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6 files changed

+44
-39
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‎nipype/algorithms/icc.py‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -44,10 +44,7 @@ def _run_interface(self, runtime):
4444
maskdata = np.logical_not(np.logical_or(maskdata == 0, np.isnan(maskdata)))
4545

4646
session_datas = [
47-
[
48-
nb.load(fname).get_fdata()[maskdata].reshape(-1, 1)
49-
for fname in sessions
50-
]
47+
[nb.load(fname).get_fdata()[maskdata].reshape(-1, 1) for fname in sessions]
5148
for sessions in self.inputs.subjects_sessions
5249
]
5350
list_of_sessions = [np.dstack(session_data) for session_data in session_datas]

‎nipype/interfaces/afni/base.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -121,7 +121,9 @@ class AFNICommandBase(CommandLine):
121121
def _run_interface(self, runtime, correct_return_codes=(0,)):
122122
if platform == "darwin":
123123
runtime.environ["DYLD_FALLBACK_LIBRARY_PATH"] = "/usr/local/afni/"
124-
return super(AFNICommandBase, self)._run_interface(runtime, correct_return_codes)
124+
return super(AFNICommandBase, self)._run_interface(
125+
runtime, correct_return_codes
126+
)
125127

126128

127129
class AFNICommandInputSpec(CommandLineInputSpec):

‎nipype/interfaces/afni/preprocess.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1842,7 +1842,9 @@ def _parse_inputs(self, skip=None):
18421842
return super(OutlierCount, self)._parse_inputs(skip)
18431843

18441844
def _run_interface(self, runtime, correct_return_codes=(0,)):
1845-
runtime = super(OutlierCount, self)._run_interface(runtime, correct_return_codes)
1845+
runtime = super(OutlierCount, self)._run_interface(
1846+
runtime, correct_return_codes
1847+
)
18461848

18471849
# Read from runtime.stdout or runtime.merged
18481850
with open(op.abspath(self.inputs.out_file), "w") as outfh:

‎nipype/interfaces/camino/dti.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1049,7 +1049,7 @@ class TrackBedpostxProbaInputSpec(TrackInputSpec):
10491049
iterations = traits.Int(
10501050
argstr="-iterations %d",
10511051
units="NA",
1052-
desc="Number of streamlines to generate at each " "seed point. The default is 1.",
1052+
desc="Number of streamlines to generate at each seed point. The default is 1.",
10531053
)
10541054

10551055

‎nipype/interfaces/spm/model.py‎

Lines changed: 35 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -456,39 +456,44 @@ def _make_matlab_command(self, _):
456456
contrasts[i].weights = cont[3]
457457
if len(cont) >= 5:
458458
contrasts[i].sessions = cont[4]
459-
script = ["""\
460-
% generated by nipype.interfaces.spm
459+
script = [
460+
"""\
461+
%% generated by nipype.interfaces.spm
461462
spm_defaults;
462463
jobs{1}.stats{1}.con.spmmat = {'%s'};
463464
load(jobs{1}.stats{1}.con.spmmat{:});
464465
SPM.swd = '%s';
465466
save(jobs{1}.stats{1}.con.spmmat{:},'SPM');
466-
names = SPM.xX.name;
467-
""" % (self.inputs.spm_mat_file, os.getcwd())]
467+
names = SPM.xX.name;"""
468+
% (self.inputs.spm_mat_file, os.getcwd())
469+
]
468470
# get names for columns
469471
if isdefined(self.inputs.group_contrast) and self.inputs.group_contrast:
470472
script += ["condnames=names;"]
471473
else:
472474
if self.inputs.use_derivs:
473475
script += [r"pat = 'Sn\([0-9]*\) (.*)';"]
474476
else:
475-
script += [r"""\
476-
pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) .*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"""]
477+
script += [
478+
r"pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) "
479+
r".*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"
480+
]
477481

478482
script += ["t = regexp(names,pat,'tokens');"]
479483
# get sessidx for columns
480484
script += [r"pat1 = 'Sn\(([0-9].*)\)\s.*';"]
481485
script += ["t1 = regexp(names,pat1,'tokens');"]
482-
script += ["""\
486+
script += [
487+
"""\
483488
for i0=1:numel(t)
484489
condnames{i0}='';
485490
condsess(i0)=0;
486491
if ~isempty(t{i0}{1})
487492
condnames{i0} = t{i0}{1}{1};
488493
condsess(i0)=str2num(t1{i0}{1}{1});
489494
end;
490-
end;
491-
"""]
495+
end;"""
496+
]
492497

493498
# BUILD CONTRAST SESSION STRUCTURE
494499
for i, contrast in enumerate(contrasts):
@@ -497,37 +502,42 @@ def _make_matlab_command(self, _):
497502
script += ["consess{%d}.tcon.convec = zeros(1,numel(names));" % (i + 1)]
498503
for c0, cond in enumerate(contrast.conditions):
499504
script += ["idx = strmatch('%s',condnames,'exact');" % cond]
500-
script += ["""\
505+
script += [
506+
"""\
501507
if isempty(idx)
502508
throw(MException('CondName:Chk', sprintf('Condition %%s not found in design','%s')));
503-
end;
504-
""" % cond]
509+
end;"""
510+
% cond
511+
]
505512
if contrast.sessions:
506513
for sno, sw in enumerate(contrast.sessions):
507514
script += ["sidx = find(condsess(idx)==%d);" % (sno + 1)]
508-
script += ["consess{%d}.tcon.convec(idx(sidx)) = %f;" % (
509-
i + 1,
510-
sw * contrast.weights[c0],
511-
)]
515+
script += [
516+
"consess{%d}.tcon.convec(idx(sidx)) = %f;"
517+
% (i + 1, sw * contrast.weights[c0],)
518+
]
512519
else:
513-
script += ["consess{%d}.tcon.convec(idx) = %f;" % (
514-
i + 1,
515-
contrast.weights[c0],
516-
)]
520+
script += [
521+
"consess{%d}.tcon.convec(idx) = %f;"
522+
% (i + 1, contrast.weights[c0],)
523+
]
517524
for i, contrast in enumerate(contrasts):
518525
if contrast.stat == "F":
519526
script += ["consess{%d}.fcon.name = '%s';" % (i + 1, contrast.name)]
520527
for cl0, fcont in enumerate(contrast.conditions):
521528
tidx = cname.index(fcont[0])
522-
script += ["consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;" %
523-
(i + 1, cl0 + 1, tidx + 1)]
529+
script += [
530+
"consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;"
531+
% (i + 1, cl0 + 1, tidx + 1)
532+
]
524533
script += ["jobs{1}.stats{1}.con.consess = consess;"]
525-
script += ["""\
534+
script += [
535+
"""\
526536
if strcmp(spm('ver'),'SPM8')
527537
spm_jobman('initcfg');
528538
jobs=spm_jobman('spm5tospm8',{jobs});
529-
end;
530-
"""]
539+
end;"""
540+
]
531541
script += ["spm_jobman('run',jobs);"]
532542
return "\n".join(script)
533543

‎nipype/sphinxext/apidoc/__init__.py‎

Lines changed: 1 addition & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -40,13 +40,7 @@ class Config(NapoleonConfig):
4040
"""
4141
_config_values = {
4242
"nipype_skip_classes": (
43-
[
44-
"Tester",
45-
"InputSpec",
46-
"OutputSpec",
47-
"Numpy",
48-
"NipypeTester",
49-
],
43+
["Tester", "InputSpec", "OutputSpec", "Numpy", "NipypeTester",],
5044
"env",
5145
),
5246
**NapoleonConfig._config_values,

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