FIX: Repair aftermath of docs refactor

.circleci/config.yml

@@ -157,13 +157,6 @@ jobs:
       - run: *_run_codecov_coverage
       - store_artifacts: *store_artifacts_kwds
       - store_test_results: *store_artifacts_kwds
-      - run:
-          name: Build docs
-          no_output_timeout: 30m
-          environment: *test_environment
-          command: bash -ux /home/circleci/nipype/.circleci/build_docs.sh
-      - store_artifacts:
-          path: /home/circleci/work/docs
       - run:
           name: Save Docker images to workspace if on master
           no_output_timeout: 60m

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

@@ -437,8 +437,7 @@ class EstimateContrast(SPMCommand):
     _jobname = "con"
 
     def _make_matlab_command(self, _):
-        """validates spm options and generates job structure
-        """
+        """Validate spm options and generate job structure."""
         contrasts = []
         cname = []
         for i, cont in enumerate(self.inputs.contrasts):
@@ -457,80 +456,90 @@ 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\n"
-        script += "spm_defaults;\n"
-        script += "jobs{1}.stats{1}.con.spmmat  = {'%s'};\n" % self.inputs.spm_mat_file
-        script += "load(jobs{1}.stats{1}.con.spmmat{:});\n"
-        script += "SPM.swd = '%s';\n" % os.getcwd()
-        script += "save(jobs{1}.stats{1}.con.spmmat{:},'SPM');\n"
-        script += "names = SPM.xX.name;\n"
+        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())
+        ]
         # get names for columns
         if isdefined(self.inputs.group_contrast) and self.inputs.group_contrast:
-            script += "condnames=names;\n"
+            script += ["condnames=names;"]
         else:
             if self.inputs.use_derivs:
-                script += r"pat = 'Sn\([0-9]*\) (.*)';\n"
+                script += [r"pat = 'Sn\([0-9]*\) (.*)';"]
             else:
-                script += (
+                script += [
                     r"pat = 'Sn\([0-9]*\) (.*)\*bf\(1\)|Sn\([0-9]*\) "
                     r".*\*bf\([2-9]\)|Sn\([0-9]*\) (.*)';"
-                    "\n"
-                )
-            script += "t = regexp(names,pat,'tokens');\n"
+                ]
+
+            script += ["t = regexp(names,pat,'tokens');"]
             # get sessidx for columns
-            script += r"pat1 = 'Sn\(([0-9].*)\)\s.*';\n"
-            script += "t1 = regexp(names,pat1,'tokens');\n"
-            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;\n"
-            )
+            script += [r"pat1 = 'Sn\(([0-9].*)\)\s.*';"]
+            script += ["t1 = regexp(names,pat1,'tokens');"]
+            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;"""
+            ]
+
         # BUILD CONTRAST SESSION STRUCTURE
         for i, contrast in enumerate(contrasts):
             if contrast.stat == "T":
-                script += "consess{%d}.tcon.name   = '%s';\n" % (i + 1, contrast.name)
-                script += "consess{%d}.tcon.convec = zeros(1,numel(names));\n" % (i + 1)
+                script += ["consess{%d}.tcon.name   = '%s';" % (i + 1, contrast.name)]
+                script += ["consess{%d}.tcon.convec = zeros(1,numel(names));" % (i + 1)]
                 for c0, cond in enumerate(contrast.conditions):
-                    script += "idx = strmatch('%s',condnames,'exact');\n" % (cond)
-                    script += (
-                        "if isempty(idx), throw(MException("
-                        "'CondName:Chk', sprintf('Condition %%s not "
-                        "found in design','%s'))); end;\n"
-                    ) % cond
+                    script += ["idx = strmatch('%s',condnames,'exact');" % cond]
+                    script += [
+                        """\
+if isempty(idx)
+  throw(MException('CondName:Chk', sprintf('Condition %%s not found in design','%s')));
+end;"""
+                        % cond
+                    ]
                     if contrast.sessions:
                         for sno, sw in enumerate(contrast.sessions):
-                            script += "sidx = find(condsess(idx)==%d);\n" % (sno + 1)
-                            script += "consess{%d}.tcon.convec(idx(sidx)) = %f;\n" % (
-                                i + 1,
-                                sw * contrast.weights[c0],
-                            )
+                            script += ["sidx = find(condsess(idx)==%d);" % (sno + 1)]
+                            script += [
+                                "consess{%d}.tcon.convec(idx(sidx)) = %f;"
+                                % (i + 1, sw * contrast.weights[c0],)
+                            ]
                     else:
-                        script += "consess{%d}.tcon.convec(idx) = %f;\n" % (
-                            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';\n" % (i + 1, contrast.name)
+                script += ["consess{%d}.fcon.name   =  '%s';" % (i + 1, contrast.name)]
                 for cl0, fcont in enumerate(contrast.conditions):
-                    try:
-                        tidx = cname.index(fcont[0])
-                    except:
-                        Exception(
-                            "Contrast Estimate: could not get index of"
-                            " T contrast. probably not defined prior "
-                            "to the F contrasts"
-                        )
-                    script += (
-                        "consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;\n"
-                    ) % (i + 1, cl0 + 1, tidx + 1)
-        script += "jobs{1}.stats{1}.con.consess = consess;\n"
-        script += (
-            "if strcmp(spm('ver'),'SPM8'), spm_jobman('initcfg');"
-            "jobs=spm_jobman('spm5tospm8',{jobs});end\n"
-        )
-        script += "spm_jobman('run',jobs);"
-        return script
+                    tidx = cname.index(fcont[0])
+                    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 += [
+            """\
+if strcmp(spm('ver'),'SPM8')
+  spm_jobman('initcfg');
+  jobs=spm_jobman('spm5tospm8',{jobs});
+end;"""
+        ]
+        script += ["spm_jobman('run',jobs);"]
+        return "\n".join(script)
 
     def _list_outputs(self):
         import scipy.io as sio

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,