FIX: PEP8 - E231 missing whitespace after ','

Author: miykael

doc/conf.py

@@ -15,7 +15,7 @@
 import sys, os
 
 nipypepath = os.path.abspath('..')
-sys.path.insert(1,nipypepath)
+sys.path.insert(1, nipypepath)
 
 import nipype
 
@@ -168,7 +168,7 @@
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'**': ['gse.html','localtoc.html', 'sidebar_versions.html', 'indexsidebar.html'],
+html_sidebars = {'**': ['gse.html', 'localtoc.html', 'sidebar_versions.html', 'indexsidebar.html'],
                  'searchresults': ['sidebar_versions.html', 'indexsidebar.html'],
                  'version': []}
 

doc/sphinxext/numpy_ext/docscrape.py

@@ -28,7 +28,7 @@ def __init__(self, data):
            String with lines separated by '\n'.
 
         """
-        if isinstance(data,list):
+        if isinstance(data, list):
             self._str = data
         else:
             self._str = data.split('\n') # store string as list of lines
@@ -80,7 +80,7 @@ def is_unindented(line):
             return (line.strip() and (len(line.lstrip()) == len(line)))
         return self.read_to_condition(is_unindented)
 
-    def peek(self,n=0):
+    def peek(self, n=0):
         if self._l + n < len(self._str):
             return self[self._l + n]
         else:
@@ -116,10 +116,10 @@ def __init__(self, docstring, config={}):
 
         self._parse()
 
-    def __getitem__(self,key):
+    def __getitem__(self, key):
         return self._parsed_data[key]
 
-    def __setitem__(self,key,val):
+    def __setitem__(self, key, val):
         if key not in self._parsed_data:
             warn("Unknown section %s" % key)
         else:
@@ -139,13 +139,13 @@ def _is_at_section(self):
         l2 = self._doc.peek(1).strip() #    ---------- or ==========
         return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1))
 
-    def _strip(self,doc):
+    def _strip(self, doc):
         i = 0
         j = 0
-        for i,line in enumerate(doc):
+        for i, line in enumerate(doc):
             if line.strip(): break
 
-        for j,line in enumerate(doc[::-1]):
+        for j, line in enumerate(doc[::-1]):
             if line.strip(): break
 
         return doc[i:len(doc)-j]
@@ -173,7 +173,7 @@ def _read_sections(self):
             else:
                 yield name, self._strip(data[2:])
 
-    def _parse_param_list(self,content):
+    def _parse_param_list(self, content):
         r = Reader(content)
         params = []
         while not r.eof():
@@ -186,7 +186,7 @@ def _parse_param_list(self,content):
             desc = r.read_to_next_unindented_line()
             desc = dedent_lines(desc)
 
-            params.append((arg_name,arg_type,desc))
+            params.append((arg_name, arg_type, desc))
 
         return params
 
@@ -288,7 +288,7 @@ def _parse(self):
         self._doc.reset()
         self._parse_summary()
 
-        for (section,content) in self._read_sections():
+        for (section, content) in self._read_sections():
             if not section.startswith('..'):
                 section = ' '.join([s.capitalize() for s in section.split(' ')])
             if section in ('Parameters', 'Returns', 'Raises', 'Warns',
@@ -314,7 +314,7 @@ def _str_indent(self, doc, indent=4):
 
     def _str_signature(self):
         if self['Signature']:
-            return [self['Signature'].replace('*','\*')] + ['']
+            return [self['Signature'].replace('*', '\*')] + ['']
         else:
             return ['']
 
@@ -334,7 +334,7 @@ def _str_param_list(self, name):
         out = []
         if self[name]:
             out += self._str_header(name)
-            for param,param_type,desc in self[name]:
+            for param, param_type, desc in self[name]:
                 out += ['%s : %s' % (param, param_type)]
                 out += self._str_indent(desc)
             out += ['']
@@ -376,7 +376,7 @@ def _str_see_also(self, func_role):
     def _str_index(self):
         idx = self['index']
         out = []
-        out += ['.. index:: %s' % idx.get('default','')]
+        out += ['.. index:: %s' % idx.get('default', '')]
         for section, references in list(idx.items()):
             if section == 'default':
                 continue
@@ -393,15 +393,15 @@ def __str__(self, func_role=''):
             out += self._str_param_list(param_list)
         out += self._str_section('Warnings')
         out += self._str_see_also(func_role)
-        for s in ('Notes','References','Examples'):
+        for s in ('Notes', 'References', 'Examples'):
             out += self._str_section(s)
         for param_list in ('Attributes', 'Methods'):
             out += self._str_param_list(param_list)
         out += self._str_index()
         return '\n'.join(out)
 
 
-def indent(str,indent=4):
+def indent(str, indent=4):
     indent_str = ' '*indent
     if str is None:
         return indent_str
@@ -433,7 +433,7 @@ def __init__(self, func, role='func', doc=None, config={}):
                 # try to read signature
                 argspec = inspect.getargspec(func)
                 argspec = inspect.formatargspec(*argspec)
-                argspec = argspec.replace('*','\*')
+                argspec = argspec.replace('*', '\*')
                 signature = '%s%s' % (func_name, argspec)
             except TypeError as e:
                 signature = '%s()' % func_name
@@ -459,7 +459,7 @@ def __str__(self):
         if self._role:
             if self._role not in roles:
                 print("Warning: invalid role %s" % self._role)
-            out += '.. %s:: %s\n    \n\n' % (roles.get(self._role,''),
+            out += '.. %s:: %s\n    \n\n' % (roles.get(self._role, ''),
                                              func_name)
 
         out += super(FunctionDoc, self).__str__(func_role=self._role)
@@ -499,7 +499,7 @@ def __init__(self, cls, doc=None, modulename='', func_doc=FunctionDoc,
     def methods(self):
         if self._cls is None:
             return []
-        return [name for name,func in inspect.getmembers(self._cls)
+        return [name for name, func in inspect.getmembers(self._cls)
                 if ((not name.startswith('_')
                      or name in self.extra_public_methods)
                     and callable(func))]
@@ -508,5 +508,5 @@ def methods(self):
     def properties(self):
         if self._cls is None:
             return []
-        return [name for name,func in inspect.getmembers(self._cls)
+        return [name for name, func in inspect.getmembers(self._cls)
                 if not name.startswith('_') and func is None]

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -42,11 +42,11 @@ def _str_param_list(self, name):
         if self[name]:
             out += self._str_field_list(name)
             out += ['']
-            for param,param_type,desc in self[name]:
+            for param, param_type, desc in self[name]:
                 out += self._str_indent(['**%s** : %s' % (param.strip(),
                                                           param_type)])
                 out += ['']
-                out += self._str_indent(desc,8)
+                out += self._str_indent(desc, 8)
                 out += ['']
         return out
 
@@ -130,7 +130,7 @@ def _str_index(self):
         if len(idx) == 0:
             return out
 
-        out += ['.. index:: %s' % idx.get('default','')]
+        out += ['.. index:: %s' % idx.get('default', '')]
         for section, references in list(idx.items()):
             if section == 'default':
                 continue
@@ -151,9 +151,9 @@ def _str_references(self):
             # Latex collects all references to a separate bibliography,
             # so we need to insert links to it
             if sphinx.__version__ >= "0.6":
-                out += ['.. only:: latex','']
+                out += ['.. only:: latex', '']
             else:
-                out += ['.. latexonly::','']
+                out += ['.. latexonly::', '']
             items = []
             for line in self['References']:
                 m = re.match(r'.. \[([a-z0-9._-]+)\]', line, re.I)
@@ -192,7 +192,7 @@ def __str__(self, indent=0, func_role="obj"):
         out += self._str_examples()
         for param_list in ('Attributes', 'Methods'):
             out += self._str_member_list(param_list)
-        out = self._str_indent(out,indent)
+        out = self._str_indent(out, indent)
         return '\n'.join(out)
 
 class SphinxFunctionDoc(SphinxDocString, FunctionDoc):

examples/dmri_camino_dti.py

@@ -65,8 +65,8 @@ def get_affine(volume):
 """
 
 info = dict(dwi=[['subject_id', 'data']],
-            bvecs=[['subject_id','bvecs']],
-            bvals=[['subject_id','bvals']])
+            bvecs=[['subject_id', 'bvecs']],
+            bvals=[['subject_id', 'bvals']])
 
 infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),
                      name="infosource")
@@ -125,7 +125,7 @@ def get_affine(volume):
 Second, diffusion tensors are fit to the voxel-order data.
 """
 
-dtifit = pe.Node(interface=camino.DTIFit(),name='dtifit')
+dtifit = pe.Node(interface=camino.DTIFit(), name='dtifit')
 
 """
 Next, a lookup table is generated from the schemefile and the
@@ -196,15 +196,15 @@ def get_affine(volume):
 fractional anisotropy and diffusivity trace maps and their associated headers.
 """
 
-fa = pe.Node(interface=camino.ComputeFractionalAnisotropy(),name='fa')
-trace = pe.Node(interface=camino.ComputeTensorTrace(),name='trace')
+fa = pe.Node(interface=camino.ComputeFractionalAnisotropy(), name='fa')
+trace = pe.Node(interface=camino.ComputeTensorTrace(), name='trace')
 dteig = pe.Node(interface=camino.ComputeEigensystem(), name='dteig')
 
 analyzeheader_fa = pe.Node(interface= camino.AnalyzeHeader(), name = "analyzeheader_fa")
 analyzeheader_fa.inputs.datatype = "double"
 analyzeheader_trace = analyzeheader_fa.clone('analyzeheader_trace')
 
-fa2nii = pe.Node(interface=misc.CreateNifti(),name='fa2nii')
+fa2nii = pe.Node(interface=misc.CreateNifti(), name='fa2nii')
 trace2nii = fa2nii.clone("trace2nii")
 
 """
@@ -213,7 +213,7 @@ def get_affine(volume):
 
 tractography = pe.Workflow(name='tractography')
 
-tractography.connect([(inputnode, bet,[("dwi","in_file")])])
+tractography.connect([(inputnode, bet, [("dwi", "in_file")])])
 
 """
 File format conversion
@@ -228,29 +228,29 @@ def get_affine(volume):
 Tensor fitting
 """
 
-tractography.connect([(image2voxel, dtifit,[['voxel_order','in_file']]),
-                      (fsl2scheme, dtifit,[['scheme','scheme_file']])
+tractography.connect([(image2voxel, dtifit, [['voxel_order', 'in_file']]),
+                      (fsl2scheme, dtifit, [['scheme', 'scheme_file']])
                       ])
 
 """
 Workflow for applying DT streamline tractogpahy
 """
 
-tractography.connect([(bet, trackdt,[("mask_file","seed_file")])])
-tractography.connect([(dtifit, trackdt,[("tensor_fitted","in_file")])])
+tractography.connect([(bet, trackdt, [("mask_file", "seed_file")])])
+tractography.connect([(dtifit, trackdt, [("tensor_fitted", "in_file")])])
 
 """
 Workflow for applying PICo
 """
 
-tractography.connect([(bet, trackpico,[("mask_file","seed_file")])])
-tractography.connect([(fsl2scheme, dtlutgen,[("scheme","scheme_file")])])
-tractography.connect([(dtlutgen, picopdfs,[("dtLUT","luts")])])
-tractography.connect([(dtifit, picopdfs,[("tensor_fitted","in_file")])])
-tractography.connect([(picopdfs, trackpico,[("pdfs","in_file")])])
+tractography.connect([(bet, trackpico, [("mask_file", "seed_file")])])
+tractography.connect([(fsl2scheme, dtlutgen, [("scheme", "scheme_file")])])
+tractography.connect([(dtlutgen, picopdfs, [("dtLUT", "luts")])])
+tractography.connect([(dtifit, picopdfs, [("tensor_fitted", "in_file")])])
+tractography.connect([(picopdfs, trackpico, [("pdfs", "in_file")])])
 
 # ProcStreamlines might throw memory errors - comment this line out in such case
-tractography.connect([(trackdt, procstreamlines,[("tracked","in_file")])])
+tractography.connect([(trackdt, procstreamlines, [("tracked", "in_file")])])
 
 
 """
@@ -262,31 +262,31 @@ def get_affine(volume):
 will be correct and readable.
 """
 
-tractography.connect([(dtifit, fa,[("tensor_fitted","in_file")])])
-tractography.connect([(fa, analyzeheader_fa,[("fa","in_file")])])
-tractography.connect([(inputnode, analyzeheader_fa,[(('dwi', get_vox_dims), 'voxel_dims'),
+tractography.connect([(dtifit, fa, [("tensor_fitted", "in_file")])])
+tractography.connect([(fa, analyzeheader_fa, [("fa", "in_file")])])
+tractography.connect([(inputnode, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'),
                                                     (('dwi', get_data_dims), 'data_dims')])])
-tractography.connect([(fa, fa2nii,[('fa','data_file')])])
-tractography.connect([(inputnode, fa2nii,[(('dwi', get_affine), 'affine')])])
-tractography.connect([(analyzeheader_fa, fa2nii,[('header', 'header_file')])])
+tractography.connect([(fa, fa2nii, [('fa', 'data_file')])])
+tractography.connect([(inputnode, fa2nii, [(('dwi', get_affine), 'affine')])])
+tractography.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])])
 
 
-tractography.connect([(dtifit, trace,[("tensor_fitted","in_file")])])
-tractography.connect([(trace, analyzeheader_trace,[("trace","in_file")])])
-tractography.connect([(inputnode, analyzeheader_trace,[(('dwi', get_vox_dims), 'voxel_dims'),
+tractography.connect([(dtifit, trace, [("tensor_fitted", "in_file")])])
+tractography.connect([(trace, analyzeheader_trace, [("trace", "in_file")])])
+tractography.connect([(inputnode, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'),
                                                        (('dwi', get_data_dims), 'data_dims')])])
-tractography.connect([(trace, trace2nii,[('trace','data_file')])])
-tractography.connect([(inputnode, trace2nii,[(('dwi', get_affine), 'affine')])])
-tractography.connect([(analyzeheader_trace, trace2nii,[('header', 'header_file')])])
+tractography.connect([(trace, trace2nii, [('trace', 'data_file')])])
+tractography.connect([(inputnode, trace2nii, [(('dwi', get_affine), 'affine')])])
+tractography.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])])
 
-tractography.connect([(dtifit, dteig,[("tensor_fitted","in_file")])])
+tractography.connect([(dtifit, dteig, [("tensor_fitted", "in_file")])])
 
-tractography.connect([(trackpico, cam2trk_pico, [('tracked','in_file')])])
-tractography.connect([(trackdt, cam2trk_dt, [('tracked','in_file')])])
-tractography.connect([(inputnode, cam2trk_pico,[(('dwi', get_vox_dims), 'voxel_dims'),
+tractography.connect([(trackpico, cam2trk_pico, [('tracked', 'in_file')])])
+tractography.connect([(trackdt, cam2trk_dt, [('tracked', 'in_file')])])
+tractography.connect([(inputnode, cam2trk_pico, [(('dwi', get_vox_dims), 'voxel_dims'),
                                                 (('dwi', get_data_dims), 'data_dims')])])
 
-tractography.connect([(inputnode, cam2trk_dt,[(('dwi', get_vox_dims), 'voxel_dims'),
+tractography.connect([(inputnode, cam2trk_dt, [(('dwi', get_vox_dims), 'voxel_dims'),
                                               (('dwi', get_data_dims), 'data_dims')])])
 
 
@@ -298,10 +298,10 @@ def get_affine(volume):
 
 workflow = pe.Workflow(name="workflow")
 workflow.base_dir = os.path.abspath('camino_dti_tutorial')
-workflow.connect([(infosource,datasource,[('subject_id', 'subject_id')]),
-                  (datasource,tractography,[('dwi','inputnode.dwi'),
-                                            ('bvals','inputnode.bvals'),
-                                            ('bvecs','inputnode.bvecs')
+workflow.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
+                  (datasource, tractography, [('dwi', 'inputnode.dwi'),
+                                            ('bvals', 'inputnode.bvals'),
+                                            ('bvecs', 'inputnode.bvecs')
                                             ])
                   ])
 """