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

@@ -652,7 +652,7 @@ def test_ReadSidecarJSON_connection(testdata_dir, field):
     "derivatives, subjects_dir",
     [
         (os.getenv("FREESURFER_HOME"), "subjects"),
-        ("/tmp", "{}/{}".format((os.getenv("FREESURFER_HOME"), "subjects"))),
+        ("/tmp", "{}/{}".format(os.getenv("FREESURFER_HOME"), "subjects")),
     ],
 )
 def test_fsdir_noaction(derivatives, subjects_dir):
@@ -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")