STY: PEP8 style correction for all warnings, and almost all errors. Except E402, E501 and E731

build_docs.py

@@ -70,7 +70,7 @@ class APIDocs(TempInstall):
 
     user_options = [
         ('None', None, 'this command has no options'),
-        ]
+    ]
 
     def run(self):
         # First build the project and install it to a temporary location.
@@ -193,5 +193,3 @@ def run(self):
             'api_docs': APIDocs,
             'clean': Clean,
             }
-
-

doc/conf.py

@@ -12,7 +12,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
+import sys
+import os
 
 nipypepath = os.path.abspath('..')
 sys.path.insert(1, nipypepath)
@@ -211,8 +212,8 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('documentation', 'nipype.tex', u'nipype Documentation',
-   u'Neuroimaging in Python team', 'manual'),
+    ('documentation', 'nipype.tex', u'nipype Documentation',
+     u'Neuroimaging in Python team', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

doc/sphinxext/autosummary_generate.py

@@ -18,7 +18,12 @@
 """
 
 from __future__ import print_function
-import glob, re, inspect, os, optparse, pydoc
+import glob
+import re
+import inspect
+import os
+import optparse
+import pydoc
 from autosummary import import_by_name
 
 try:
@@ -76,7 +81,7 @@ def main():
         f = open(fn, 'w')
 
         try:
-            f.write('%s\n%s\n\n' % (name, '='*len(name)))
+            f.write('%s\n%s\n\n' % (name, '=' * len(name)))
 
             if inspect.isclass(obj):
                 if issubclass(obj, Exception):
@@ -205,7 +210,7 @@ def get_documented_in_lines(lines, module=None, filename=None):
                     current_module = name
                     documented.update(get_documented_in_docstring(
                         name, filename=filename))
-                elif current_module and not name.startswith(current_module+'.'):
+                elif current_module and not name.startswith(current_module + '.'):
                     name = "%s.%s" % (current_module, name)
                 documented.setdefault(name, []).append(
                     (filename, current_title, "auto" + m.group(1), None))

doc/sphinxext/numpy_ext/docscrape.py

@@ -67,7 +67,7 @@ def read_to_condition(self, condition_func):
                 return self[start:self._l]
             self._l += 1
             if self.eof():
-                return self[start:self._l+1]
+                return self[start:self._l + 1]
         return []
 
     def read_to_next_empty_line(self):
@@ -114,7 +114,7 @@ def __init__(self, docstring, config={}):
             'References': '',
             'Examples': '',
             'index': {}
-            }
+        }
 
         self._parse()
 
@@ -139,18 +139,20 @@ def _is_at_section(self):
             return True
 
         l2 = self._doc.peek(1).strip()  # ---------- or ==========
-        return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1))
+        return l2.startswith('-' * len(l1)) or l2.startswith('=' * len(l1))
 
     def _strip(self, doc):
         i = 0
         j = 0
         for i, line in enumerate(doc):
-            if line.strip(): break
+            if line.strip():
+                break
 
         for j, line in enumerate(doc[::-1]):
-            if line.strip(): break
+            if line.strip():
+                break
 
-        return doc[i:len(doc)-j]
+        return doc[i:len(doc) - j]
 
     def _read_to_next_section(self):
         section = self._doc.read_to_next_empty_line()
@@ -227,7 +229,8 @@ def push_item(name, rest):
         rest = []
 
         for line in content:
-            if not line.strip(): continue
+            if not line.strip():
+                continue
 
             m = self._name_rgx.match(line)
             if m and line[m.end():].strip().startswith(':'):
@@ -306,12 +309,12 @@ def _parse(self):
     # string conversion routines
 
     def _str_header(self, name, symbol='-'):
-        return [name, len(name)*symbol]
+        return [name, len(name) * symbol]
 
     def _str_indent(self, doc, indent=4):
         out = []
         for line in doc:
-            out += [' '*indent + line]
+            out += [' ' * indent + line]
         return out
 
     def _str_signature(self):
@@ -351,7 +354,8 @@ def _str_section(self, name):
         return out
 
     def _str_see_also(self, func_role):
-        if not self['See Also']: return []
+        if not self['See Also']:
+            return []
         out = []
         out += self._str_header("See Also")
         last_had_desc = True
@@ -404,7 +408,7 @@ def __str__(self, func_role=''):
 
 
 def indent(str, indent=4):
-    indent_str = ' '*indent
+    indent_str = ' ' * indent
     if str is None:
         return indent_str
     lines = str.split('\n')
@@ -417,7 +421,7 @@ def dedent_lines(lines):
 
 
 def header(text, style='-'):
-    return text + '\n' + style*len(text) + '\n'
+    return text + '\n' + style * len(text) + '\n'
 
 
 class FunctionDoc(NumpyDocString):
@@ -504,9 +508,9 @@ def methods(self):
         if self._cls is None:
             return []
         return [name for name, func in inspect.getmembers(self._cls)
-                if ((not name.startswith('_')
-                     or name in self.extra_public_methods)
-                    and callable(func))]
+                if ((not name.startswith('_') or
+                     name in self.extra_public_methods) and
+                    callable(func))]
 
     @property
     def properties(self):

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -1,5 +1,8 @@
 from __future__ import absolute_import
-import re, inspect, textwrap, pydoc
+import re
+import inspect
+import textwrap
+import pydoc
 import sphinx
 from .docscrape import NumpyDocString, FunctionDoc, ClassDoc
 from nipype.external.six import string_types
@@ -20,7 +23,7 @@ def _str_field_list(self, name):
     def _str_indent(self, doc, indent=4):
         out = []
         for line in doc:
-            out += [' '*indent + line]
+            out += [' ' * indent + line]
         return out
 
     def _str_signature(self):
@@ -87,7 +90,7 @@ def _str_member_list(self, name):
             if others:
                 maxlen_0 = max([len(x[0]) for x in others])
                 maxlen_1 = max([len(x[1]) for x in others])
-                hdr = "="*maxlen_0 + "  " + "="*maxlen_1 + "  " + "="*10
+                hdr = "=" * maxlen_0 + "  " + "=" * maxlen_1 + "  " + "=" * 10
                 fmt = '%%%ds  %%%ds  ' % (maxlen_0, maxlen_1)
                 n_indent = maxlen_0 + maxlen_1 + 4
                 out += [hdr]
@@ -164,8 +167,8 @@ def _str_references(self):
     def _str_examples(self):
         examples_str = "\n".join(self['Examples'])
 
-        if (self.use_plots and 'import matplotlib' in examples_str
-                and 'plot::' not in examples_str):
+        if (self.use_plots and 'import matplotlib' in examples_str and
+                'plot::' not in examples_str):
             out = []
             out += self._str_header('Examples')
             out += ['.. plot::', '']

doc/sphinxext/numpy_ext/numpydoc.py

@@ -24,7 +24,9 @@
 if sphinx.__version__ < '1.0.1':
     raise RuntimeError("Sphinx 1.0.1 or newer is required")
 
-import os, re, pydoc
+import os
+import re
+import pydoc
 from .docscrape_sphinx import get_doc_object, SphinxDocString
 from sphinx.util.compat import Directive
 import inspect
@@ -39,14 +41,14 @@ def mangle_docstrings(app, what, name, obj, options, lines,
     if what == 'module':
         # Strip top title
         title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*',
-                              re.I |re.S)
+                              re.I | re.S)
         lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n")
     else:
         doc = get_doc_object(obj, what, u"\n".join(lines), config=cfg)
         lines[:] = str(doc).split(u"\n")
 
     if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
-        obj.__name__:
+            obj.__name__:
         if hasattr(obj, '__module__'):
             v = dict(full_name=u"%s.%s" % (obj.__module__, obj.__name__))
         else:
@@ -87,8 +89,10 @@ def mangle_signature(app, what, name, obj, options, sig, retann):
              'initializes x; see ' in pydoc.getdoc(obj.__init__))):
         return '', ''
 
-    if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')): return
-    if not hasattr(obj, '__doc__'): return
+    if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')):
+        return
+    if not hasattr(obj, '__doc__'):
+        return
 
     doc = SphinxDocString(pydoc.getdoc(obj))
     if doc['Signature']:
@@ -176,4 +180,3 @@ def run(self):
             return base_directive.run(self)
 
     return directive
-

examples/dmri_camino_dti.py

@@ -268,7 +268,7 @@ def get_affine(volume):
 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')])])
+                                                     (('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')])])
@@ -277,7 +277,7 @@ def get_affine(volume):
 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')])])
+                                                        (('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')])])
@@ -287,10 +287,10 @@ def get_affine(volume):
 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')])])
+                                                 (('dwi', get_data_dims), 'data_dims')])])
 
 tractography.connect([(inputnode, cam2trk_dt, [(('dwi', get_vox_dims), 'voxel_dims'),
-                                              (('dwi', get_data_dims), 'data_dims')])])
+                                               (('dwi', get_data_dims), 'data_dims')])])
 
 
 """
@@ -303,9 +303,9 @@ def get_affine(volume):
 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')
-                                            ])
+                                              ('bvals', 'inputnode.bvals'),
+                                              ('bvecs', 'inputnode.bvecs')
+                                              ])
                   ])
 """
 The following functions run the whole workflow and produce a .dot and .png graph of the processing pipeline.

examples/dmri_connectivity.py

@@ -464,7 +464,7 @@ def select_aparc_annot(list_of_files):
 mapping.connect([(dtifit, fa, [("tensor_fitted", "in_file")])])
 mapping.connect([(fa, analyzeheader_fa, [("fa", "in_file")])])
 mapping.connect([(inputnode, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'),
-                                               (('dwi', get_data_dims), 'data_dims')])])
+                                                (('dwi', get_data_dims), 'data_dims')])])
 mapping.connect([(fa, fa2nii, [('fa', 'data_file')])])
 mapping.connect([(inputnode, fa2nii, [(('dwi', get_affine), 'affine')])])
 mapping.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])])
@@ -473,7 +473,7 @@ def select_aparc_annot(list_of_files):
 mapping.connect([(dtifit, trace, [("tensor_fitted", "in_file")])])
 mapping.connect([(trace, analyzeheader_trace, [("trace", "in_file")])])
 mapping.connect([(inputnode, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'),
-                                                  (('dwi', get_data_dims), 'data_dims')])])
+                                                   (('dwi', get_data_dims), 'data_dims')])])
 mapping.connect([(trace, trace2nii, [('trace', 'data_file')])])
 mapping.connect([(inputnode, trace2nii, [(('dwi', get_affine), 'affine')])])
 mapping.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])])
@@ -490,7 +490,7 @@ def select_aparc_annot(list_of_files):
                  (camino2trackvis, trk2camino, [['trackvis', 'in_file']])
                  ])
 mapping.connect([(inputnode, camino2trackvis, [(('dwi', get_vox_dims), 'voxel_dims'),
-                                              (('dwi', get_data_dims), 'data_dims')])])
+                                               (('dwi', get_data_dims), 'data_dims')])])
 
 """
 Here the CMTK connectivity mapping nodes are connected.
@@ -571,11 +571,11 @@ def select_aparc_annot(list_of_files):
 connectivity.connect([
                     (infosource, datasource, [('subject_id', 'subject_id')]),
                     (datasource, mapping, [('dwi', 'inputnode.dwi'),
-                                         ('bvals', 'inputnode.bvals'),
-                                         ('bvecs', 'inputnode.bvecs')
-                                         ]),
-        (infosource, mapping, [('subject_id', 'inputnode.subject_id')])
-                ])
+                                           ('bvals', 'inputnode.bvals'),
+                                           ('bvecs', 'inputnode.bvecs')
+                                           ]),
+    (infosource, mapping, [('subject_id', 'inputnode.subject_id')])
+])
 
 """
 The following functions run the whole workflow and produce graphs describing the processing pipeline.

examples/dmri_connectivity_advanced.py

@@ -56,7 +56,8 @@
 import nipype.interfaces.cmtk as cmtk
 import nipype.interfaces.dipy as dipy
 import inspect
-import os, os.path as op                      # system functions
+import os
+import os.path as op                      # system functions
 from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
 from nipype.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
 from nipype.utils.misc import package_check
@@ -580,11 +581,11 @@
 connectivity.connect([
                     (infosource, datasource, [('subject_id', 'subject_id')]),
                     (datasource, mapping, [('dwi', 'inputnode.dwi'),
-                                         ('bvals', 'inputnode.bvals'),
-                                         ('bvecs', 'inputnode.bvecs')
-                                         ]),
-        (infosource, mapping, [('subject_id', 'inputnode.subject_id')])
-                ])
+                                           ('bvals', 'inputnode.bvals'),
+                                           ('bvecs', 'inputnode.bvecs')
+                                           ]),
+    (infosource, mapping, [('subject_id', 'inputnode.subject_id')])
+])
 
 """
 The following functions run the whole workflow and produce a .dot and .png graph of the processing pipeline.