FIX: PEP8 - E302 expected 2 blank lines, found 1

Author: miykael

build_docs.py

@@ -29,6 +29,8 @@
 
 ################################################################################
 # Distutils Command class for installing nipype to a temporary location.
+
+
 class TempInstall(Command):
     temp_install_dir = os.path.join('build', 'install')
 
@@ -166,6 +168,8 @@ def finalize_options(self):
 
 ################################################################################
 # Distutils Command class to clean
+
+
 class Clean(clean):
 
     def run(self):

doc/sphinxext/autosummary_generate.py

@@ -26,6 +26,7 @@
 except ImportError:
     import_phantom_module = lambda x: x
 
+
 def main():
     p = optparse.OptionParser(__doc__.strip())
     p.add_option("-p", "--phantom", action="store", type="string",
@@ -95,16 +96,19 @@ def main():
         finally:
             f.close()
 
+
 def format_modulemember(name, directive):
     parts = name.split('.')
     mod, name = '.'.join(parts[:-1]), parts[-1]
     return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
 
+
 def format_classmember(name, directive):
     parts = name.split('.')
     mod, name = '.'.join(parts[:-2]), '.'.join(parts[-2:])
     return ".. currentmodule:: %s\n\n.. %s:: %s\n" % (mod, directive, name)
 
+
 def get_documented(filenames):
     """
     Find out what items are documented in source/*.rst
@@ -119,6 +123,7 @@ def get_documented(filenames):
         f.close()
     return documented
 
+
 def get_documented_in_docstring(name, module=None, filename=None):
     """
     Find out what items are documented in the given object's docstring.
@@ -135,6 +140,7 @@ def get_documented_in_docstring(name, module=None, filename=None):
         print("Failed to import '%s': %s" % (name, e))
     return {}
 
+
 def get_documented_in_lines(lines, module=None, filename=None):
     """
     Find out what items are documented in the given lines

doc/sphinxext/ipython_console_highlighting.py

@@ -25,6 +25,7 @@
 # -----------------------------------------------------------------------------
 # Code begins - classes and functions
 
+
 class IPythonConsoleLexer(Lexer):
     """
     For IPython console output or doctests, such as:

doc/sphinxext/numpy_ext/docscrape.py

@@ -411,10 +411,12 @@ def indent(str, indent=4):
     lines = str.split('\n')
     return '\n'.join(indent_str + l for l in lines)
 
+
 def dedent_lines(lines):
     """Deindent a list of lines maximally"""
     return textwrap.dedent("\n".join(lines)).split("\n")
 
+
 def header(text, style='-'):
     return text + '\n' + style*len(text) + '\n'
 

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -195,21 +195,25 @@ def __str__(self, indent=0, func_role="obj"):
         out = self._str_indent(out, indent)
         return '\n'.join(out)
 
+
 class SphinxFunctionDoc(SphinxDocString, FunctionDoc):
     def __init__(self, obj, doc=None, config={}):
         self.use_plots = config.get('use_plots', False)
         FunctionDoc.__init__(self, obj, doc=doc, config=config)
 
+
 class SphinxClassDoc(SphinxDocString, ClassDoc):
     def __init__(self, obj, doc=None, func_doc=None, config={}):
         self.use_plots = config.get('use_plots', False)
         ClassDoc.__init__(self, obj, doc=doc, func_doc=None, config=config)
 
+
 class SphinxObjDoc(SphinxDocString):
     def __init__(self, obj, doc=None, config={}):
         self._f = obj
         SphinxDocString.__init__(self, doc, config=config)
 
+
 def get_doc_object(obj, what=None, doc=None, config={}):
     if what is None:
         if inspect.isclass(obj):

doc/sphinxext/numpy_ext/numpydoc.py

@@ -29,6 +29,7 @@
 from sphinx.util.compat import Directive
 import inspect
 
+
 def mangle_docstrings(app, what, name, obj, options, lines,
                       reference_offset=[0]):
 
@@ -78,6 +79,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
 
     reference_offset[0] += len(references)
 
+
 def mangle_signature(app, what, name, obj, options, sig, retann):
     # Do not try to inspect classes that don't define `__init__`
     if (inspect.isclass(obj) and
@@ -93,6 +95,7 @@ def mangle_signature(app, what, name, obj, options, sig, retann):
         sig = re.sub(u"^[^(]*", u"", doc['Signature'])
         return sig, u''
 
+
 def setup(app, get_doc_object_=get_doc_object):
     global get_doc_object
     get_doc_object = get_doc_object_
@@ -115,6 +118,7 @@ def setup(app, get_doc_object_=get_doc_object):
 from sphinx.domains.c import CDomain
 from sphinx.domains.python import PythonDomain
 
+
 class ManglingDomainBase(object):
     directive_mangling_map = {}
 
@@ -127,6 +131,7 @@ def wrap_mangling_directives(self):
             self.directives[name] = wrap_mangling_directive(
                 self.directives[name], objtype)
 
+
 class NumpyPythonDomain(ManglingDomainBase, PythonDomain):
     name = 'np'
     directive_mangling_map = {
@@ -139,6 +144,7 @@ class NumpyPythonDomain(ManglingDomainBase, PythonDomain):
         'attribute': 'attribute',
     }
 
+
 class NumpyCDomain(ManglingDomainBase, CDomain):
     name = 'np-c'
     directive_mangling_map = {
@@ -149,6 +155,7 @@ class NumpyCDomain(ManglingDomainBase, CDomain):
         'var': 'object',
     }
 
+
 def wrap_mangling_directive(base_directive, objtype):
     class directive(base_directive):
         def run(self):

examples/dmri_camino_dti.py

@@ -33,6 +33,7 @@
 (fmri_spm_face.py) also implements this inferral of voxel size from the data.
 """
 
+
 def get_vox_dims(volume):
     import nibabel as nb
     if isinstance(volume, list):
@@ -42,6 +43,7 @@ def get_vox_dims(volume):
     voxdims = hdr.get_zooms()
     return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]
 
+
 def get_data_dims(volume):
     import nibabel as nb
     if isinstance(volume, list):
@@ -51,6 +53,7 @@ def get_data_dims(volume):
     datadims = hdr.get_data_shape()
     return [int(datadims[0]), int(datadims[1]), int(datadims[2])]
 
+
 def get_affine(volume):
     import nibabel as nb
     nii = nb.load(volume)

examples/dmri_connectivity.py

@@ -71,6 +71,7 @@
 regions.
 """
 
+
 def get_vox_dims(volume):
     import nibabel as nb
     if isinstance(volume, list):
@@ -80,6 +81,7 @@ def get_vox_dims(volume):
     voxdims = hdr.get_zooms()
     return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]
 
+
 def get_data_dims(volume):
     import nibabel as nb
     if isinstance(volume, list):
@@ -89,17 +91,20 @@ def get_data_dims(volume):
     datadims = hdr.get_data_shape()
     return [int(datadims[0]), int(datadims[1]), int(datadims[2])]
 
+
 def get_affine(volume):
     import nibabel as nb
     nii = nb.load(volume)
     return nii.get_affine()
 
+
 def select_aparc(list_of_files):
     for in_file in list_of_files:
         if 'aparc+aseg.mgz' in in_file:
             idx = list_of_files.index(in_file)
     return list_of_files[idx]
 
+
 def select_aparc_annot(list_of_files):
     for in_file in list_of_files:
         if '.aparc.annot' in in_file:

examples/dmri_dtk_dti.py

@@ -189,6 +189,7 @@
 datasink = pe.Node(interface=nio.DataSink(), name='datasink')
 datasink.inputs.base_directory = os.path.abspath('dtiresults')
 
+
 def getstripdir(subject_id):
     return os.path.join(os.path.abspath('data/workingdir/dwiproc'), '_subject_id_%s' % subject_id)
 

examples/dmri_fsl_dti.py

@@ -239,6 +239,7 @@
 datasink = pe.Node(interface=nio.DataSink(), name='datasink')
 datasink.inputs.base_directory = os.path.abspath('dtiresults')
 
+
 def getstripdir(subject_id):
     import os
     return os.path.join(os.path.abspath('data/workingdir/dwiproc'), '_subject_id_%s' % subject_id)