sty: black

Author: oesteban

nipype/algorithms/icc.py

@@ -44,10 +44,7 @@ def _run_interface(self, runtime):
         maskdata = np.logical_not(np.logical_or(maskdata == 0, np.isnan(maskdata)))
 
         session_datas = [
-            [
-                nb.load(fname).get_fdata()[maskdata].reshape(-1, 1)
-                for fname in sessions
-            ]
+            [nb.load(fname).get_fdata()[maskdata].reshape(-1, 1) for fname in sessions]
             for sessions in self.inputs.subjects_sessions
         ]
         list_of_sessions = [np.dstack(session_data) for session_data in session_datas]

nipype/interfaces/afni/base.py

@@ -121,7 +121,9 @@ class AFNICommandBase(CommandLine):
     def _run_interface(self, runtime, correct_return_codes=(0,)):
         if platform == "darwin":
             runtime.environ["DYLD_FALLBACK_LIBRARY_PATH"] = "/usr/local/afni/"
-        return super(AFNICommandBase, self)._run_interface(runtime, correct_return_codes)
+        return super(AFNICommandBase, self)._run_interface(
+            runtime, correct_return_codes
+        )
 
 
 class AFNICommandInputSpec(CommandLineInputSpec):

nipype/interfaces/afni/preprocess.py

@@ -1842,7 +1842,9 @@ def _parse_inputs(self, skip=None):
         return super(OutlierCount, self)._parse_inputs(skip)
 
     def _run_interface(self, runtime, correct_return_codes=(0,)):
-        runtime = super(OutlierCount, self)._run_interface(runtime, correct_return_codes)
+        runtime = super(OutlierCount, self)._run_interface(
+            runtime, correct_return_codes
+        )
 
         # Read from runtime.stdout or runtime.merged
         with open(op.abspath(self.inputs.out_file), "w") as outfh:

nipype/interfaces/camino/dti.py

@@ -1049,7 +1049,7 @@ class TrackBedpostxProbaInputSpec(TrackInputSpec):
     iterations = traits.Int(
         argstr="-iterations %d",
         units="NA",
-        desc="Number of streamlines to generate at each " "seed point. The default is 1.",
+        desc="Number of streamlines to generate at each seed point. The default is 1.",
     )
 
 

nipype/interfaces/spm/model.py

@@ -456,39 +456,44 @@ def _make_matlab_command(self, _):
                 contrasts[i].weights = cont[3]
             if len(cont) >= 5:
                 contrasts[i].sessions = cont[4]
-        script = ["""\
-% generated by nipype.interfaces.spm
+        script = [
+            """\
+%% generated by nipype.interfaces.spm
 spm_defaults;
 jobs{1}.stats{1}.con.spmmat  = {'%s'};
 load(jobs{1}.stats{1}.con.spmmat{:});
 SPM.swd = '%s';
 save(jobs{1}.stats{1}.con.spmmat{:},'SPM');
-names = SPM.xX.name;
-""" % (self.inputs.spm_mat_file, os.getcwd())]
+names = SPM.xX.name;"""
+            % (self.inputs.spm_mat_file, os.getcwd())
+        ]
         # get names for columns
         if isdefined(self.inputs.group_contrast) and self.inputs.group_contrast:
             script += ["condnames=names;"]
         else:
             if self.inputs.use_derivs:
                 script += [r"pat = 'Sn\([0-9]*\) (.*)';"]
             else:
-                script += [r"""\
-pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) .*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"""]
+                script += [
+                    r"pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) "
+                    r".*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"
+                ]
 
             script += ["t = regexp(names,pat,'tokens');"]
             # get sessidx for columns
             script += [r"pat1 = 'Sn\(([0-9].*)\)\s.*';"]
             script += ["t1 = regexp(names,pat1,'tokens');"]
-            script += ["""\
+            script += [
+                """\
 for i0=1:numel(t)
   condnames{i0}='';
   condsess(i0)=0;
   if ~isempty(t{i0}{1})
     condnames{i0} = t{i0}{1}{1};
     condsess(i0)=str2num(t1{i0}{1}{1});
   end;
-end;
-"""]
+end;"""
+            ]
 
         # BUILD CONTRAST SESSION STRUCTURE
         for i, contrast in enumerate(contrasts):
@@ -497,37 +502,42 @@ def _make_matlab_command(self, _):
                 script += ["consess{%d}.tcon.convec = zeros(1,numel(names));" % (i + 1)]
                 for c0, cond in enumerate(contrast.conditions):
                     script += ["idx = strmatch('%s',condnames,'exact');" % cond]
-                    script += ["""\
+                    script += [
+                        """\
 if isempty(idx)
   throw(MException('CondName:Chk', sprintf('Condition %%s not found in design','%s')));
-end;
-""" % cond]
+end;"""
+                        % cond
+                    ]
                     if contrast.sessions:
                         for sno, sw in enumerate(contrast.sessions):
                             script += ["sidx = find(condsess(idx)==%d);" % (sno + 1)]
-                            script += ["consess{%d}.tcon.convec(idx(sidx)) = %f;" % (
-                                i + 1,
-                                sw * contrast.weights[c0],
-                            )]
+                            script += [
+                                "consess{%d}.tcon.convec(idx(sidx)) = %f;"
+                                % (i + 1, sw * contrast.weights[c0],)
+                            ]
                     else:
-                        script += ["consess{%d}.tcon.convec(idx) = %f;" % (
-                            i + 1,
-                            contrast.weights[c0],
-                        )]
+                        script += [
+                            "consess{%d}.tcon.convec(idx) = %f;"
+                            % (i + 1, contrast.weights[c0],)
+                        ]
         for i, contrast in enumerate(contrasts):
             if contrast.stat == "F":
                 script += ["consess{%d}.fcon.name   =  '%s';" % (i + 1, contrast.name)]
                 for cl0, fcont in enumerate(contrast.conditions):
                     tidx = cname.index(fcont[0])
-                    script += ["consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;" %
-                               (i + 1, cl0 + 1, tidx + 1)]
+                    script += [
+                        "consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;"
+                        % (i + 1, cl0 + 1, tidx + 1)
+                    ]
         script += ["jobs{1}.stats{1}.con.consess = consess;"]
-        script += ["""\
+        script += [
+            """\
 if strcmp(spm('ver'),'SPM8')
   spm_jobman('initcfg');
   jobs=spm_jobman('spm5tospm8',{jobs});
-end;
-"""]
+end;"""
+        ]
         script += ["spm_jobman('run',jobs);"]
         return "\n".join(script)
 

nipype/sphinxext/apidoc/__init__.py

@@ -40,13 +40,7 @@ class Config(NapoleonConfig):
     """
     _config_values = {
         "nipype_skip_classes": (
-            [
-                "Tester",
-                "InputSpec",
-                "OutputSpec",
-                "Numpy",
-                "NipypeTester",
-            ],
+            ["Tester", "InputSpec", "OutputSpec", "Numpy", "NipypeTester",],
             "env",
         ),
         **NapoleonConfig._config_values,