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FIX: PEP8 - E127 continuation line over-indented for visual indent
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+427
-427
lines changed

‎build_docs.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -141,12 +141,12 @@ def zip_docs(self):
141141
# require zlib.
142142
try:
143143
zf = zipfile.ZipFile(target_file, 'w',
144-
compression=zipfile.ZIP_DEFLATED)
144+
compression=zipfile.ZIP_DEFLATED)
145145
except RuntimeError:
146146
warnings.warn('zlib not installed, storing the docs '
147-
'without compression')
147+
'without compression')
148148
zf = zipfile.ZipFile(target_file, 'w',
149-
compression=zipfile.ZIP_STORED)
149+
compression=zipfile.ZIP_STORED)
150150

151151
for root, dirs, files in os.walk(DOC_BUILD_DIR):
152152
relative = relative_path(root)

‎doc/sphinxext/numpy_ext/numpydoc.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ def mangle_docstrings(app, what, name, obj, options, lines,
4545
lines[:] = str(doc).split(u"\n")
4646

4747
if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \
48-
obj.__name__:
48+
obj.__name__:
4949
if hasattr(obj, '__module__'):
5050
v = dict(full_name=u"%s.%s" % (obj.__module__, obj.__name__))
5151
else:

‎examples/dmri_connectivity.py

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -386,10 +386,10 @@ def select_aparc_annot(list_of_files):
386386
"""
387387

388388
mapping.connect([(inputnode, image2voxel, [("dwi", "in_file")]),
389-
(inputnode, fsl2scheme, [("bvecs", "bvec_file"),
390-
("bvals", "bval_file")]),
391-
(image2voxel, dtifit,[['voxel_order','in_file']]),
392-
(fsl2scheme, dtifit,[['scheme','scheme_file']])
389+
(inputnode, fsl2scheme, [("bvecs", "bvec_file"),
390+
("bvals", "bval_file")]),
391+
(image2voxel, dtifit,[['voxel_order','in_file']]),
392+
(fsl2scheme, dtifit,[['scheme','scheme_file']])
393393
])
394394

395395
"""
@@ -481,8 +481,8 @@ def select_aparc_annot(list_of_files):
481481
"""
482482

483483
mapping.connect([(track, camino2trackvis, [('tracked','in_file')]),
484-
(track, vtkstreamlines,[['tracked','in_file']]),
485-
(camino2trackvis, trk2camino,[['trackvis','in_file']])
484+
(track, vtkstreamlines,[['tracked','in_file']]),
485+
(camino2trackvis, trk2camino,[['trackvis','in_file']])
486486
])
487487
mapping.connect([(inputnode, camino2trackvis,[(('dwi', get_vox_dims), 'voxel_dims'),
488488
(('dwi', get_data_dims), 'data_dims')])])
@@ -566,8 +566,8 @@ def select_aparc_annot(list_of_files):
566566
connectivity.connect([
567567
(infosource,datasource,[('subject_id', 'subject_id')]),
568568
(datasource,mapping,[('dwi','inputnode.dwi'),
569-
('bvals','inputnode.bvals'),
570-
('bvecs','inputnode.bvecs')
569+
('bvals','inputnode.bvals'),
570+
('bvecs','inputnode.bvecs')
571571
]),
572572
(infosource,mapping,[('subject_id','inputnode.subject_id')])
573573
])

‎examples/dmri_connectivity_advanced.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -417,14 +417,14 @@
417417
"""
418418

419419
mapping.connect([(inputnode, fsl2mrtrix, [("bvecs", "bvec_file"),
420-
("bvals", "bval_file")])])
420+
("bvals", "bval_file")])])
421421
mapping.connect([(inputnode, eddycorrect,[("dwi","inputnode.in_file")])])
422422
mapping.connect([(eddycorrect, dwi2tensor,[("outputnode.eddy_corrected","in_file")])])
423423
mapping.connect([(fsl2mrtrix, dwi2tensor,[("encoding_file","encoding_file")])])
424424

425425
mapping.connect([(dwi2tensor, tensor2vector,[['tensor','in_file']]),
426-
(dwi2tensor, tensor2adc,[['tensor','in_file']]),
427-
(dwi2tensor, tensor2fa,[['tensor','in_file']]),
426+
(dwi2tensor, tensor2adc,[['tensor','in_file']]),
427+
(dwi2tensor, tensor2fa,[['tensor','in_file']]),
428428
])
429429
mapping.connect([(tensor2fa, MRmult_merge,[("FA","in1")])])
430430
mapping.connect([(tensor2fa, MRconvert_fa,[("FA","in_file")])])
@@ -580,8 +580,8 @@
580580
connectivity.connect([
581581
(infosource,datasource,[('subject_id', 'subject_id')]),
582582
(datasource,mapping,[('dwi','inputnode.dwi'),
583-
('bvals','inputnode.bvals'),
584-
('bvecs','inputnode.bvecs')
583+
('bvals','inputnode.bvals'),
584+
('bvecs','inputnode.bvecs')
585585
]),
586586
(infosource,mapping,[('subject_id','inputnode.subject_id')])
587587
])

‎examples/dmri_dtk_odf.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -192,12 +192,12 @@
192192
dwiproc.connect([
193193
(infosource,datasource,[('subject_id', 'subject_id')]),
194194
(datasource,compute_ODF,[('dwi','fslroi.in_file'),
195-
('bvals','hardi_mat.bvals'),
196-
('bvecs','hardi_mat.bvecs'),
197-
('dwi','eddycorrect.inputnode.in_file')]),
195+
('bvals','hardi_mat.bvals'),
196+
('bvecs','hardi_mat.bvecs'),
197+
('dwi','eddycorrect.inputnode.in_file')]),
198198
(compute_ODF,tractography,[('bet.mask_file','odf_tracker.mask1_file'),
199-
('odf_recon.ODF','odf_tracker.ODF'),
200-
('odf_recon.max','odf_tracker.max')
199+
('odf_recon.ODF','odf_tracker.ODF'),
200+
('odf_recon.max','odf_tracker.max')
201201
])
202202
])
203203

‎examples/dmri_mrtrix_dti.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -176,14 +176,14 @@
176176
tractography = pe.Workflow(name='tractography')
177177

178178
tractography.connect([(inputnode, fsl2mrtrix, [("bvecs", "bvec_file"),
179-
("bvals", "bval_file")])])
179+
("bvals", "bval_file")])])
180180
tractography.connect([(inputnode, gunzip,[("dwi","in_file")])])
181181
tractography.connect([(gunzip, dwi2tensor,[("out_file","in_file")])])
182182
tractography.connect([(fsl2mrtrix, dwi2tensor,[("encoding_file","encoding_file")])])
183183

184184
tractography.connect([(dwi2tensor, tensor2vector,[['tensor','in_file']]),
185-
(dwi2tensor, tensor2adc,[['tensor','in_file']]),
186-
(dwi2tensor, tensor2fa,[['tensor','in_file']]),
185+
(dwi2tensor, tensor2adc,[['tensor','in_file']]),
186+
(dwi2tensor, tensor2fa,[['tensor','in_file']]),
187187
])
188188
tractography.connect([(tensor2fa, MRmult_merge,[("FA","in1")])])
189189

@@ -251,8 +251,8 @@
251251
dwiproc.connect([
252252
(infosource,datasource,[('subject_id', 'subject_id')]),
253253
(datasource,tractography,[('dwi','inputnode.dwi'),
254-
('bvals','inputnode.bvals'),
255-
('bvecs','inputnode.bvecs')
254+
('bvals','inputnode.bvals'),
255+
('bvecs','inputnode.bvecs')
256256
])
257257
])
258258

‎examples/fmri_ants_openfmri.py

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -111,11 +111,11 @@ def create_reg_workflow(name='registration'):
111111
register = pe.Workflow(name=name)
112112

113113
inputnode = pe.Node(interface=niu.IdentityInterface(fields=['source_files',
114-
'mean_image',
115-
'anatomical_image',
116-
'target_image',
117-
'target_image_brain',
118-
'config_file']),
114+
'mean_image',
115+
'anatomical_image',
116+
'target_image',
117+
'target_image_brain',
118+
'config_file']),
119119
name='inputspec')
120120
outputnode = pe.Node(interface=niu.IdentityInterface(fields=['func2anat_transform',
121121
'anat2target_transform',
@@ -568,8 +568,8 @@ def get_subjectinfo(subject_id, base_dir, task_id, model_id):
568568
runs = [int(val[-3:]) for val in files]
569569
run_ids.insert(idx, runs)
570570
json_info = os.path.join(base_dir, subject_id, 'BOLD',
571-
'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]),
572-
'bold_scaninfo.json')
571+
'task%03d_run%03d' % (task_id, run_ids[task_id - 1][0]),
572+
'bold_scaninfo.json')
573573
if os.path.exists(json_info):
574574
import json
575575
with open(json_info, 'rt') as fp:
@@ -763,7 +763,7 @@ def get_contrasts(contrast_file, task_id, conds):
763763
name="art")
764764

765765
modelspec = pe.Node(interface=model.SpecifyModel(),
766-
name="modelspec")
766+
name="modelspec")
767767
modelspec.inputs.input_units = 'secs'
768768

769769
def check_behav_list(behav, run_id, conds):
@@ -861,7 +861,7 @@ def sort_copes(copes, varcopes, contrasts):
861861
('varcopes', 'inputspec.varcopes'),
862862
('n_runs', 'l2model.num_copes')]),
863863
(modelfit, fixed_fx, [('outputspec.dof_file',
864-
'inputspec.dof_files'),
864+
'inputspec.dof_files'),
865865
])
866866
])
867867

@@ -895,9 +895,9 @@ def merge_files(copes, varcopes, zstats):
895895
function=merge_files),
896896
name='merge_files')
897897
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc,
898-
[('copes', 'copes'),
899-
('varcopes', 'varcopes'),
900-
('zstats', 'zstats'),
898+
[('copes', 'copes'),
899+
('varcopes', 'varcopes'),
900+
('zstats', 'zstats'),
901901
])])
902902
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
903903

@@ -992,16 +992,16 @@ def get_subs(subject_id, conds, run_id, model_id, task_id):
992992
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
993993
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
994994
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
995-
[('res4d', 'res4d'),
996-
('copes', 'copes'),
997-
('varcopes', 'varcopes'),
998-
('zstats', 'zstats'),
999-
('tstats', 'tstats')])
995+
[('res4d', 'res4d'),
996+
('copes', 'copes'),
997+
('varcopes', 'varcopes'),
998+
('zstats', 'zstats'),
999+
('tstats', 'tstats')])
10001000
])
10011001
wf.connect([(modelfit.get_node('modelgen'), datasink,
1002-
[('design_cov', 'qa.model'),
1003-
('design_image', 'qa.model.@matrix_image'),
1004-
('design_file', 'qa.model.@matrix'),
1002+
[('design_cov', 'qa.model'),
1003+
('design_image', 'qa.model.@matrix_image'),
1004+
('design_file', 'qa.model.@matrix'),
10051005
])])
10061006
wf.connect([(preproc, datasink, [('outputspec.motion_parameters',
10071007
'qa.motion'),

‎examples/fmri_fsl_reuse.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -69,9 +69,9 @@
6969

7070
level1_workflow.connect([(preproc, art, [('outputspec.motion_parameters',
7171
'realignment_parameters'),
72-
('outputspec.realigned_files',
73-
'realigned_files'),
74-
('outputspec.mask', 'mask_file')]),
72+
('outputspec.realigned_files',
73+
'realigned_files'),
74+
('outputspec.mask', 'mask_file')]),
7575
(preproc, modelspec, [('outputspec.highpassed_files',
7676
'functional_runs'),
7777
('outputspec.motion_parameters',
@@ -106,8 +106,8 @@ def num_copes(files):
106106
'flameo.mask_file')]),
107107
(modelfit, fixed_fx, [(('outputspec.copes', sort_copes),
108108
'inputspec.copes'),
109-
('outputspec.dof_file',
110-
'inputspec.dof_files'),
109+
('outputspec.dof_file',
110+
'inputspec.dof_files'),
111111
(('outputspec.varcopes',
112112
sort_copes),
113113
'inputspec.varcopes'),

‎examples/fmri_nipy_glm.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -258,12 +258,12 @@ def subjectinfo(subject_id):
258258
(modelspec, model_estimate,[('session_info','session_info')]),
259259
(compute_mask, model_estimate, [('brain_mask','mask')]),
260260
(model_estimate, contrast_estimate, [("beta","beta"),
261-
("nvbeta","nvbeta"),
262-
("s2","s2"),
263-
("dof", "dof"),
264-
("axis", "axis"),
265-
("constants", "constants"),
266-
("reg_names", "reg_names")])
261+
("nvbeta","nvbeta"),
262+
("s2","s2"),
263+
("dof", "dof"),
264+
("axis", "axis"),
265+
("constants", "constants"),
266+
("reg_names", "reg_names")])
267267
])
268268

269269
if __name__ == '__main__':

‎examples/fmri_openfmri.py

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -236,7 +236,7 @@ def get_contrasts(contrast_file, task_id, conds):
236236
name="art")
237237

238238
modelspec = pe.Node(interface=model.SpecifyModel(),
239-
name="modelspec")
239+
name="modelspec")
240240
modelspec.inputs.input_units = 'secs'
241241

242242
def check_behav_list(behav):
@@ -296,13 +296,13 @@ def num_copes(files):
296296
'flameo.mask_file')]),
297297
(modelfit, fixed_fx, [(('outputspec.copes', sort_copes),
298298
'inputspec.copes'),
299-
('outputspec.dof_file',
300-
'inputspec.dof_files'),
301-
(('outputspec.varcopes',
302-
sort_copes),
303-
'inputspec.varcopes'),
304-
(('outputspec.copes', num_copes),
305-
'l2model.num_copes'),
299+
('outputspec.dof_file',
300+
'inputspec.dof_files'),
301+
(('outputspec.varcopes',
302+
sort_copes),
303+
'inputspec.varcopes'),
304+
(('outputspec.copes', num_copes),
305+
'l2model.num_copes'),
306306
])
307307
])
308308

@@ -329,9 +329,9 @@ def merge_files(copes, varcopes, zstats):
329329
function=merge_files),
330330
name='merge_files')
331331
wf.connect([(fixed_fx.get_node('outputspec'), mergefunc,
332-
[('copes', 'copes'),
333-
('varcopes', 'varcopes'),
334-
('zstats', 'zstats'),
332+
[('copes', 'copes'),
333+
('varcopes', 'varcopes'),
334+
('zstats', 'zstats'),
335335
])])
336336
wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files')
337337

@@ -393,11 +393,11 @@ def get_subs(subject_id, conds, model_id, task_id):
393393
wf.connect(contrastgen, 'contrasts', subsgen, 'conds')
394394
wf.connect(subsgen, 'substitutions', datasink, 'substitutions')
395395
wf.connect([(fixed_fx.get_node('outputspec'), datasink,
396-
[('res4d', 'res4d'),
397-
('copes', 'copes'),
398-
('varcopes', 'varcopes'),
399-
('zstats', 'zstats'),
400-
('tstats', 'tstats')])
396+
[('res4d', 'res4d'),
397+
('copes', 'copes'),
398+
('varcopes', 'varcopes'),
399+
('zstats', 'zstats'),
400+
('tstats', 'tstats')])
401401
])
402402
wf.connect([(splitfunc, datasink,
403403
[('copes', 'copes.mni'),

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