Merge pull request #817 from DimitriPapadopoulos/pyupgrade

MNT: Pyupgrade suggestions

docs/conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-#
 # Configuration file for the Sphinx documentation builder.
 #
 # This file does only contain a selection of the most common options. For a

niworkflows/engine/__init__.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """

niworkflows/engine/workflows.py

@@ -43,7 +43,7 @@ def __init__(self, name, base_dir=None):
             path to workflow storage
 
         """
-        super(LiterateWorkflow, self).__init__(name, base_dir)
+        super().__init__(name, base_dir)
         self.__desc__ = None
         self.__postdesc__ = None
 

niworkflows/interfaces/bids.py

@@ -253,7 +253,7 @@ class BIDSDataGrabber(SimpleInterface):
     def __init__(self, *args, **kwargs):
         anat_only = kwargs.pop("anat_only")
         anat_derivatives = kwargs.pop("anat_derivatives", None)
-        super(BIDSDataGrabber, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         if anat_only is not None:
             self._require_funcs = not anat_only
         self._require_t1w = anat_derivatives is None
@@ -820,12 +820,12 @@ class ReadSidecarJSON(SimpleInterface):
     def __init__(self, fields=None, undef_fields=False, **inputs):
         from bids.utils import listify
 
-        super(ReadSidecarJSON, self).__init__(**inputs)
+        super().__init__(**inputs)
         self._fields = listify(fields or [])
         self._undef_fields = undef_fields
 
     def _outputs(self):
-        base = super(ReadSidecarJSON, self)._outputs()
+        base = super()._outputs()
         if self._fields:
             base = add_traits(base, self._fields)
         return base

niworkflows/interfaces/fixes.py

@@ -61,7 +61,7 @@ class FixHeaderApplyTransforms(ApplyTransforms):
 
     def _run_interface(self, runtime, correct_return_codes=(0,)):
         # Run normally
-        runtime = super(FixHeaderApplyTransforms, self)._run_interface(
+        runtime = super()._run_interface(
             runtime, correct_return_codes
         )
 
@@ -100,7 +100,7 @@ class FixHeaderRegistration(Registration):
 
     def _run_interface(self, runtime, correct_return_codes=(0,)):
         # Run normally
-        runtime = super(FixHeaderRegistration, self)._run_interface(
+        runtime = super()._run_interface(
             runtime, correct_return_codes
         )
 
@@ -143,12 +143,12 @@ def __init__(self, *args, **kwargs):
         """Add a private property to keep the path to the right input."""
         self._input_image = None
         self._negative_values = False
-        super(FixN4BiasFieldCorrection, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
 
     def _format_arg(self, name, trait_spec, value):
         if name == "input_image":
             return trait_spec.argstr % self._input_image
-        return super(FixN4BiasFieldCorrection, self)._format_arg(
+        return super()._format_arg(
             name, trait_spec, value
         )
 
@@ -166,9 +166,9 @@ def _parse_inputs(self, skip=None):
             newnii.to_filename(self._input_image)
             self._negative_values = True
 
-        return super(FixN4BiasFieldCorrection, self)._parse_inputs(skip=skip)
+        return super()._parse_inputs(skip=skip)
 
     def _list_outputs(self):
-        outputs = super(FixN4BiasFieldCorrection, self)._list_outputs()
+        outputs = super()._list_outputs()
         outputs["negative_values"] = self._negative_values
         return outputs

niworkflows/interfaces/freesurfer.py

@@ -80,10 +80,10 @@ def _num_vols(self):
     def cmdline(self):
         if self._num_vols() == 1:
             return "echo Only one time point!"
-        return super(StructuralReference, self).cmdline
+        return super().cmdline
 
     def _list_outputs(self):
-        outputs = super(StructuralReference, self)._list_outputs()
+        outputs = super()._list_outputs()
         if self._num_vols() == 1:
             in_file = self.inputs.in_files[0]
             outputs["out_file"] = in_file
@@ -117,7 +117,7 @@ class MakeMidthickness(fs.MRIsExpand):
 
     @property
     def cmdline(self):
-        cmd = super(MakeMidthickness, self).cmdline
+        cmd = super().cmdline
         if not isdefined(self.inputs.graymid) or len(self.inputs.graymid) < 1:
             return cmd
 
@@ -217,7 +217,7 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class TruncateLTA(object):
+class TruncateLTA:
     """
     Truncate long filenames in LTA files.
 
@@ -247,7 +247,7 @@ def _post_run_hook(self, runtime):
 
             fix_lta_length(lta_file)
 
-        runtime = super(TruncateLTA, self)._post_run_hook(runtime)
+        runtime = super()._post_run_hook(runtime)
         return runtime
 
 

niworkflows/interfaces/header.py

@@ -67,14 +67,14 @@ def __init__(self, fields=None, **inputs):
         if isinstance(self._fields, str):
             self._fields = [self._fields]
 
-        super(CopyXForm, self).__init__(**inputs)
+        super().__init__(**inputs)
 
         add_traits(self.inputs, self._fields)
         for f in set(self._fields).intersection(list(inputs.keys())):
             setattr(self.inputs, f, inputs[f])
 
     def _outputs(self):
-        base = super(CopyXForm, self)._outputs()
+        base = super()._outputs()
         if self._fields:
             fields = self._fields.copy()
             if "in_file" in fields:

niworkflows/interfaces/nilearn.py

@@ -241,10 +241,10 @@ def _run_interface(self, runtime):
         self._mask_file = os.path.join(runtime.cwd, "mask_file.nii.gz")
 
         runtime.returncode = 0
-        return super(ComputeEPIMask, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _list_outputs(self):
-        outputs = super(ComputeEPIMask, self)._list_outputs()
+        outputs = super()._list_outputs()
         outputs["mask_file"] = self._mask_file
         return outputs
 
@@ -261,7 +261,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(ComputeEPIMask, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 def _enhance_t2_contrast(in_file, newpath=None, offset=0.5):

niworkflows/interfaces/norm.py

@@ -148,7 +148,7 @@ def __init__(self, **inputs):
         self._reference_image = None
         self.retry = 1
         self.terminal_output = "file"
-        super(SpatialNormalization, self).__init__(**inputs)
+        super().__init__(**inputs)
 
     def _get_settings(self):
         """

niworkflows/interfaces/patches.py

@@ -40,7 +40,7 @@ def _run_interface(self, runtime):
         failures = 0
         while True:
             try:
-                runtime = super(RobustACompCor, self)._run_interface(runtime)
+                runtime = super()._run_interface(runtime)
                 break
             except LinAlgError:
                 failures += 1
@@ -63,7 +63,7 @@ def _run_interface(self, runtime):
         failures = 0
         while True:
             try:
-                runtime = super(RobustTCompCor, self)._run_interface(runtime)
+                runtime = super()._run_interface(runtime)
                 break
             except LinAlgError:
                 failures += 1

niworkflows/interfaces/reportlets/base.py

@@ -189,7 +189,7 @@ class ReportingInterface(reporting.ReportCapableInterface):
     output_spec = reporting.ReportCapableOutputSpec
 
     def __init__(self, generate_report=True, **kwargs):
-        super(ReportingInterface, self).__init__(
+        super().__init__(
             generate_report=generate_report, **kwargs
         )
 

niworkflows/interfaces/reportlets/masks.py

@@ -57,7 +57,7 @@ def _run_interface(self, runtime):
         if self.generate_report:
             self.inputs.mask = True
 
-        return super(BETRPT, self)._run_interface(runtime)
+        return super()._run_interface(runtime)
 
     def _post_run_hook(self, runtime):
         """generates a report showing slices from each axis of an arbitrary
@@ -74,7 +74,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(BETRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _BrainExtractionInputSpecRPT(
@@ -117,7 +117,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(BrainExtractionRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ACompCorInputSpecRPT(nrb._SVGReportCapableInputSpec, confounds.CompCorInputSpec):
@@ -153,7 +153,7 @@ def _post_run_hook(self, runtime):
             self._mask_file,
         )
 
-        return super(ACompCorRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _TCompCorInputSpecRPT(
@@ -195,7 +195,7 @@ def _post_run_hook(self, runtime):
             self.aggregate_outputs(runtime=runtime).high_variance_masks,
         )
 
-        return super(TCompCorRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _SimpleShowMaskInputSpec(nrb._SVGReportCapableInputSpec):
@@ -212,7 +212,7 @@ def _post_run_hook(self, runtime):
         self._seg_files = [self.inputs.mask_file]
         self._masked = True
 
-        return super(SimpleShowMaskRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ROIsPlotInputSpecRPT(nrb._SVGReportCapableInputSpec):

niworkflows/interfaces/reportlets/registration.py

@@ -78,7 +78,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(SpatialNormalizationRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ANTSRegistrationInputSpecRPT(
@@ -106,7 +106,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(ANTSRegistrationRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ANTSApplyTransformsInputSpecRPT(
@@ -134,7 +134,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(ANTSApplyTransformsRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ApplyTOPUPInputSpecRPT(
@@ -169,7 +169,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(ApplyTOPUPRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _FUGUEInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.preprocess.FUGUEInputSpec):
@@ -198,7 +198,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(FUGUERPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _FLIRTInputSpecRPT(nrb._SVGReportCapableInputSpec, fsl.preprocess.FLIRTInputSpec):
@@ -225,7 +225,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(FLIRTRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ApplyXFMInputSpecRPT(
@@ -291,7 +291,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(BBRegisterRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _MRICoregInputSpecRPT(
@@ -342,7 +342,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(MRICoregRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _SimpleBeforeAfterInputSpecRPT(nrb._SVGReportCapableInputSpec):
@@ -373,7 +373,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        return super(SimpleBeforeAfterRPT, self)._post_run_hook(runtime)
+        return super()._post_run_hook(runtime)
 
 
 class _ResampleBeforeAfterInputSpecRPT(_SimpleBeforeAfterInputSpecRPT):
@@ -411,7 +411,7 @@ def _post_run_hook(self, runtime):
             self._moving_image,
         )
 
-        runtime = super(ResampleBeforeAfterRPT, self)._post_run_hook(runtime)
+        runtime = super()._post_run_hook(runtime)
         NIWORKFLOWS_LOG.info("Successfully created report (%s)", self._out_report)
         os.unlink(fname)