STY: Use f-strings where possible

These have been changed manually.

docs/sphinxext/docscrape.py

@@ -326,8 +326,9 @@ def parse_item_name(text):
                 description = line_match.group("desc")
                 if line_match.group("trailing") and description:
                     self._error_location(
-                        "Unexpected comma or period after function list at index %d of "
-                        'line "%s"' % (line_match.end("trailing"), line),
+                        "Unexpected comma or period after function list "
+                        f"at index {line_match.end('trailing')} of line "
+                        f'"{line}"',
                         error=False,
                     )
             if not description and line.startswith(" "):
@@ -414,8 +415,8 @@ def _parse(self):
                 section = " ".join(section)
                 if self.get(section):
                     self._error_location(
-                        "The section %s appears twice in  %s"
-                        % (section, "\n".join(self._doc._str))
+                        f"The section {section} appears twice "
+                        f"in  {'\n'.join(self._doc._str)}"
                     )
 
             if section in ("Parameters", "Other Parameters", "Attributes", "Methods"):

docs/sphinxext/github.py

@@ -37,7 +37,7 @@ def make_link_node(rawtext, app, type, slug, options):
         if not base.endswith('/'):
             base += '/'
     except AttributeError as err:
-        raise ValueError('github_project_url configuration value is not set (%s)' % str(err))
+        raise ValueError(f'github_project_url configuration value is not set ({err})')
 
     ref = base + type + '/' + slug + '/'
     set_classes(options)
@@ -71,19 +71,19 @@ def ghissue_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
     except ValueError:
         msg = inliner.reporter.error(
             'GitHub issue number must be a number greater than or equal to 1; '
-            '"%s" is invalid.' % text, line=lineno)
+            f'"{text}" is invalid.', line=lineno)
         prb = inliner.problematic(rawtext, rawtext, msg)
         return [prb], [msg]
     app = inliner.document.settings.env.app
-    #app.info('issue %r' % text)
+    #app.info(f'issue {text!r}')
     if 'pull' in name.lower():
         category = 'pull'
     elif 'issue' in name.lower():
         category = 'issues'
     else:
         msg = inliner.reporter.error(
             'GitHub roles include "ghpull" and "ghissue", '
-            '"%s" is invalid.' % name, line=lineno)
+            f'"{name}" is invalid.', line=lineno)
         prb = inliner.problematic(rawtext, rawtext, msg)
         return [prb], [msg]
     node = make_link_node(rawtext, app, category, str(issue_num), options)
@@ -105,7 +105,7 @@ def ghuser_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
     :param content: The directive content for customization.
     """
     app = inliner.document.settings.env.app
-    #app.info('user link %r' % text)
+    #app.info(f'user link {text!r}')
     ref = 'https://www.github.com/' + text
     node = nodes.reference(rawtext, text, refuri=ref, **options)
     return [node], []
@@ -126,15 +126,15 @@ def ghcommit_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
     :param content: The directive content for customization.
     """
     app = inliner.document.settings.env.app
-    #app.info('user link %r' % text)
+    #app.info(f'user link {text!r}')
     try:
         base = app.config.github_project_url
         if not base:
             raise AttributeError
         if not base.endswith('/'):
             base += '/'
     except AttributeError as err:
-        raise ValueError('github_project_url configuration value is not set (%s)' % str(err))
+        raise ValueError(f'github_project_url configuration value is not set ({err})')
 
     ref = base + text
     node = nodes.reference(rawtext, text[:6], refuri=ref, **options)

docs/sphinxext/math_dollar.py

@@ -33,7 +33,7 @@ def dollars_to_math(source):
     def repl(matchobj):
         global _data
         s = matchobj.group(0)
-        t = "___XXX_REPL_%d___" % len(_data)
+        t = f"___XXX_REPL_{len(_data)}___"
         _data[t] = s
         return t
     s = re.sub(r"({[^{}$]*\$[^{}$]*\$[^{}]*})", repl, s)

niworkflows/__about__.py

@@ -29,9 +29,7 @@
 from datetime import datetime
 
 __packagename__ = "niworkflows"
-__copyright__ = "Copyright {}, The NiPreps Developers".format(
-    datetime.now().year
-)
+__copyright__ = f"Copyright {datetime.now().year}, The NiPreps Developers"
 __credits__ = [
     "Oscar Esteban",
     "Ross Blair",

niworkflows/anat/ants.py

@@ -721,19 +721,19 @@ def init_atropos_wf(
 
     # De-pad
     depad_mask = pe.Node(
-        ImageMath(operation="PadImage", op2="-%d" % padding), name="23_depad_mask"
+        ImageMath(operation="PadImage", op2=f"-{padding}"), name="23_depad_mask"
     )
     depad_segm = pe.Node(
-        ImageMath(operation="PadImage", op2="-%d" % padding), name="24_depad_segm"
+        ImageMath(operation="PadImage", op2=f"-{padding}"), name="24_depad_segm"
     )
     depad_gm = pe.Node(
-        ImageMath(operation="PadImage", op2="-%d" % padding), name="25_depad_gm"
+        ImageMath(operation="PadImage", op2=f"-{padding}"), name="25_depad_gm"
     )
     depad_wm = pe.Node(
-        ImageMath(operation="PadImage", op2="-%d" % padding), name="26_depad_wm"
+        ImageMath(operation="PadImage", op2=f"-{padding}"), name="26_depad_wm"
     )
     depad_csf = pe.Node(
-        ImageMath(operation="PadImage", op2="-%d" % padding), name="27_depad_csf"
+        ImageMath(operation="PadImage", op2=f"-{padding}"), name="27_depad_csf"
     )
 
     msk_conform = pe.Node(niu.Function(function=_conform_mask), name="msk_conform")
@@ -1061,7 +1061,7 @@ def _select_labels(in_segm, labels):
     for label in labels:
         newnii = nii.__class__(np.uint8(label_data == label), nii.affine, nii.header)
         newnii.set_data_dtype("uint8")
-        out_file = fname_presuffix(in_segm, suffix="_class-%02d" % label, newpath=cwd)
+        out_file = fname_presuffix(in_segm, suffix=f"_class-{label:%02d}", newpath=cwd)
         newnii.to_filename(out_file)
         out_files.append(out_file)
     return out_files

niworkflows/data/__init__.py

@@ -110,7 +110,7 @@ class Loader:
     .. automethod:: cached
     """
 
-    def __init__(self, anchor: Union[str, ModuleType]):
+    def __init__(self, anchor: str | ModuleType):
         self._anchor = anchor
         self.files = files(anchor)
         self.exit_stack = ExitStack()

niworkflows/func/tests/test_util.py

@@ -85,11 +85,10 @@
     parameters = zip(bold_datasets, exp_masks)
 
     if not bold_datasets:
+        _folder_contents = "\n".join([str(p) for p in datapath.glob("ds*/*.nii.gz")])
         raise RuntimeError(
             f"Data folder <{datapath}> was provided, but no images were found. "
-            "Folder contents:\n{}".format(
-                "\n".join([str(p) for p in datapath.glob("ds*/*.nii.gz")])
-            )
+            f"Folder contents:\n{_folder_contents}"
         )
 
 

niworkflows/interfaces/bids.py

@@ -857,8 +857,7 @@ def _run_interface(self, runtime):
         for fname in self._fields:
             if not self._undef_fields and fname not in metadata:
                 raise KeyError(
-                    'Metadata field "%s" not found for file %s'
-                    % (fname, self.inputs.in_file)
+                    f'Metadata field "{fname}" not found for file {self.inputs.in_file}'
                 )
             self._results[fname] = metadata.get(fname, Undefined)
         return runtime
@@ -944,7 +943,7 @@ def _run_interface(self, runtime):
                 if dest.exists():
                     continue
                 else:
-                    raise FileNotFoundError("Expected to find '%s' to copy" % source)
+                    raise FileNotFoundError(f"Expected to find '{source}' to copy")
 
             if (
                 space == 'fsaverage'

niworkflows/interfaces/confounds.py

@@ -298,13 +298,13 @@ def spike_regressors(
     mask = reduce((lambda x, y: x | y), mask.values())
 
     for lag in lags:
-        mask = set([m + lag for m in mask]) | mask
+        mask = {m + lag for m in mask} | mask
 
     mask = mask.intersection(indices)
     if minimum_contiguous is not None:
         post_final = data.shape[0] + 1
-        epoch_length = np.diff(sorted(mask | set([-1, post_final]))) - 1
-        epoch_end = sorted(mask | set([post_final]))
+        epoch_length = np.diff(sorted(mask | {-1, post_final})) - 1
+        epoch_end = sorted(mask | {post_final})
         for end, length in zip(epoch_end, epoch_length):
             if length < minimum_contiguous:
                 mask = mask | set(range(end - length, end))
@@ -357,7 +357,7 @@ def temporal_derivatives(order, variables, data):
     if 0 in order:
         data_deriv[0] = data[variables]
         variables_deriv[0] = variables
-        order = set(order) - set([0])
+        order = set(order) - {0}
     for o in order:
         variables_deriv[o] = [f"{v}_derivative{o}" for v in variables]
         data_deriv[o] = np.tile(np.nan, data[variables].shape)
@@ -400,7 +400,7 @@ def exponential_terms(order, variables, data):
     if 1 in order:
         data_exp[1] = data[variables]
         variables_exp[1] = variables
-        order = set(order) - set([1])
+        order = set(order) - {1}
     for o in order:
         variables_exp[o] = [f"{v}_power{o}" for v in variables]
         data_exp[o] = data[variables] ** o

niworkflows/interfaces/freesurfer.py

@@ -139,7 +139,7 @@ def cmdline(self):
         if source is None:
             return cmd
 
-        return "cp {} {}".format(source, self._list_outputs()["out_file"])
+        return f"cp {source} {self._list_outputs()['out_file']}"
 
 
 class _FSInjectBrainExtractedInputSpec(BaseInterfaceInputSpec):

niworkflows/interfaces/header.py

@@ -100,7 +100,7 @@ def _run_interface(self, runtime):
                 _copyxform(
                     self.inputs.hdr_file,
                     out_name,
-                    message="CopyXForm (niworkflows v%s)" % __version__,
+                    message=f"CopyXForm (niworkflows v{__version__})",
                 )
                 self._results[f].append(out_name)
 
@@ -543,10 +543,7 @@ def _run_interface(self, runtime):
             img.to_filename(out_fname)
 
         if warning_txt:
-            snippet = '<h3 class="elem-title">%s</h3>\n%s\n' % (
-                warning_txt,
-                description,
-            )
+            snippet = f'<h3 class="elem-title">{warning_txt}</h3>\n{description}\n'
             with open(out_report, "w") as fobj:
                 fobj.write(indent(snippet, "\t" * 3))
 

niworkflows/interfaces/images.py

@@ -139,7 +139,7 @@ def _run_interface(self, runtime):
             filenii = nb.load(f)
             filenii = nb.squeeze_image(filenii)
             if len(filenii.shape) == 5:
-                raise RuntimeError("Input image (%s) is 5D." % f)
+                raise RuntimeError(f"Input image ({f}) is 5D.")
             if filenii.dataobj.ndim == 4:
                 nii_list += nb.four_to_three(filenii)
             else:

niworkflows/interfaces/itk.py

@@ -188,7 +188,7 @@ def _applytfms(args):
 
     in_file, in_xform, ifargs, index, newpath = args
     out_file = fname_presuffix(
-        in_file, suffix="_xform-%05d" % index, newpath=newpath, use_ext=True
+        in_file, suffix=f"_xform-{index:05d}", newpath=newpath, use_ext=True
     )
 
     copy_dtype = ifargs.pop("copy_dtype", False)
@@ -250,8 +250,8 @@ def _arrange_xfms(transforms, num_files, tmp_folder):
 
         if nxforms != num_files:
             raise RuntimeError(
-                "Number of transforms (%d) found in the ITK file does not match"
-                " the number of input image files (%d)." % (nxforms, num_files)
+                f"Number of transforms ({nxforms}) found in the ITK file does"
+                f" not match the number of input image files ({num_files})."
             )
 
         # At this point splitting transforms will be necessary, generate a base name
@@ -262,7 +262,7 @@ def _arrange_xfms(transforms, num_files, tmp_folder):
         split_xfms = []
         for xform_i in range(nxforms):
             # Find start token to extract
-            startidx = tfdata.index("#Transform %d" % xform_i)
+            startidx = tfdata.index(f"#Transform {xform_i}")
             next_xform = base_xform + tfdata[startidx + 1:startidx + 4] + [""]
             xfm_file = out_base(xform_i)
             with open(xfm_file, "w") as out_xfm:

niworkflows/interfaces/nibabel.py

@@ -661,9 +661,8 @@ def _gen_reference(
     # Keep 0, 2, 3, 4 unchanged
     resampled.header.set_qform(xform, int(xform_code))
     resampled.header.set_sform(xform, int(xform_code))
-    resampled.header["descrip"] = "reference image generated by %s." % (
-        message or "(unknown software)"
-    )
+    message = message or "(unknown software)"
+    resampled.header["descrip"] = f"reference image generated by {message}."
     resampled.to_filename(out_file)
     return out_file
 

niworkflows/interfaces/norm.py

@@ -162,9 +162,7 @@ def _get_settings(self):
             return self.inputs.settings
 
         # Define a prefix for output files based on the modality of the moving image.
-        filestart = "{}-mni_registration_{}_".format(
-            self.inputs.moving.lower(), self.inputs.flavor
-        )
+        filestart = f"{self.inputs.moving.lower()}-mni_registration_{self.inputs.flavor}_"
 
         data_dir = load_data()
         # Get a list of settings files that match the flavor.
@@ -224,7 +222,7 @@ def _run_interface(self, runtime):
                 NIWORKFLOWS_LOG.warning("Retry #%d failed.", self.retry)
                 # Save outputs (if available)
                 term_out = _write_outputs(
-                    interface_result.runtime, ".nipype-%04d" % self.retry
+                    interface_result.runtime, f".nipype-{self.retry:04d}"
                 )
                 if term_out:
                     NIWORKFLOWS_LOG.warning(
@@ -243,7 +241,7 @@ def _run_interface(self, runtime):
 
         # If all tries fail, raise an error.
         raise RuntimeError(
-            "Robust spatial normalization failed after %d retries." % (self.retry - 1)
+            f"Robust spatial normalization failed after {self.retry - 1} retries."
         )
 
     def _get_ants_args(self):
@@ -435,10 +433,9 @@ def _get_ants_args(self):
             self._reference_image = ref_template
             if not op.isfile(self._reference_image):
                 raise ValueError(
-                    """\
-The registration reference must be an existing file, but path "%s" \
+                    f"""\
+The registration reference must be an existing file, but path "{ref_template}" \
 cannot be found."""
-                    % ref_template
                 )
 
             # Get the template specified by the user.

niworkflows/interfaces/reportlets/masks.py

@@ -140,7 +140,7 @@ def _post_run_hook(self, runtime):
         if len(self.inputs.mask_files) != 1:
             raise ValueError(
                 "ACompCorRPT only supports a single input mask. "
-                "A list %s was found." % self.inputs.mask_files
+                f"A list {self.inputs.mask_files} was found."
             )
         self._anat_file = self.inputs.realigned_file
         self._mask_file = self.inputs.mask_files[0]
@@ -182,7 +182,7 @@ def _post_run_hook(self, runtime):
         if isinstance(high_variance_masks, list):
             raise ValueError(
                 "TCompCorRPT only supports a single output high variance mask. "
-                "A list %s was found." % high_variance_masks
+                f"A list {high_variance_masks} was found."
             )
         self._anat_file = self.inputs.realigned_file
         self._mask_file = high_variance_masks

niworkflows/interfaces/surf.py

@@ -509,13 +509,12 @@ def _run_interface(self, runtime):
             "VolGeomC_A": "0.0",
             "VolGeomC_S": "0.0",
         }
-        meta["AnatomicalStructurePrimary"] = "Cortex%s" % (
-            "Left" if self.inputs.surf_key.startswith("lh") else "Right"
-        )
+        _lr = "Left" if self.inputs.surf_key.startswith("lh") else "Right"
+        meta["AnatomicalStructurePrimary"] = f"Cortex{_lr}"
         meta["AnatomicalStructureSecondary"] = SECONDARY_ANAT_STRUC[
             self.inputs.surf_key.split(".")[-1]
         ]
-        meta["Name"] = "%s_average.gii" % self.inputs.surf_key
+        meta["Name"] = f"{self.inputs.surf_key}_average.gii"
 
         out_file = Path(runtime.cwd) / meta["Name"]
         out_file = ply2gii(self.inputs.in_file, meta, out_file=out_file)
@@ -754,7 +753,7 @@ def ply2gii(in_file, metadata, out_file=None):
     metadata.update(
         zip(
             ("SurfaceCenterX", "SurfaceCenterY", "SurfaceCenterZ"),
-            ["%.4f" % c for c in surf.centroid],
+            [f"{c:.4f}" for c in surf.centroid],
         )
     )
 

niworkflows/interfaces/tests/test_bids.py

@@ -661,7 +661,7 @@ def test_fsdir_noaction(derivatives, subjects_dir):
     res = bintfs.BIDSFreeSurferDir(
         derivatives=derivatives, subjects_dir=subjects_dir, freesurfer_home=fshome
     ).run()
-    assert res.outputs.subjects_dir == "%s/subjects" % fshome
+    assert res.outputs.subjects_dir == f"{fshome}/subjects"
 
 
 @pytest.mark.skipif(not os.getenv("FREESURFER_HOME"), reason="No FreeSurfer")

niworkflows/interfaces/tests/test_cifti.py

@@ -79,7 +79,7 @@ def test__create_cifti_image(tmp_path):
         cifti_file = _create_cifti_image(bold_file, volume_label, dummy_fnames, dummy_fnames, 2.0)
 
     cimg = nb.load(cifti_file)
-    series, bm = [cimg.header.get_axis(i) for i in (0, 1)]
+    series, bm = (cimg.header.get_axis(i) for i in (0, 1))
     assert len(series) == 1  # Time
     assert len(bm) == 8  # Voxel
 

niworkflows/interfaces/tests/test_images.py

@@ -58,13 +58,13 @@ def test_signal_extraction_equivalence(tmp_path, nvols, nmasks, ext, factor):
     se1 = nl.SignalExtraction(
         in_file=img_fname,
         label_files=masks_fname,
-        class_labels=["a%d" % i for i in range(nmasks)],
+        class_labels=[f"a{i}" for i in range(nmasks)],
         out_file=nlsignals,
     )
     se2 = im.SignalExtraction(
         in_file=img_fname,
         label_files=masks_fname,
-        class_labels=["a%d" % i for i in range(nmasks)],
+        class_labels=[f"a{i}" for i in range(nmasks)],
         out_file=imsignals,
     )
 

niworkflows/interfaces/tests/test_itk.py

@@ -52,7 +52,7 @@ def test_applytfms(tmpdir, ext, copy_dtype, in_dtype):
     args = (in_file, in_xform, ifargs, 0, str(tmpdir))
     out_file, cmdline = _applytfms(args)
 
-    assert out_file == str(tmpdir / ("src_xform-%05d%s" % (0, ext)))
+    assert out_file == str(tmpdir / ("src_xform-{0:05d}{ext}"))
 
     out_nii = nb.load(out_file)
     assert np.allclose(nii.affine, out_nii.affine)

niworkflows/interfaces/tests/test_utility.py

@@ -36,7 +36,7 @@ def test_KeySelect():
 
 
 def test_tsv2json(tmp_path):
-    Path.write_bytes(tmp_path / 'empty.tsv', bytes())
+    Path.write_bytes(tmp_path / 'empty.tsv', b'')
     res = _tsv2json(tmp_path / 'empty.tsv', None, 'any_column')
     assert res == {}
     res = _tsv2json(tmp_path / 'empty.tsv', None, 'any_column', additional_metadata={'a': 'b'})

niworkflows/interfaces/utility.py

@@ -169,7 +169,8 @@ def __init__(self, keys=None, fields=None, **inputs):
 
         _invalid = set(self.input_spec.class_editable_traits()).intersection(fields)
         if _invalid:
-            raise ValueError("Some fields are invalid (%s)." % ", ".join(_invalid))
+            _invalid = ", ".join(_invalid)
+            raise ValueError(f"Some fields are invalid ({_invalid}).")
 
         self._fields = fields
 
@@ -196,7 +197,7 @@ def _check_len(self, name, new):
             return
 
         if name == "key" and new not in self.inputs.keys:
-            raise ValueError('Selected key "%s" not found in the index' % new)
+            raise ValueError(f'Selected key "{new}" not found in the index')
 
         if name in self._fields:
             if isinstance(new, str) or len(new) < 1:
@@ -532,10 +533,10 @@ def _tsv2json(
     re_to_snake = r"(^.+?|.*?)((?<![_A-Z])[A-Z]|(?<![_0-9])[0-9]+)"
 
     def snake(match):
-        return "{}_{}".format(match.group(1).lower(), match.group(2).lower())
+        return f"{match.group(1).lower()}_{match.group(2).lower()}"
 
     def camel(match):
-        return "{}{}".format(match.group(1), match.group(2).upper())
+        return f"{match.group(1)}{match.group(2).upper()}"
 
     # from fmriprep
     def less_breakable(a_string):

niworkflows/interfaces/workbench.py

@@ -282,7 +282,7 @@ def _format_arg(self, opt, spec, val):
         if opt in ["current_area", "new_area"]:
             if not self.inputs.area_surfs and not self.inputs.area_metrics:
                 raise ValueError(
-                    "{} was set but neither area_surfs or" " area_metrics were set".format(opt)
+                    f"{opt} was set but neither area_surfs or" " area_metrics were set"
                 )
         if opt == "method":
             if (

niworkflows/reports/core.py

@@ -43,7 +43,7 @@
     if "Configuration 'figures' already exists" != str(e):
         raise
 
-PLURAL_SUFFIX = defaultdict(str("s").format, [("echo", "es")])
+PLURAL_SUFFIX = defaultdict("s".format, [("echo", "es")])
 SVG_SNIPPET = [
     """\
 <object class="svg-reportlet" type="image/svg+xml" data="./{0}">
@@ -548,7 +548,7 @@ def generate_reports(
 
         logger = logging.getLogger("cli")
         error_list = ", ".join(
-            "%s (%d)" % (subid, err)
+            f"{subid} ({err})"
             for subid, err in zip(subject_list, report_errors)
             if err
         )

niworkflows/tests/test_confounds.py

@@ -37,7 +37,7 @@ def _smoke_test_report(report_interface, artifact_name):
     save_artifacts = os.getenv("SAVE_CIRCLE_ARTIFACTS", False)
     if save_artifacts:
         copy(out_report, os.path.join(save_artifacts, artifact_name))
-    assert os.path.isfile(out_report), 'Report "%s" does not exist' % out_report
+    assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'
 
 
 def _expand_test(model_formula):

niworkflows/tests/test_segmentation.py

@@ -47,7 +47,7 @@ def _smoke_test_report(report_interface, artifact_name):
         save_artifacts = os.getenv("SAVE_CIRCLE_ARTIFACTS", False)
         if save_artifacts:
             copy(out_report, os.path.join(save_artifacts, artifact_name))
-        assert os.path.isfile(out_report), 'Report "%s" does not exist' % out_report
+        assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'
 
 
 @pytest.mark.skipif(not has_fsl, reason="No FSL")
@@ -129,7 +129,7 @@ def test_ROIsPlot2(tmp_path):
     for i in range(1, 5):
         seg = np.zeros_like(newdata, dtype="uint8")
         seg[(newdata > 0) & (newdata <= i)] = 1
-        out_file = str(tmp_path / ("segments%02d.nii.gz" % i))
+        out_file = str(tmp_path / (f"segments{i:02d}.nii.gz"))
         nb.Nifti1Image(seg, im.affine, hdr).to_filename(out_file)
         out_files.append(out_file)
     roi_rpt = ROIsPlot(

niworkflows/tests/test_utils.py

@@ -88,6 +88,6 @@ def test_compression(tmp_path):
     size = int(os.stat(uncompressed).st_size)
     size_compress = int(os.stat(compressed).st_size)
     assert size >= size_compress, (
-        "The uncompressed report is smaller (%d)"
-        "than the compressed report (%d)" % (size, size_compress)
+        f"The uncompressed report is smaller (size)"
+        f"than the compressed report (size_compress)"
     )

niworkflows/utils/images.py

@@ -95,7 +95,8 @@ def _copyxform(ref_image, out_image, message=None):
     header = resampled.header.copy()
     header.set_qform(qform, int(qform_code))
     header.set_sform(sform, int(sform_code))
-    header["descrip"] = "xform matrices modified by %s." % (message or "(unknown)")
+    message = message or "(unknown)"
+    header["descrip"] = f"xform matrices modified by {message}."
 
     newimg = resampled.__class__(resampled.dataobj, orig.affine, header)
     newimg.to_filename(out_image)

niworkflows/utils/misc.py

@@ -155,7 +155,7 @@ def fix_multi_T1w_source_name(in_files):
 
     base, in_file = os.path.split(in_file)
     subject_label = in_file.split("_", 1)[0].split("-")[1]
-    return os.path.join(base, "sub-%s_T1w.nii.gz" % subject_label)
+    return os.path.join(base, f"sub-{subject_label}_T1w.nii.gz")
 
 
 def add_suffix(in_files, suffix):

niworkflows/utils/spaces.py

@@ -170,24 +170,25 @@ def __attrs_post_init__(self):
         if self.space in self._standard_spaces:
             object.__setattr__(self, "standard", True)
 
-        _cohorts = ["%s" % t for t in _tfapi.TF_LAYOUT.get_cohorts(template=self.space)]
+        _cohorts = [f"{t}" for t in _tfapi.TF_LAYOUT.get_cohorts(template=self.space)]
         if "cohort" in self.spec:
             if not _cohorts:
                 raise ValueError(
-                    'standard space "%s" does not accept a cohort '
-                    "specification." % self.space
+                    f'standard space "{self.space}" does not accept a cohort '
+                    "specification."
                 )
 
-            if str(self.spec["cohort"]) not in _cohorts:
+            _cohort = str(self.spec["cohort"])
+            if _cohort not in _cohorts:
                 raise ValueError(
-                    'standard space "%s" does not contain any cohort '
-                    'named "%s".' % (self.space, self.spec["cohort"])
+                    f'standard space "{self.space}" does not contain any cohort '
+                    f'named "{_cohort}".'
                 )
         elif _cohorts:
-            _cohorts = ", ".join(['"cohort-%s"' % c for c in _cohorts])
+            _cohorts = ", ".join([f'"cohort-{c}"' for c in _cohorts])
             raise ValueError(
-                'standard space "%s" is not fully defined.\n'
-                "Set a valid cohort selector from: %s." % (self.space, _cohorts)
+                f'standard space "{self.space}" is not fully defined.\n'
+                f"Set a valid cohort selector from: {_cohorts}."
             )
 
     @property
@@ -244,8 +245,8 @@ def _check_name(self, attribute, value):
         valid = list(self._standard_spaces) + NONSTANDARD_REFERENCES
         if value not in valid:
             raise ValueError(
-                'space identifier "%s" is invalid.\nValid '
-                "identifiers are: %s" % (value, ", ".join(valid))
+                f'space identifier "{value}" is invalid.\n'
+                f"Valid identifiers are: {', '.join(valid)}"
             )
 
     def __str__(self):
@@ -529,7 +530,7 @@ def __str__(self):
 
         """
         spaces = ", ".join([str(s) for s in self.references]) or "<none>."
-        return "Spatial References: %s" % spaces
+        return f"Spatial References: {spaces}"
 
     @property
     def references(self):
@@ -563,14 +564,14 @@ def append(self, value):
             self._refs += [self.check_space(value)]
             return
 
-        raise ValueError('space "%s" already in spaces.' % str(value))
+        raise ValueError(f'space "{value}" already in spaces.')
 
     def insert(self, index, value, error=True):
         """Concatenate one more space."""
         if value not in self:
             self._refs.insert(index, self.check_space(value))
         elif error is True:
-            raise ValueError('space "%s" already in spaces.' % str(value))
+            raise ValueError(f'space "{value}" already in spaces.')
 
     def get_spaces(self, standard=True, nonstandard=True, dim=(2, 3)):
         """

niworkflows/viz/plots.py

@@ -426,7 +426,7 @@ def spikesplot(
             ax.set_xlabel("time (frame #)")
         else:
             ax.set_xlabel("time (s)")
-            ax.set_xticklabels(["%.02f" % t for t in (tr * np.array(xticks)).tolist()])
+            ax.set_xticklabels([f"{t:.02f}" for t in (tr * np.array(xticks)).tolist()])
 
     # Handle Y axis
     ylabel = "slice-wise noise average on background"
@@ -488,7 +488,7 @@ def spikesplot(
 
     # if yticks:
     #     # ax.set_yticks(yticks)
-    #     # ax.set_yticklabels(['%.02f' % y for y in yticks])
+    #     # ax.set_yticklabels([f'{y:.02f}' for y in yticks])
     #     # Plot maximum and minimum horizontal lines
     #     ax.plot((0, ntsteps - 1), (yticks[0], yticks[0]), 'k:')
     #     ax.plot((0, ntsteps - 1), (yticks[-1], yticks[-1]), 'k:')
@@ -577,13 +577,13 @@ def confoundplot(
         else:
             ax_ts.set_xlabel("time (s)")
             labels = tr * np.array(xticks)
-            ax_ts.set_xticklabels(["%.02f" % t for t in labels.tolist()])
+            ax_ts.set_xticklabels([f"{t:%.02f}" for t in labels.tolist()])
     else:
         ax_ts.set_xticklabels([])
 
     if name is not None:
         if units is not None:
-            name += " [%s]" % units
+            name += f" [{units}]"
 
         ax_ts.annotate(
             name,
@@ -651,10 +651,11 @@ def confoundplot(
         stdv = 0
         p95 = 0
 
+    units = units or ""
     stats_label = (
-        r"max: {max:.3f}{units} $\bullet$ mean: {mean:.3f}{units} "
-        r"$\bullet$ $\sigma$: {sigma:.3f}"
-    ).format(max=maxv, mean=mean, units=units or "", sigma=stdv)
+        fr"max: {maxv:.3f}{units} $\bullet$ mean: {mean:.3f}{units} "
+        fr"$\bullet$ $\sigma$: {stdv:.3f}"
+    )
     ax_ts.annotate(
         stats_label,
         xy=(0.98, 0.7),
@@ -678,7 +679,7 @@ def confoundplot(
     # Annotate percentile 95
     ax_ts.plot((0, ntsteps - 1), [p95] * 2, linewidth=0.1, color="lightgray")
     ax_ts.annotate(
-        "%.2f" % p95,
+        f"{p95:%.2f}",
         xy=(0, p95),
         xytext=(-1, 0),
         textcoords="offset points",
@@ -695,7 +696,7 @@ def confoundplot(
         ax_ts.plot((0, ntsteps - 1), [thr] * 2, linewidth=0.2, color="dimgray")
 
         ax_ts.annotate(
-            "%.2f" % thr,
+            f"{thr:.2f}",
             xy=(0, thr),
             xytext=(-1, 0),
             textcoords="offset points",
@@ -822,14 +823,14 @@ def compcor_variance_plot(
             ax[m].text(
                 0,
                 100 * thr,
-                "{:.0f}".format(100 * thr),
+                f"{100 * thr:.0f}",
                 fontsize="x-small",
                 bbox=bbox_txt,
             )
             ax[m].text(
                 varexp[thr][0],
                 25,
-                "{} components explain\n{:.0f}% of variance".format(varexp[thr][0], 100 * thr),
+                f"{varexp[thr][0]} components explain\n{100 * thr:.0f}% of variance",
                 rotation=90,
                 horizontalalignment="center",
                 fontsize="xx-small",