(xor=['autocorr_estimate_only', 'fit_armodel', 'tukey_window', 'multitaper_product', 'use_pava', 'autocorr_noestimate'],argstr='-tukey %d',),
                     use_pava = dict(argstr='-pava',),
-                    )
+                     )
     input_map2 = dict(args = dict(argstr='%s',),
                      autocorr_estimate_only = dict(xor=['autocorr_estimate_only', 'fit_armodel', 'tukey_window', 'multitaper_product', 'use_pava', 'autocorr_noestimate'],argstr='--ac',),
                      autocorr_noestimate = dict(xor=['autocorr_estimate_only', 'fit_armodel', 'tukey_window', 'multitaper_product', 'use_pava', 'autocorr_noestimate'],argstr='--noest',),
diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py
@@ -144,7 +144,7 @@ def _run_interface(self, runtime):
                hrf_model=self.inputs.hrf_model,
                add_regs=reg_vals,
                add_reg_names=reg_names
-               )
+                                                       )
         if self.inputs.normalize_design_matrix:
             for i in range(len(self._reg_names)-1):
                 design_matrix[:,i] = ((design_matrix[:,i] -
diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
@@ -375,8 +375,8 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
                                  (self.procs[jobid].overwrite == False or
                                    (self.procs[jobid].overwrite == None and
                                     not self.procs[jobid]._interface.always_run)
-                                 )
-                               ):
+                                  )
+                                ):
                                 continue_with_submission = False
                                 self._task_finished_cb(jobid)
                                 self._remove_node_dirs()
diff --git a/nipype/utils/misc.py b/nipype/utils/misc.py
@@ -93,7 +93,7 @@ def create_function_from_source(function_source, imports=None):
                           "They cannot be declared either interactively or inside",
                           "another function or inline in the connect string. Any",
                           "imports should be done inside the function"
-                           ])
+                          ])
         raise RuntimeError(msg)
     ns_funcs = list(set(ns) - set(import_keys + ['__builtins__']))
     assert len(ns_funcs) == 1, "Function or inputs are ill-defined"
diff --git a/nipype/workflows/dmri/camino/connectivity_mapping.py b/nipype/workflows/dmri/camino/connectivity_mapping.py
@@ -59,7 +59,7 @@ def create_connectivity_pipeline(name="connectivity"):
                                                                   "bvals",
                                                                   "subjects_dir",
                                                                   "resolution_network_file",
-                                                                  ]),
+                                                                        ]),
                          name="inputnode_within")
 
     FreeSurferSource = pe.Node(interface=nio.FreeSurferSource(), name='fssource')
@@ -279,7 +279,7 @@ def create_connectivity_pipeline(name="connectivity"):
                                                     ("bvals", "bval_file")]),
                            (image2voxel, dtifit,[['voxel_order','in_file']]),
                            (fsl2scheme, dtifit,[['scheme','scheme_file']])
-                          ])
+                     ])
 
     """
     Nifti conversions for the subject's stripped brain image from Freesurfer:
@@ -372,7 +372,7 @@ def create_connectivity_pipeline(name="connectivity"):
     mapping.connect([(track, camino2trackvis, [('tracked','in_file')]),
                            (track, vtkstreamlines,[['tracked','in_file']]),
                            (camino2trackvis, trk2camino,[['trackvis','in_file']])
-                          ])
+                     ])
     mapping.connect([(inputnode_within, camino2trackvis,[(('dwi', get_vox_dims), 'voxel_dims'),
         (('dwi', get_data_dims), 'data_dims')])])
 
@@ -475,7 +475,7 @@ def create_connectivity_pipeline(name="connectivity"):
                                               ("subject_id", "inputnode_within.subject_id"),
                                               ("subjects_dir", "inputnode_within.subjects_dir"),
                                               ("resolution_network_file", "inputnode_within.resolution_network_file")])
-                                              ])
+                          ])
 
     connectivity.connect([(mapping, outputnode, [("camino2trackvis.trackvis", "tracts"),
         ("CFFConverter.connectome_file", "connectome"),
diff --git a/nipype/workflows/dmri/camino/group_connectivity.py b/nipype/workflows/dmri/camino/group_connectivity.py
@@ -94,6 +94,6 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_
                                               ("outputnode.networks", "@l1output.networks"),
                                               ("outputnode.mean_fiber_length", "@l1output.mean_fiber_length"),
                                               ("outputnode.fiber_length_std", "@l1output.fiber_length_std"),
-                                              ])])
+                                               ])])
     l1pipeline.connect([(group_infosource, datasink,[('group_id','@group_id')])])
     return l1pipeline
diff --git a/nipype/workflows/dmri/connectivity/group_connectivity.py b/nipype/workflows/dmri/connectivity/group_connectivity.py
@@ -176,8 +176,7 @@ def create_merge_network_results_by_group_workflow(group_list, group_id, data_di
     group_infosource.inputs.group_id = group_id
 
     l2infosource = pe.Node(interface=util.IdentityInterface(fields=['group_id',
-    'merged',
-    ]), name='l2infosource')
+        'merged']), name='l2infosource')
 
     l2source = pe.Node(
         nio.DataGrabber(
diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py
diff --git a/nipype/workflows/dmri/fsl/tbss.py b/nipype/workflows/dmri/fsl/tbss.py
diff --git a/nipype/workflows/dmri/mrtrix/connectivity_mapping.py b/nipype/workflows/dmri/mrtrix/connectivity_mapping.py
diff --git a/nipype/workflows/dmri/mrtrix/diffusion.py b/nipype/workflows/dmri/mrtrix/diffusion.py
diff --git a/nipype/workflows/dmri/mrtrix/group_connectivity.py b/nipype/workflows/dmri/mrtrix/group_connectivity.py
diff --git a/nipype/workflows/fmri/fsl/preprocess.py b/nipype/workflows/fmri/fsl/preprocess.py
diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
diff --git a/setup.py b/setup.py
diff --git a/tools/setup.py b/tools/setup.py
