STY: Apply ruff/pyupgrade rule UP032

UP032 Use f-string instead of `format` call

Co-authored-by: Chris Markiewicz <[email protected]>

Author: DimitriPapadopoulos

nipype/algorithms/confounds.py

@@ -608,8 +608,7 @@ def _run_interface(self, runtime):
 
         if len(imgseries.shape) != 4:
             raise ValueError(
-                "{} expected a 4-D nifti file. Input {} has "
-                "{} dimensions (shape {})".format(
+                "{} expected a 4-D nifti file. Input {} has {} dimensions (shape {})".format(  # noqa: UP032
                     self._header,
                     self.inputs.realigned_file,
                     len(imgseries.shape),
@@ -648,8 +647,7 @@ def _run_interface(self, runtime):
 
                 if TR == 0:
                     raise ValueError(
-                        "{} cannot detect repetition time from image - "
-                        "Set the repetition_time input".format(self._header)
+                        f"{self._header} cannot detect repetition time from image - Set the repetition_time input"
                     )
 
         if isdefined(self.inputs.variance_threshold):
@@ -753,8 +751,7 @@ def _run_interface(self, runtime):
                 f.write("\t".join(["component"] + list(metadata.keys())) + "\n")
                 for i in zip(components_names, *metadata.values()):
                     f.write(
-                        "{0[0]}\t{0[1]}\t{0[2]:.10f}\t"
-                        "{0[3]:.10f}\t{0[4]:.10f}\t{0[5]}\n".format(i)
+                        f"{i[0]}\t{i[1]}\t{i[2]:.10f}\t{i[3]:.10f}\t{i[4]:.10f}\t{i[5]}\n"
                     )
 
         return runtime
@@ -1398,9 +1395,7 @@ def compute_noise_components(
         if imgseries.shape[:3] != mask.shape:
             raise ValueError(
                 "Inputs for CompCor, timeseries and mask, do not have "
-                "matching spatial dimensions ({} and {}, respectively)".format(
-                    imgseries.shape[:3], mask.shape
-                )
+                f"matching spatial dimensions ({imgseries.shape[:3]} and {mask.shape}, respectively)"
             )
 
         voxel_timecourses = imgseries[mask, :]

nipype/caching/memory.py

@@ -86,7 +86,7 @@ def __call__(self, **kwargs):
         return out
 
     def __repr__(self):
-        return "{}({}.{}), base_dir={})".format(
+        return "{}({}.{}), base_dir={})".format(  # noqa: UP032
             self.__class__.__name__,
             self.interface.__module__,
             self.interface.__name__,

nipype/interfaces/ants/registration.py

@@ -204,7 +204,7 @@ def _transformation_constructor(self):
         return "".join(retval)
 
     def _regularization_constructor(self):
-        return "--regularization {}[{},{}]".format(
+        return "--regularization {}[{},{}]".format(  # noqa: UP032
             self.inputs.regularization,
             self.inputs.regularization_gradient_field_sigma,
             self.inputs.regularization_deformation_field_sigma,
@@ -1241,7 +1241,7 @@ def _format_winsorize_image_intensities(self):
                 )
             )
         self._quantilesDone = True
-        return "--winsorize-image-intensities [ {}, {} ]".format(
+        return "--winsorize-image-intensities [ {}, {} ]".format(  # noqa: UP032
             self.inputs.winsorize_lower_quantile,
             self.inputs.winsorize_upper_quantile,
         )
@@ -1268,12 +1268,12 @@ def _get_initial_transform_filenames(self):
     def _format_arg(self, opt, spec, val):
         if opt == "fixed_image_mask":
             if isdefined(self.inputs.moving_image_mask):
-                return "--masks [ {}, {} ]".format(
+                return "--masks [ {}, {} ]".format(  # noqa: UP032
                     self.inputs.fixed_image_mask,
                     self.inputs.moving_image_mask,
                 )
             else:
-                return "--masks %s" % self.inputs.fixed_image_mask
+                return "--masks {}".format(self.inputs.fixed_image_mask)  # noqa: UP032
         elif opt == "transforms":
             return self._format_registration()
         elif opt == "initial_moving_transform":
@@ -1308,18 +1308,20 @@ def _format_arg(self, opt, spec, val):
             out_filename = self._get_outputfilenames(inverse=False)
             inv_out_filename = self._get_outputfilenames(inverse=True)
             if out_filename and inv_out_filename:
-                return "--output [ {}, {}, {} ]".format(
+                return "--output [ {}, {}, {} ]".format(  # noqa: UP032
                     self.inputs.output_transform_prefix,
                     out_filename,
                     inv_out_filename,
                 )
             elif out_filename:
-                return "--output [ {}, {} ]".format(
+                return "--output [ {}, {} ]".format(  # noqa: UP032
                     self.inputs.output_transform_prefix,
                     out_filename,
                 )
             else:
-                return "--output %s" % self.inputs.output_transform_prefix
+                return "--output {}".format(  # noqa: UP032
+                    self.inputs.output_transform_prefix,
+                )
         elif opt == "winsorize_upper_quantile" or opt == "winsorize_lower_quantile":
             if not self._quantilesDone:
                 return self._format_winsorize_image_intensities()
@@ -1590,7 +1592,7 @@ class MeasureImageSimilarity(ANTSCommand):
     def _metric_constructor(self):
         retval = (
             '--metric {metric}["{fixed_image}","{moving_image}",{metric_weight},'
-            "{radius_or_number_of_bins},{sampling_strategy},{sampling_percentage}]".format(
+            "{radius_or_number_of_bins},{sampling_strategy},{sampling_percentage}]".format(  # noqa: UP032
                 metric=self.inputs.metric,
                 fixed_image=self.inputs.fixed_image,
                 moving_image=self.inputs.moving_image,
@@ -1604,13 +1606,13 @@ def _metric_constructor(self):
 
     def _mask_constructor(self):
         if self.inputs.moving_image_mask:
-            retval = '--masks ["{fixed_image_mask}","{moving_image_mask}"]'.format(
+            retval = '--masks ["{fixed_image_mask}","{moving_image_mask}"]'.format(  # noqa: UP032
                 fixed_image_mask=self.inputs.fixed_image_mask,
                 moving_image_mask=self.inputs.moving_image_mask,
             )
         else:
-            retval = '--masks "{fixed_image_mask}"'.format(
-                fixed_image_mask=self.inputs.fixed_image_mask
+            retval = '--masks "{}"'.format(  # noqa: UP032
+                fixed_image_mask=self.inputs.fixed_image_mask,
             )
         return retval
 
@@ -1870,9 +1872,7 @@ def _list_outputs(self):
                 f"00_{self.inputs.output_prefix}_AffineTransform.mat"
             )
             outputs["displacement_field"] = os.path.abspath(
-                "01_{}_DisplacementFieldTransform.nii.gz".format(
-                    self.inputs.output_prefix
-                )
+                f"01_{self.inputs.output_prefix}_DisplacementFieldTransform.nii.gz"
             )
         if self.inputs.process == "assemble":
             outputs["out_file"] = os.path.abspath(self.inputs.out_file)

nipype/interfaces/base/core.py

@@ -849,8 +849,8 @@ def _filename_from_source(self, name, chain=None):
 
             if not isinstance(ns, (str, bytes)):
                 raise ValueError(
-                    "name_source of '{}' trait should be an input trait "
-                    "name, but a type {} object was found".format(name, type(ns))
+                    f"name_source of '{name}' trait should be an input trait "
+                    f"name, but a type {type(ns)} object was found"
                 )
 
             if isdefined(getattr(self.inputs, ns)):

nipype/interfaces/base/specs.py

@@ -142,10 +142,7 @@ def _deprecated_warn(self, obj, name, old, new):
                 raise TraitError(msg)
             else:
                 if trait_spec.new_name:
-                    msg += "Unsetting old value {}; setting new value {}.".format(
-                        name,
-                        trait_spec.new_name,
-                    )
+                    msg += f"Unsetting old value {name}; setting new value {trait_spec.new_name}."
                 warn(msg)
                 if trait_spec.new_name:
                     self.trait_set(

nipype/interfaces/cmtk/parcellation.py

@@ -315,15 +315,10 @@ def create_annot_label(subject_id, subjects_dir, fs_dir, parcellation_name):
     )
     runCmd(mri_cmd, log)
     runCmd("mris_volmask %s" % subject_id, log)
-    mri_cmd = 'mri_convert -i "{}/mri/ribbon.mgz" -o "{}/mri/ribbon.nii.gz"'.format(
-        op.join(subjects_dir, subject_id),
-        op.join(subjects_dir, subject_id),
-    )
+    subject_path = op.join(subjects_dir, subject_id)
+    mri_cmd = f'mri_convert -i "{subject_path}/mri/ribbon.mgz" -o "{subject_path}/mri/ribbon.nii.gz"'
     runCmd(mri_cmd, log)
-    mri_cmd = 'mri_convert -i "{}/mri/aseg.mgz" -o "{}/mri/aseg.nii.gz"'.format(
-        op.join(subjects_dir, subject_id),
-        op.join(subjects_dir, subject_id),
-    )
+    mri_cmd = f'mri_convert -i "{subject_path}/mri/aseg.mgz" -o "{subject_path}/mri/aseg.nii.gz"'
     runCmd(mri_cmd, log)
 
     iflogger.info("[ DONE ]")

nipype/interfaces/dtitk/base.py

@@ -42,11 +42,10 @@ def __init__(self, *args, **kwargs):
         rename_idx = classes.index("DTITKRenameMixin")
         new_name = classes[rename_idx + 1]
         warnings.warn(
-            "The {} interface has been renamed to {}\n"
+            f"The {dep_name} interface has been renamed to {new_name}\n"
             "Please see the documentation for DTI-TK "
             "interfaces, as some inputs have been "
-            "added or renamed for clarity."
-            "".format(dep_name, new_name),
+            "added or renamed for clarity.",
             DeprecationWarning,
         )
         super().__init__(*args, **kwargs)

nipype/interfaces/freesurfer/preprocess.py

@@ -729,10 +729,7 @@ def cmdline(self):
         outdir = self._get_outdir()
         cmd = []
         if not os.path.exists(outdir):
-            cmdstr = "{} -c \"import os; os.makedirs('{}')\"".format(
-                op.basename(sys.executable),
-                outdir,
-            )
+            cmdstr = f"{op.basename(sys.executable)} -c \"import os; os.makedirs('{outdir}')\""
             cmd.extend([cmdstr])
         infofile = os.path.join(outdir, "shortinfo.txt")
         if not os.path.exists(infofile):
@@ -741,12 +738,7 @@ def cmdline(self):
         files = self._get_filelist(outdir)
         for infile, outfile in files:
             if not os.path.exists(outfile):
-                single_cmd = "{}{} {} {}".format(
-                    self._cmd_prefix,
-                    self.cmd,
-                    infile,
-                    os.path.join(outdir, outfile),
-                )
+                single_cmd = f"{self._cmd_prefix}{self.cmd} {infile} {os.path.join(outdir, outfile)}"
                 cmd.extend([single_cmd])
         return "; ".join(cmd)
 

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -65,11 +65,7 @@ def test_fitmsparams(create_files_in_directory):
     # .inputs based parameters setting
     fit.inputs.in_files = filelist
     fit.inputs.out_dir = outdir
-    assert fit.cmdline == "mri_ms_fitparms  {} {} {}".format(
-        filelist[0],
-        filelist[1],
-        outdir,
-    )
+    assert fit.cmdline == f"mri_ms_fitparms  {filelist[0]} {filelist[1]} {outdir}"
 
     # constructor based parameter setting
     fit2 = freesurfer.FitMSParams(
@@ -184,9 +180,7 @@ def test_bbregister(create_files_in_directory):
         base, _ = os.path.splitext(base)
 
     assert bbr.cmdline == (
-        "bbregister --t2 --init-fsl "
-        "--reg {base}_bbreg_fsaverage.dat "
-        "--mov {full} --s fsaverage".format(full=filelist[0], base=base)
+        f"bbregister --t2 --init-fsl --reg {base}_bbreg_fsaverage.dat --mov {filelist[0]} --s fsaverage"
     )
 
 

nipype/interfaces/freesurfer/tests/test_utils.py

@@ -210,10 +210,7 @@ def test_mrisexpand(tmpdir):
     nd_res = expand_nd.run()
 
     # Commandlines differ
-    node_cmdline = (
-        "mris_expand -T 60 -pial {cwd}/lh.pial {cwd}/lh.smoothwm "
-        "1 expandtmp".format(cwd=nd_res.runtime.cwd)
-    )
+    node_cmdline = f"mris_expand -T 60 -pial {nd_res.runtime.cwd}/lh.pial {nd_res.runtime.cwd}/lh.smoothwm 1 expandtmp"
     assert nd_res.runtime.cmdline == node_cmdline
 
     # Check output

nipype/interfaces/freesurfer/utils.py

@@ -355,8 +355,7 @@ def _format_arg(self, name, spec, value):
                 if ext != filemap[value]:
                     if ext in filemap.values():
                         raise ValueError(
-                            "Cannot create {} file with extension "
-                            "{}".format(value, ext)
+                            f"Cannot create {value} file with extension {ext}"
                         )
                     else:
                         logger.warning(
@@ -595,8 +594,7 @@ def _format_arg(self, name, spec, value):
                 if ext != filemap[value]:
                     if ext in filemap.values():
                         raise ValueError(
-                            "Cannot create {} file with extension "
-                            "{}".format(value, ext)
+                            f"Cannot create {value} file with extension {ext}"
                         )
                     else:
                         logger.warning(
@@ -998,10 +996,8 @@ def _format_arg(self, name, spec, value):
                 if len(value) == 2:
                     return "-fminmax %.3f %.3f" % value
                 else:
-                    return "-fminmax {:.3f} {:.3f} -fmid {:.3f}".format(
-                        value[0],
-                        value[2],
-                        value[1],
+                    return (
+                        f"-fminmax {value[0]:.3f} {value[2]:.3f} -fmid {value[1]:.3f}"
                     )
         elif name == "annot_name" and isdefined(value):
             # Matching annot by name needs to strip the leading hemi and trailing
@@ -1015,11 +1011,7 @@ def _format_arg(self, name, spec, value):
 
     def _run_interface(self, runtime):
         if not isdefined(self.inputs.screenshot_stem):
-            stem = "{}_{}_{}".format(
-                self.inputs.subject_id,
-                self.inputs.hemi,
-                self.inputs.surface,
-            )
+            stem = f"{self.inputs.subject_id}_{self.inputs.hemi}_{self.inputs.surface}"
         else:
             stem = self.inputs.screenshot_stem
             stem_args = self.inputs.stem_template_args
@@ -1085,11 +1077,7 @@ def _write_tcl_script(self):
     def _list_outputs(self):
         outputs = self._outputs().get()
         if not isdefined(self.inputs.screenshot_stem):
-            stem = "{}_{}_{}".format(
-                self.inputs.subject_id,
-                self.inputs.hemi,
-                self.inputs.surface,
-            )
+            stem = f"{self.inputs.subject_id}_{self.inputs.hemi}_{self.inputs.surface}"
         else:
             stem = self.inputs.screenshot_stem
             stem_args = self.inputs.stem_template_args

nipype/interfaces/fsl/preprocess.py

@@ -1319,9 +1319,9 @@ def _format_arg(self, name, spec, value):
             if name == "out_intensitymap_file":
                 value = self._list_outputs()[name]
             value = [FNIRT.intensitymap_file_basename(v) for v in value]
-            assert len(set(value)) == 1, "Found different basenames for {}: {}".format(
-                name, value
-            )
+            assert (
+                len(set(value)) == 1
+            ), f"Found different basenames for {name}: {value}"
             return spec.argstr % value[0]
         if name in list(self.filemap.keys()):
             return spec.argstr % self._list_outputs()[name]

nipype/interfaces/fsl/tests/test_maths.py

@@ -401,9 +401,7 @@ def test_binarymaths(create_files_in_directory_plus_output_type):
                 assert maths.cmdline == f"fslmaths a.nii -{op} b.nii c.nii"
             else:
                 maths.inputs.operand_value = ent
-                assert maths.cmdline == "fslmaths a.nii -{} {:.8f} c.nii".format(
-                    op, ent
-                )
+                assert maths.cmdline == f"fslmaths a.nii -{op} {ent:.8f} c.nii"
 
     # Test that we don't need to ask for an out file
     for op in ops:
@@ -461,9 +459,7 @@ def test_tempfilt(create_files_in_directory_plus_output_type):
     for win in windows:
         filt.inputs.highpass_sigma = win[0]
         filt.inputs.lowpass_sigma = win[1]
-        assert filt.cmdline == "fslmaths a.nii -bptf {:.6f} {:.6f} b.nii".format(
-            win[0], win[1]
-        )
+        assert filt.cmdline == f"fslmaths a.nii -bptf {win[0]:.6f} {win[1]:.6f} b.nii"
 
     # Test that we don't need to ask for an out file
     filt = fsl.TemporalFilter(in_file="a.nii", highpass_sigma=64)

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -240,12 +240,7 @@ def test_flirt(setup_flirt):
     pth, fname, ext = split_filename(infile)
     outfile = fsl_name(flirter, "%s_flirt" % fname)
     outmat = "%s_flirt.mat" % fname
-    realcmd = "flirt -in {} -ref {} -out {} -omat {}".format(
-        infile,
-        reffile,
-        outfile,
-        outmat,
-    )
+    realcmd = f"flirt -in {infile} -ref {reffile} -out {outfile} -omat {outmat}"
     assert flirter.cmdline == realcmd
 
     # test apply_xfm option
@@ -433,14 +428,7 @@ def test_fnirt(setup_flirt):
                 " --iout=%s" % (infile, log, flag, strval, reffile, iout)
             )
         elif item in ("in_fwhm", "intensity_mapping_model"):
-            cmd = "fnirt --in={} {}={} --logout={} --ref={} --iout={}".format(
-                infile,
-                flag,
-                strval,
-                log,
-                reffile,
-                iout,
-            )
+            cmd = f"fnirt --in={infile} {flag}={strval} --logout={log} --ref={reffile} --iout={iout}"
         elif item.startswith("apply"):
             cmd = (
                 "fnirt %s=%s "