FIX: PEP8 - missing whitespace around operator (E225) or arithmetic operator (E226) - 2nd clean up

Author: miykael

doc/sphinxext/autosummary_generate.py

@@ -81,7 +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):
@@ -210,7 +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):
@@ -139,7 +139,7 @@ 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
@@ -152,7 +152,7 @@ def _strip(self, doc):
             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()
@@ -309,12 +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):
@@ -408,7 +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')
@@ -421,7 +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):

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -23,7 +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):
@@ -90,7 +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]

doc/sphinxext/numpy_ext/numpydoc.py

@@ -41,7 +41,7 @@ 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)

examples/fmri_ants_openfmri.py

@@ -217,7 +217,7 @@ def create_reg_workflow(name='registration'):
     reg.inputs.convergence_window_size = [20] * 2 + [5]
     reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
     reg.inputs.sigma_units = ['vox'] * 3
-    reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]]
+    reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
     reg.inputs.use_estimate_learning_rate_once = [True] * 3
     reg.inputs.use_histogram_matching = [False] * 2 + [True]
     reg.inputs.winsorize_lower_quantile = 0.005
@@ -428,7 +428,7 @@ def create_fs_reg_workflow(name='registration'):
     reg.inputs.convergence_window_size = [20] * 2 + [5]
     reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
     reg.inputs.sigma_units = ['vox'] * 3
-    reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]]
+    reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
     reg.inputs.use_estimate_learning_rate_once = [True] * 3
     reg.inputs.use_histogram_matching = [False] * 2 + [True]
     reg.inputs.winsorize_lower_quantile = 0.005

examples/fmri_freesurfer_smooth.py

@@ -450,7 +450,7 @@
 def subjectinfo(subject_id):
     from nipype.interfaces.base import Bunch
     from copy import deepcopy
-    print("Subject ID: %s\n" %str(subject_id))
+    print("Subject ID: %s\n" % str(subject_id))
     output = []
     names = ['Task-Odd', 'Task-Even']
     for r in range(4):
@@ -539,7 +539,7 @@ def subjectinfo(subject_id):
 
 
 def getsubs(subject_id):
-    subs = [('_subject_id_%s/' %subject_id, '')]
+    subs = [('_subject_id_%s/' % subject_id, '')]
     return subs
 
 # store relevant outputs from various stages of the 1st level analysis
@@ -579,7 +579,7 @@ def getsubs(subject_id):
 l2inputnode = pe.Node(interface=util.IdentityInterface(fields=['contrasts',
                                                                'hemi']),
                       name='inputnode')
-l2inputnode.iterables = [('contrasts', list(range(1, len(contrasts)+1))),
+l2inputnode.iterables = [('contrasts', list(range(1, len(contrasts) + 1))),
                          ('hemi', ['lh', 'rh'])]
 
 """
@@ -610,7 +610,7 @@ def ordersubjects(files, subj_list):
     outlist = []
     for s in subj_list:
         for f in files:
-            if '/%s/' %s in f:
+            if '/%s/' % s in f:
                 outlist.append(f)
                 continue
     print(outlist)

examples/fmri_fsl.py

@@ -191,7 +191,7 @@ def getmiddlevolume(func):
 
 
 def getthreshop(thresh):
-    return '-thr %.10f -Tmin -bin' %(0.1*thresh[0][1])
+    return '-thr %.10f -Tmin -bin' % (0.1 * thresh[0][1])
 preproc.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string')
 
 """
@@ -259,11 +259,11 @@ def getthreshop(thresh):
 
 
 def getbtthresh(medianvals):
-    return [0.75*val for val in medianvals]
+    return [0.75 * val for val in medianvals]
 
 
 def getusans(x):
-    return [[tuple([val[0], 0.75*val[1]])] for val in x]
+    return [[tuple([val[0], 0.75 * val[1]])] for val in x]
 
 preproc.connect(maskfunc2, 'out_file', smooth, 'in_file')
 preproc.connect(medianval, ('out_stat', getbtthresh), smooth, 'brightness_threshold')

examples/fmri_fsl_feeds.py

@@ -79,7 +79,7 @@
 modelspec.inputs.time_repetition = TR
 modelspec.inputs.high_pass_filter_cutoff = 100
 modelspec.inputs.subject_info = [Bunch(conditions=['Visual', 'Auditory'],
-                                 onsets=[list(range(0, int(180*TR), 60)), list(range(0, int(180*TR), 90))],
+                                 onsets=[list(range(0, int(180 * TR), 60)), list(range(0, int(180 * TR), 90))],
                                  durations=[[30], [45]],
                                  amplitudes=None,
                                  tmod=None,

examples/fmri_fsl_reuse.py

@@ -202,7 +202,7 @@ def num_copes(files):
 def subjectinfo(subject_id):
     from nipype.interfaces.base import Bunch
     from copy import deepcopy
-    print("Subject ID: %s\n" %str(subject_id))
+    print("Subject ID: %s\n" % str(subject_id))
     output = []
     names = ['Task-Odd', 'Task-Even']
     for r in range(4):

examples/fmri_nipy_glm.py

@@ -159,7 +159,7 @@
 def subjectinfo(subject_id):
     from nipype.interfaces.base import Bunch
     from copy import deepcopy
-    print("Subject ID: %s\n" %str(subject_id))
+    print("Subject ID: %s\n" % str(subject_id))
     output = []
     names = ['Task-Odd', 'Task-Even']
     for r in range(4):