STY: pyupgrade + black

doc/conf.py

@@ -1,5 +1,3 @@
-# emacs: -*- coding: utf-8; mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set fileencoding=utf-8 ft=python sts=4 ts=4 sw=4 et:
 #
 # nipype documentation build configuration file, created by
 # sphinx-quickstart on Mon Jul 20 12:30:18 2009.
@@ -151,8 +149,8 @@
 master_doc = "index"
 
 # General information about the project.
-project = u"nipype"
-copyright = u"2009-21, Neuroimaging in Python team"
+project = "nipype"
+copyright = "2009-21, Neuroimaging in Python team"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

nipype/__init__.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """
@@ -26,14 +25,14 @@
     import faulthandler
 
     faulthandler.enable()
-except (ImportError, IOError) as e:
+except (ImportError, OSError) as e:
     pass
 
 config = NipypeConfig()
 logging = Logging(config)
 
 
-class NipypeTester(object):
+class NipypeTester:
     def __call__(self, doctests=True, parallel=False):
         try:
             import pytest

nipype/algorithms/__init__.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """

nipype/algorithms/confounds.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """
@@ -150,7 +149,7 @@ class ComputeDVARS(BaseInterface):
 
     def __init__(self, **inputs):
         self._results = {}
-        super(ComputeDVARS, self).__init__(**inputs)
+        super().__init__(**inputs)
 
     def _gen_fname(self, suffix, ext=None):
         fname, in_ext = op.splitext(op.basename(self.inputs.in_file))
@@ -165,7 +164,7 @@ def _gen_fname(self, suffix, ext=None):
         if ext.startswith("."):
             ext = ext[1:]
 
-        return op.abspath("{}_{}.{}".format(fname, suffix, ext))
+        return op.abspath(f"{fname}_{suffix}.{ext}")
 
     def _run_interface(self, runtime):
         dvars = compute_dvars(
@@ -584,7 +583,7 @@ class CompCor(SimpleInterface):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(CompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "CompCor"
 
     def _run_interface(self, runtime):
@@ -713,7 +712,7 @@ def _run_interface(self, runtime):
                 self.inputs.pre_filter
             ]
             ncols = filter_basis.shape[1] if filter_basis.size > 0 else 0
-            header = ["{}{:02d}".format(ftype, i) for i in range(ncols)]
+            header = [f"{ftype}{i:02d}" for i in range(ncols)]
             if skip_vols:
                 old_basis = filter_basis
                 # nrows defined above
@@ -724,7 +723,7 @@ def _run_interface(self, runtime):
                     filter_basis[skip_vols:, :ncols] = old_basis
                 filter_basis[:skip_vols, -skip_vols:] = np.eye(skip_vols)
                 header.extend(
-                    ["NonSteadyStateOutlier{:02d}".format(i) for i in range(skip_vols)]
+                    [f"NonSteadyStateOutlier{i:02d}" for i in range(skip_vols)]
                 )
             np.savetxt(
                 self._results["pre_filter_file"],
@@ -747,7 +746,7 @@ def _run_interface(self, runtime):
             not_retained = np.where(np.logical_not(metadata["retained"]))
             components_names[retained] = components_header
             components_names[not_retained] = [
-                "dropped{}".format(i) for i in range(len(not_retained[0]))
+                f"dropped{i}" for i in range(len(not_retained[0]))
             ]
             with open(self._results["metadata_file"], "w") as f:
                 f.write("\t".join(["component"] + list(metadata.keys())) + "\n")
@@ -768,7 +767,7 @@ def _make_headers(self, num_col):
             if isdefined(self.inputs.header_prefix)
             else self._header
         )
-        headers = ["{}{:02d}".format(header, i) for i in range(num_col)]
+        headers = [f"{header}{i:02d}" for i in range(num_col)]
         return headers
 
 
@@ -781,7 +780,7 @@ class ACompCor(CompCor):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(ACompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "aCompCor"
 
 
@@ -807,7 +806,7 @@ class TCompCorInputSpec(CompCorInputSpec):
 class TCompCorOutputSpec(CompCorOutputSpec):
     # and all the fields in CompCorOutputSpec
     high_variance_masks = OutputMultiPath(
-        File(exists=True), desc=(("voxels exceeding the variance" " threshold"))
+        File(exists=True), desc=("voxels exceeding the variance" " threshold")
     )
 
 
@@ -832,7 +831,7 @@ class TCompCor(CompCor):
 
     def __init__(self, *args, **kwargs):
         """exactly the same as compcor except the header"""
-        super(TCompCor, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._header = "tCompCor"
         self._mask_files = []
 
@@ -854,7 +853,7 @@ def _process_masks(self, mask_images, timeseries=None):
             out_image = nb.Nifti1Image(mask_data, affine=img.affine, header=img.header)
 
             # save mask
-            mask_file = os.path.abspath("mask_{:03d}.nii.gz".format(i))
+            mask_file = os.path.abspath(f"mask_{i:03d}.nii.gz")
             out_image.to_filename(mask_file)
             IFLOGGER.debug(
                 "tCompcor computed and saved mask of shape %s to " "mask_file %s",
@@ -866,7 +865,7 @@ def _process_masks(self, mask_images, timeseries=None):
         return out_images
 
     def _list_outputs(self):
-        outputs = super(TCompCor, self)._list_outputs()
+        outputs = super()._list_outputs()
         outputs["high_variance_masks"] = self._mask_files
         return outputs
 
@@ -1136,7 +1135,7 @@ def plot_confound(tseries, figsize, name, units=None, series_tr=None, normalize=
 
     xlabel = "Frame #"
     if series_tr is not None:
-        xlabel = "Frame # ({} sec TR)".format(series_tr)
+        xlabel = f"Frame # ({series_tr} sec TR)"
     ax.set_xlabel(xlabel)
     ylim = ax.get_ylim()
 
@@ -1280,17 +1279,15 @@ def combine_mask_files(mask_files, mask_method=None, mask_index=None):
                 mask_index = 0
             else:
                 raise ValueError(
-                    (
-                        "When more than one mask file is provided, "
-                        "one of merge_method or mask_index must be "
-                        "set"
-                    )
+                    "When more than one mask file is provided, "
+                    "one of merge_method or mask_index must be "
+                    "set"
                 )
         if mask_index < len(mask_files):
             mask = nb.load(mask_files[mask_index])
             return [mask]
         raise ValueError(
-            ("mask_index {0} must be less than number of mask " "files {1}").format(
+            ("mask_index {} must be less than number of mask " "files {}").format(
                 mask_index, len(mask_files)
             )
         )

nipype/algorithms/icc.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import os
 from functools import lru_cache
 import numpy as np

nipype/algorithms/mesh.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """
@@ -30,7 +29,7 @@ class TVTKBaseInterface(BaseInterface):
     def __init__(self, **inputs):
         if VTKInfo.no_tvtk():
             raise ImportError("This interface requires tvtk to run.")
-        super(TVTKBaseInterface, self).__init__(**inputs)
+        super().__init__(**inputs)
 
 
 class WarpPointsInputSpec(BaseInterfaceInputSpec):
@@ -92,7 +91,7 @@ def _gen_fname(self, in_file, suffix="generated", ext=None):
 
         if ext[0] == ".":
             ext = ext[1:]
-        return op.abspath("%s_%s.%s" % (fname, suffix, ext))
+        return op.abspath(f"{fname}_{suffix}.{ext}")
 
     def _run_interface(self, runtime):
         import nibabel as nb
@@ -423,7 +422,7 @@ class P2PDistance(ComputeMeshWarp):
     """
 
     def __init__(self, **inputs):
-        super(P2PDistance, self).__init__(**inputs)
+        super().__init__(**inputs)
         IFLOGGER.warning(
             "This interface has been deprecated since 1.0, please "
             "use ComputeMeshWarp"

nipype/algorithms/metrics.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """

nipype/algorithms/misc.py

@@ -1,4 +1,3 @@
-# -*- 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:
 """Miscellaneous algorithms."""
@@ -494,7 +493,7 @@ def merge_csvs(in_list):
             try:
                 in_array = np.loadtxt(in_file, delimiter=",", skiprows=1)
             except ValueError:
-                with open(in_file, "r") as first:
+                with open(in_file) as first:
                     header_line = first.readline()
 
                 header_list = header_line.split(",")
@@ -671,7 +670,7 @@ def _run_interface(self, runtime):
             iflogger.info(
                 'Row headings have been provided. Adding "labels"' "column header."
             )
-            prefix = '"{p}","'.format(p=self.inputs.row_heading_title)
+            prefix = f'"{self.inputs.row_heading_title}","'
             csv_headings = prefix + '","'.join(itertools.chain(headings)) + '"\n'
             rowheadingsBool = True
         else:
@@ -772,7 +771,7 @@ class AddCSVColumn(BaseInterface):
     output_spec = AddCSVColumnOutputSpec
 
     def _run_interface(self, runtime):
-        in_file = open(self.inputs.in_file, "r")
+        in_file = open(self.inputs.in_file)
         _, name, ext = split_filename(self.inputs.out_file)
         if not ext == ".csv":
             ext = ".csv"
@@ -808,12 +807,12 @@ class AddCSVRowInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
     def __setattr__(self, key, value):
         if key not in self.copyable_trait_names():
             if not isdefined(value):
-                super(AddCSVRowInputSpec, self).__setattr__(key, value)
+                super().__setattr__(key, value)
             self._outputs[key] = value
         else:
             if key in self._outputs:
                 self._outputs[key] = value
-            super(AddCSVRowInputSpec, self).__setattr__(key, value)
+            super().__setattr__(key, value)
 
 
 class AddCSVRowOutputSpec(TraitedSpec):
@@ -850,7 +849,7 @@ class AddCSVRow(BaseInterface):
     output_spec = AddCSVRowOutputSpec
 
     def __init__(self, infields=None, force_run=True, **kwargs):
-        super(AddCSVRow, self).__init__(**kwargs)
+        super().__init__(**kwargs)
         undefined_traits = {}
         self._infields = infields
         self._have_lock = False
@@ -882,10 +881,8 @@ def _run_interface(self, runtime):
             from warnings import warn
 
             warn(
-                (
-                    "Python module filelock was not found: AddCSVRow will not be"
-                    " thread-safe in multi-processor execution"
-                )
+                "Python module filelock was not found: AddCSVRow will not be"
+                " thread-safe in multi-processor execution"
             )
 
         input_dict = {}
@@ -926,7 +923,7 @@ def _list_outputs(self):
         return outputs
 
     def _outputs(self):
-        return self._add_output_traits(super(AddCSVRow, self)._outputs())
+        return self._add_output_traits(super()._outputs())
 
     def _add_output_traits(self, base):
         return base
@@ -1070,7 +1067,7 @@ def _run_interface(self, runtime):
     def _gen_output_filename(self):
         if not isdefined(self.inputs.out_file):
             _, base, ext = split_filename(self.inputs.in_file)
-            out_file = os.path.abspath("%s_SNR%03.2f%s" % (base, self.inputs.snr, ext))
+            out_file = os.path.abspath(f"{base}_SNR{self.inputs.snr:03.2f}{ext}")
         else:
             out_file = self.inputs.out_file
 
@@ -1121,7 +1118,7 @@ def gen_noise(self, image, mask=None, snr_db=10.0, dist="normal", bg_dist="norma
             im_noise = np.sqrt((image + stde_1) ** 2 + (stde_2) ** 2)
         else:
             raise NotImplementedError(
-                ("Only normal and rician distributions " "are supported")
+                "Only normal and rician distributions " "are supported"
             )
 
         return im_noise
@@ -1547,7 +1544,7 @@ class CalculateMedian(BaseInterface):
     output_spec = CalculateMedianOutputSpec
 
     def __init__(self, *args, **kwargs):
-        super(CalculateMedian, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         self._median_files = []
 
     def _gen_fname(self, suffix, idx=None, ext=None):
@@ -1569,10 +1566,10 @@ def _gen_fname(self, suffix, idx=None, ext=None):
         if self.inputs.median_file:
             outname = self.inputs.median_file
         else:
-            outname = "{}_{}".format(fname, suffix)
+            outname = f"{fname}_{suffix}"
         if idx:
             outname += str(idx)
-        return op.abspath("{}.{}".format(outname, ext))
+        return op.abspath(f"{outname}.{ext}")
 
     def _run_interface(self, runtime):
         total = None