Merge branch 'master' into replace_imghdr

Author: effigies

nipype/algorithms/misc.py

@@ -684,7 +684,7 @@ def _run_interface(self, runtime):
 
         output_array = merge_csvs(self.inputs.in_files)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
 
         out_file = op.abspath(name + ext)
@@ -725,7 +725,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file
@@ -771,7 +771,7 @@ class AddCSVColumn(BaseInterface):
     def _run_interface(self, runtime):
         in_file = open(self.inputs.in_file)
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
 
@@ -791,7 +791,7 @@ def _run_interface(self, runtime):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         _, name, ext = split_filename(self.inputs.out_file)
-        if not ext == ".csv":
+        if ext != ".csv":
             ext = ".csv"
         out_file = op.abspath(name + ext)
         outputs["csv_file"] = out_file

nipype/algorithms/modelgen.py

@@ -161,7 +161,7 @@ def bids_gen_info(
     for bids_event_file in bids_event_files:
         with open(bids_event_file) as f:
             f_events = csv.DictReader(f, skipinitialspace=True, delimiter="\t")
-            events = [{k: v for k, v in row.items()} for row in f_events]
+            events = list(f_events)
         if not condition_column:
             condition_column = "_trial_type"
             for i in events:

nipype/algorithms/tests/test_CompCor.py

@@ -287,9 +287,9 @@ def run_cc(
                 components_metadata = [
                     line.rstrip().split("\t") for line in metadata_file
                 ]
-                components_metadata = {
-                    i: j for i, j in zip(components_metadata[0], components_metadata[1])
-                }
+                components_metadata = dict(
+                    zip(components_metadata[0], components_metadata[1])
+                )
                 assert components_metadata == expected_metadata
 
         return ccresult

nipype/algorithms/tests/test_modelgen.py

@@ -122,7 +122,7 @@ def test_modelgen_spm_concat(tmpdir):
     s = SpecifySPMModel()
     s.inputs.input_units = "secs"
     s.inputs.concatenate_runs = True
-    setattr(s.inputs, "output_units", "secs")
+    s.inputs.output_units = "secs"
     assert s.inputs.output_units == "secs"
     s.inputs.functional_runs = [filename1, filename2]
     s.inputs.time_repetition = 6
@@ -147,7 +147,7 @@ def test_modelgen_spm_concat(tmpdir):
     )
 
     # Test case of scans as output units instead of seconds
-    setattr(s.inputs, "output_units", "scans")
+    s.inputs.output_units = "scans"
     assert s.inputs.output_units == "scans"
     s.inputs.subject_info = deepcopy(info)
     res = s.run()

nipype/interfaces/afni/base.py

@@ -326,6 +326,4 @@ def _cmd_prefix(self):
 
 def no_afni():
     """Check whether AFNI is not available."""
-    if Info.version() is None:
-        return True
-    return False
+    return Info.version() is None

nipype/interfaces/afni/model.py

@@ -636,7 +636,7 @@ def _parse_inputs(self, skip=None):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 
@@ -722,7 +722,7 @@ class Synthesize(AFNICommand):
     def _list_outputs(self):
         outputs = self.output_spec().get()
 
-        for key in outputs.keys():
+        for key in outputs:
             if isdefined(self.inputs.get()[key]):
                 outputs[key] = os.path.abspath(self.inputs.get()[key])
 

nipype/interfaces/afni/utils.py

@@ -234,7 +234,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
             m = re.search(pattern, line)
             if m:
                 d = m.groupdict()
-                outputs.trait_set(**{k: int(d[k]) for k in d.keys()})
+                outputs.trait_set(**{k: int(v) for k, v in d.items()})
         return outputs
 
 
@@ -3244,11 +3244,11 @@ def _run_interface(self, runtime):
             for line in runtime.stdout.split("\n")
             if line.strip().startswith("GCOR = ")
         ][-1]
-        setattr(self, "_gcor", float(gcor_line[len("GCOR = ") :]))
+        self._gcor = float(gcor_line[len("GCOR = ") :])
         return runtime
 
     def _list_outputs(self):
-        return {"out": getattr(self, "_gcor")}
+        return {"out": self._gcor}
 
 
 class AxializeInputSpec(AFNICommandInputSpec):

nipype/interfaces/ants/segmentation.py

@@ -194,7 +194,7 @@ def _format_arg(self, opt, spec, val):
                         priors_paths[0] % i for i in range(1, n_classes + 1)
                     ]
 
-                if not all([os.path.exists(p) for p in priors_paths]):
+                if not all(os.path.exists(p) for p in priors_paths):
                     raise FileNotFoundError(
                         "One or more prior images do not exist: "
                         "%s." % ", ".join(priors_paths)

nipype/interfaces/ants/utils.py

@@ -536,7 +536,7 @@ def _format_arg(self, opt, spec, val):
         return super()._format_arg(opt, spec, val)
 
     def _list_outputs(self):
-        return getattr(self, "_output")
+        return self._output
 
 
 class AverageAffineTransformInputSpec(ANTSCommandInputSpec):

nipype/interfaces/base/core.py

@@ -486,7 +486,7 @@ def load_inputs_from_json(self, json_file, overwrite=True):
         if not overwrite:
             def_inputs = list(self.inputs.get_traitsfree().keys())
 
-        new_inputs = list(set(list(inputs_dict.keys())) - set(def_inputs))
+        new_inputs = set(inputs_dict) - set(def_inputs)
         for key in new_inputs:
             if hasattr(self.inputs, key):
                 setattr(self.inputs, key, inputs_dict[key])