FIX: PEP8 - E122 continuation line missing indentation or outdented

Author: miykael

doc/sphinxext/numpy_ext/numpydoc.py

@@ -46,7 +46,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
         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:

examples/rsfmri_vol_surface_preprocessing.py

@@ -869,7 +869,7 @@ def get_names(files, suffix):
                      iterfield=['timeseries_file'],
                      name='getsubcortts')
     ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
-    list(range(49, 55)) + [58]
+        list(range(49, 55)) + [58]
     ts2txt.inputs.label_file = \
         os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
                          '2mm_v2.nii.gz'))

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -859,7 +859,7 @@ def get_names(files, suffix):
                      iterfield=['timeseries_file'],
                      name='getsubcortts')
     ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
-    list(range(49, 55)) + [58]
+        list(range(49, 55)) + [58]
     ts2txt.inputs.label_file = \
         os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
                          '2mm_v2.nii.gz'))

nipype/algorithms/modelgen.py

@@ -315,10 +315,10 @@ def _generate_standard_design(self, infolist,
                         sessinfo[i]['cond'][cid]['amplitudes'] = \
                             info.amplitudes[cid]
                     if hasattr(info, 'tmod') and info.tmod and \
-                    len(info.tmod) > cid:
+                        len(info.tmod) > cid:
                         sessinfo[i]['cond'][cid]['tmod'] = info.tmod[cid]
                     if hasattr(info, 'pmod') and info.pmod and \
-                    len(info.pmod) > cid:
+                        len(info.pmod) > cid:
                         if info.pmod[cid]:
                             sessinfo[i]['cond'][cid]['pmod'] = []
                             for j, name in enumerate(info.pmod[cid].name):
@@ -334,7 +334,7 @@ def _generate_standard_design(self, infolist,
                 for j, r in enumerate(info.regressors):
                     sessinfo[i]['regress'].insert(j, dict(name='', val=[]))
                     if hasattr(info, 'regressor_names') and \
-                    info.regressor_names is not None:
+                        info.regressor_names is not None:
                         sessinfo[i]['regress'][j]['name'] = \
                             info.regressor_names[j]
                     else:

nipype/algorithms/rapidart.py

@@ -377,7 +377,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
                     vol = data[:, :, :, t0]
                     # Use an SPM like approach
                     mask_tmp = vol > \
-                    (_nanmean(vol) / self.inputs.global_threshold)
+                        (_nanmean(vol) / self.inputs.global_threshold)
                     mask = mask * mask_tmp
                 for t0 in range(timepoints):
                     vol = data[:, :, :, t0]
@@ -391,7 +391,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
                 for t0 in range(timepoints):
                     vol = data[:, :, :, t0]
                     mask_tmp = vol > \
-                    (_nanmean(vol) / self.inputs.global_threshold)
+                        (_nanmean(vol) / self.inputs.global_threshold)
                     mask[:, :, :, t0] = mask_tmp
                     g[t0] = np.nansum(vol * mask_tmp) / np.nansum(mask_tmp)
         elif masktype == 'file':  # uses a mask image to determine intensity

nipype/fixes/numpy/testing/noseclasses.py

@@ -81,7 +81,7 @@ def _find(self, tests, obj, name, module, source_lines, globs, seen):
 
         # Local shorthands
         from inspect import isroutine, isclass, ismodule, isfunction, \
-        ismethod
+            ismethod
 
         # Look for tests in a module's contained objects.
         if ismodule(obj) and self._recurse:

nipype/interfaces/ants/legacy.py

@@ -250,7 +250,7 @@ def _list_outputs(self):
 
             outputs['template_files'].append(os.path.realpath(file_))
             outputs['final_template_file'] = \
-            os.path.realpath('%stemplate.nii.gz' %
+                os.path.realpath('%stemplate.nii.gz' %
                              self.inputs.out_prefix)
         outputs['subject_outfiles'] = []
         for filename in self.inputs.in_files:

nipype/interfaces/base.py

@@ -1500,7 +1500,7 @@ def _run_interface(self, runtime, correct_return_codes=[0]):
         runtime = run_command(runtime, output=self.inputs.terminal_output,
                               redirect_x=self._redirect_x)
         if runtime.returncode is None or \
-        runtime.returncode not in correct_return_codes:
+            runtime.returncode not in correct_return_codes:
             self.raise_exception(runtime)
 
         return runtime

nipype/interfaces/fsl/tests/test_dti.py

@@ -169,7 +169,7 @@ def test_randomise2():
     results = rand3.run(input_4D='infile3',
                         output_rootname='outfile3')
     yield assert_equal, results.runtime.cmdline, \
-    'randomise -i infile3 -o outfile3'
+        'randomise -i infile3 -o outfile3'
 
     # test arguments for opt_map
     opt_map = {'demean_data':                        ('-D', True),
@@ -252,7 +252,7 @@ def test_Randomise_parallel():
     results = rand3.run(input_4D='infile3',
                         output_rootname='outfile3')
     yield assert_equal, results.runtime.cmdline, \
-    'randomise_parallel -i infile3 -o outfile3'
+        'randomise_parallel -i infile3 -o outfile3'
 
     # test arguments for opt_map
     opt_map = {'demean_data':                        ('-D', True),
@@ -371,7 +371,7 @@ def test_Vec_reg():
                        affineTmat='tmat3.mat',)
 
     yield assert_equal, results.runtime.cmdline, \
-    'vecreg -i infile3 -o outfile3 -r MNI152 -t tmat3.mat'
+        'vecreg -i infile3 -o outfile3 -r MNI152 -t tmat3.mat'
     yield assert_not_equal, results.runtime.returncode, 0
     yield assert_equal, results.interface.inputs.infile, 'infile3'
     yield assert_equal, results.interface.inputs.outfile, 'outfile3'

nipype/interfaces/tests/test_io.py

@@ -200,9 +200,9 @@ def test_datasink_substitutions():
     setattr(ds.inputs, '@outdir', files)
     ds.run()
     yield assert_equal, \
-    sorted([os.path.basename(x) for
+        sorted([os.path.basename(x) for
             x in glob.glob(os.path.join(outdir, '*'))]), \
-    ['!-yz-b.n', 'ABABAB.n']  # so we got re used 2nd and both patterns
+        ['!-yz-b.n', 'ABABAB.n']  # so we got re used 2nd and both patterns
     shutil.rmtree(indir)
     shutil.rmtree(outdir)
 
@@ -249,9 +249,9 @@ def test_s3datasink_substitutions():
     setattr(ds.inputs, '@outdir', files)
     ds.run()
     yield assert_equal, \
-    sorted([os.path.basename(x) for
+        sorted([os.path.basename(x) for
             x in glob.glob(os.path.join(outdir, '*'))]), \
-    ['!-yz-b.n', 'ABABAB.n']  # so we got re used 2nd and both patterns
+        ['!-yz-b.n', 'ABABAB.n']  # so we got re used 2nd and both patterns
 
     bkt = conn.get_bucket(ds.inputs.bucket)
     bkt_files = list(k for k in bkt.list())

nipype/pipeline/plugins/base.py

@@ -233,7 +233,7 @@ def run(self, graph, config, updatehash=False):
         # setup polling - TODO: change to threaded model
         notrun = []
         while np.any(self.proc_done == False) | \
-        np.any(self.proc_pending == True):
+            np.any(self.proc_pending == True):
             toappend = []
             # trigger callbacks for any pending results
             while self.pending_tasks:

nipype/pipeline/plugins/dagman.py

@@ -130,7 +130,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                 if not wrapper_cmd is None:
                     specs['executable'] = wrapper_cmd
                     specs['nodescript'] = \
-                    '%s %s %s' % (wrapper_args % specs,  # give access to variables
+                        '%s %s %s' % (wrapper_args % specs,  # give access to variables
                                   sys.executable,
                                   pyscript)
                 submitspec = template % specs

tools/github.py

@@ -93,6 +93,6 @@ def get_file_url(object):
         info = nipype.get_info()
         shortfile = os.path.join('nipype', filename.split('nipype/')[-1])
         uri = 'http://github.com/nipy/nipype/tree/%s/%s#L%d' % \
-        (info['commit_hash'],
+            (info['commit_hash'],
          shortfile, lines[1])
     return uri