chore: Manual ruff fixes [ignore-rev]

Author: effigies

.maint/update_authors.py

@@ -130,10 +130,11 @@ def get_git_lines(fname='line-contributors.txt'):
     if not lines:
         raise RuntimeError(
             """\
-Could not find line-contributors from git repository.%s"""
-            % """ \
+Could not find line-contributors from git repository.{}""".format(
+                """ \
 git-line-summary not found, please install git-extras. """
-            * (cmd[0] is None)
+                * (cmd[0] is None)
+            )
         )
     return [' '.join(line.strip().split()[1:-1]) for line in lines if '%' in line]
 
@@ -219,7 +220,7 @@ def zenodo(
         elif isinstance(creator['affiliation'], list):
             creator['affiliation'] = creator['affiliation'][0]
 
-    Path(zenodo_file).write_text('%s\n' % json.dumps(zenodo, indent=2, ensure_ascii=False))
+    Path(zenodo_file).write_text(f'{json.dumps(zenodo, indent=2, ensure_ascii=False)}\n')
 
 
 @cli.command()
@@ -266,10 +267,8 @@ def _aslist(value):
 
     aff_indexes = [
         ', '.join(
-            [
-                '%d' % (affiliations.index(a) + 1)
-                for a in _aslist(author.get('affiliation', 'Unaffiliated'))
-            ]
+            str(affiliations.index(a) + 1)
+            for a in _aslist(author.get('affiliation', 'Unaffiliated'))
         )
         for author in hits
     ]
@@ -280,15 +279,13 @@ def _aslist(value):
             file=sys.stderr,
         )
 
-    print('Authors (%d):' % len(hits))
-    print(
-        '%s.'
-        % '; '.join(['%s \\ :sup:`%s`\\ ' % (i['name'], idx) for i, idx in zip(hits, aff_indexes)])
-    )
+    print(f'Authors ({len(hits)}):')
+    print('; '.join([rf'{i["name"]} \ :sup:`{idx}`\ ' for i, idx in zip(hits, aff_indexes)]) + '.')
 
     print(
-        '\n\nAffiliations:\n%s'
-        % '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n{}'.format(
+            '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        )
     )
 
 

docs/tools/apigen.py

@@ -217,14 +217,10 @@ def _parse_module_with_import(self, uri):
                 continue
             obj = mod.__dict__[obj_str]
             # Check if function / class defined in module
-            if not self.other_defines and not getmodule(obj) == mod:
+            if not self.other_defines and getmodule(obj) != mod:
                 continue
             # figure out if obj is a function or class
-            if (
-                hasattr(obj, 'func_name')
-                or isinstance(obj, BuiltinFunctionType)
-                or isinstance(obj, FunctionType)
-            ):
+            if hasattr(obj, 'func_name') or isinstance(obj, (BuiltinFunctionType, FunctionType)):
                 functions.append(obj_str)
             else:
                 try:
@@ -278,7 +274,7 @@ def generate_api_doc(self, uri):
 
         # Make a shorter version of the uri that omits the package name for
         # titles
-        uri_short = re.sub(r'^%s\.' % self.package_name, '', uri)
+        uri_short = re.sub(rf'^{self.package_name}\.', '', uri)
 
         head = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
         body = ''
@@ -345,7 +341,7 @@ def _survives_exclude(self, matchstr, match_type):
         elif match_type == 'package':
             patterns = self.package_skip_patterns
         else:
-            raise ValueError('Cannot interpret match type "%s"' % match_type)
+            raise ValueError(f'Cannot interpret match type "{match_type}"')
         # Match to URI without package name
         L = len(self.package_name)
         if matchstr[:L] == self.package_name:
@@ -426,7 +422,7 @@ def write_modules_api(self, modules, outdir):
         written_modules = []
 
         for ulm, mods in module_by_ulm.items():
-            print('Generating docs for %s:' % ulm)
+            print(f'Generating docs for {ulm}:')
             document_head = []
             document_body = []
 
@@ -506,5 +502,5 @@ def write_index(self, outdir, froot='gen', relative_to=None):
         w('=' * len(title) + '\n\n')
         w('.. toctree::\n\n')
         for f in self.written_modules:
-            w('   %s\n' % os.path.join(relpath, f))
+            w(f'   {os.path.join(relpath, f)}\n')
         idx.close()

docs/tools/buildmodref.py

@@ -14,7 +14,7 @@
 
 
 def abort(error):
-    print('*WARNING* API documentation not generated: %s' % error)
+    print(f'*WARNING* API documentation not generated: {error}')
     exit()
 
 
@@ -41,7 +41,7 @@ def writeapi(package, outdir, source_version, other_defines=True):
     docwriter = ApiDocWriter(package, rst_extension='.rst', other_defines=other_defines)
 
     docwriter.package_skip_patterns += [
-        r'\.%s$' % package,
+        rf'\.{package}$',
         r'.*test.*$',
         r'\.version.*$',
     ]

sdcflows/cli/parser.py

@@ -22,7 +22,6 @@
 #
 """Standalone command line executable for estimation of fieldmaps."""
 
-import re
 from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
 from functools import partial
 from pathlib import Path
@@ -46,9 +45,7 @@ def _parse_participant_labels(value):
     ['s060']
 
     """
-    return sorted(
-        set(re.sub(r'^sub-', '', item.strip()) for item in re.split(r'\s+', f'{value}'.strip()))
-    )
+    return sorted({item.removeprefix('sub-') for item in value.split()})
 
 
 def _parser():
@@ -301,12 +298,10 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
+        suggested_path = bids_dir / 'derivatives' / f'sdcflows_{version.split("+")[0]}'
         parser.error(
             'The selected output folder is the same as the input BIDS folder. '
-            'Please modify the output path (suggestion: %s).'
-            % bids_dir
-            / 'derivatives'
-            / ('sdcflows_%s' % version.split('+')[0])
+            f'Please modify the output path (suggestion: {suggested_path}).'
         )
 
     if bids_dir in work_dir.parents:

sdcflows/config.py

@@ -124,6 +124,8 @@
     from importlib_metadata import version as get_version
 
 # Ignore annoying warnings
+import contextlib
+
 from sdcflows import __version__
 from sdcflows._warnings import logging
 
@@ -220,7 +222,7 @@
 class _Config:
     """An abstract class forbidding instantiation."""
 
-    _paths = tuple()
+    _paths = ()
 
     def __init__(self):
         """Avert instantiation."""
@@ -239,10 +241,8 @@ def load(cls, settings, init=True):
                 setattr(cls, k, v)
 
         if init:
-            try:
+            with contextlib.suppress(AttributeError):
                 cls.init()
-            except AttributeError:
-                pass
 
     @classmethod
     def get(cls):

sdcflows/fieldmaps.py

@@ -342,7 +342,7 @@ def __attrs_post_init__(self):
 
         # Fieldmap option 1: actual field-mapping sequences
         fmap_types = suffix_set.intersection(('fieldmap', 'phasediff', 'phase1', 'phase2'))
-        if len(fmap_types) > 1 and fmap_types - set(('phase1', 'phase2')):
+        if len(fmap_types) > 1 and fmap_types - {'phase1', 'phase2'}:
             raise TypeError(f'Incompatible suffices found: <{",".join(fmap_types)}>.')
 
         if fmap_types:
@@ -403,7 +403,7 @@ def __attrs_post_init__(self):
 
         if _pepolar_estimation and not anat_types:
             self.method = MODALITIES[pepolar_types.pop()]
-            _pe = set(f.metadata['PhaseEncodingDirection'] for f in self.sources)
+            _pe = {f.metadata['PhaseEncodingDirection'] for f in self.sources}
             if len(_pe) == 1:
                 raise ValueError(
                     f'Only one phase-encoding direction <{_pe.pop()}> found across sources.'
@@ -418,9 +418,9 @@ def __attrs_post_init__(self):
             # No method has been identified -> fail.
             raise ValueError('Insufficient sources to estimate a fieldmap.')
 
-        intents_meta = set(
+        intents_meta = {
             el for f in self.sources for el in listify(f.metadata.get('IntendedFor') or [])
-        )
+        }
 
         # Register this estimation method
         if not self.bids_id:

sdcflows/interfaces/bspline.py

@@ -628,7 +628,7 @@ def _fix_topup_fieldcoeff(in_coeff, fmap_ref, pe_dir, out_file=None):
         )
     )
     header['cal_min'] = -header['cal_max']
-    header.set_intent('estimate', tuple(), name='B-Spline coefficients')
+    header.set_intent('estimate', (), name='B-Spline coefficients')
 
     # Write out fixed (generalized) coefficients
     coeffnii.__class__(coeffnii.dataobj, newaff, header).to_filename(out_file)

sdcflows/interfaces/reportlets.py

@@ -61,7 +61,7 @@ class FieldmapReportlet(reporting.ReportCapableInterface):
     def __init__(self, **kwargs):
         """Instantiate FieldmapReportlet."""
         self._n_cuts = kwargs.pop('n_cuts', self._n_cuts)
-        super(FieldmapReportlet, self).__init__(generate_report=True, **kwargs)
+        super().__init__(generate_report=True, **kwargs)
 
     def _run_interface(self, runtime):
         return runtime
@@ -77,7 +77,7 @@ def _generate_report(self):
         fmapnii = nb.squeeze_image(rotate_affine(load_img(self.inputs.fieldmap), rot=canonical_r))
 
         if fmapnii.dataobj.ndim == 4:
-            for i, tstep in enumerate(nb.four_to_three(fmapnii)):
+            for tstep in nb.four_to_three(fmapnii):
                 if np.any(np.asanyarray(tstep.dataobj) != 0):
                     fmapnii = tstep
                     break

sdcflows/interfaces/utils.py

@@ -196,20 +196,20 @@ def _run_interface(self, runtime):
 
         # Identity transform
         if np.array_equal(img2target, [[0, 1], [1, 1], [2, 1]]):
-            self._results = dict(
-                out_file=self.inputs.in_file,
-                pe_dir=self.inputs.pe_dir,
-            )
+            self._results = {
+                'out_file': self.inputs.in_file,
+                'pe_dir': self.inputs.pe_dir,
+            }
             return runtime
 
         reoriented = img.as_reoriented(img2target)
 
         pe_dirs = [reorient_pedir(pe_dir, img2target) for pe_dir in self.inputs.pe_dir]
 
-        self._results = dict(
-            out_file=fname_presuffix(self.inputs.in_file, suffix=target, newpath=runtime.cwd),
-            pe_dir=pe_dirs,
-        )
+        self._results = {
+            'out_file': fname_presuffix(self.inputs.in_file, suffix=target, newpath=runtime.cwd),
+            'pe_dir': pe_dirs,
+        }
 
         reoriented.to_filename(self._results['out_file'])
 
@@ -405,7 +405,7 @@ def _flatten(inlist, max_trs=50, out_dir=None):
     out_dir = Path(out_dir) if out_dir is not None else Path()
 
     output = []
-    for i, (path, meta) in enumerate(inlist):
+    for path, meta in inlist:
         img = nb.load(path)
         if len(img.shape) == 3:
             output.append((path, meta))

sdcflows/transform.py

@@ -52,7 +52,7 @@
 from collections.abc import Sequence
 from functools import partial
 from pathlib import Path
-from typing import Callable, Tuple
+from typing import Callable
 from warnings import warn
 
 import attr
@@ -72,7 +72,7 @@
 def _sdc_unwarp(
     data: np.ndarray,
     coordinates: np.ndarray,
-    pe_info: Tuple[int, float],
+    pe_info: tuple[int, float],
     hmc_xfm: np.ndarray | None,
     jacobian: bool,
     fmap_hz: np.ndarray,
@@ -121,7 +121,7 @@ def _sdc_unwarp(
 async def worker(
     data: np.ndarray,
     coordinates: np.ndarray,
-    pe_info: Tuple[int, float],
+    pe_info: tuple[int, float],
     hmc_xfm: np.ndarray,
     func: Callable,
     semaphore: asyncio.Semaphore,
@@ -137,7 +137,7 @@ async def unwarp_parallel(
     fulldataset: np.ndarray,
     coordinates: np.ndarray,
     fmap_hz: np.ndarray,
-    pe_info: Sequence[Tuple[int, float]],
+    pe_info: Sequence[tuple[int, float]],
     xfms: Sequence[np.ndarray],
     jacobian: bool,
     order: int = 3,
@@ -464,7 +464,8 @@ def apply(
         if self.mapped is not None:
             warn(
                 'The fieldmap has been already fit, the user is responsible for '
-                'ensuring the parameters of the EPI target are consistent.'
+                'ensuring the parameters of the EPI target are consistent.',
+                stacklevel=2,
             )
         else:
             # Generate warp field (before ensuring positive cosines)
@@ -519,7 +520,8 @@ def apply(
             warn(
                 'Head-motion compensating (realignment) transforms are ignored when applying '
                 'the unwarp with SDCFlows. This feature will be enabled as soon as unit tests '
-                'are implemented for its quality assurance.'
+                'are implemented for its quality assurance.',
+                stacklevel=1,
             )
 
         # Resample
@@ -733,7 +735,7 @@ def grid_bspline_weights(target_nii, ctrl_nii, dtype='float32'):
         0,
         atol=1e-3,
     ):
-        warn("Image's and B-Spline's grids are not aligned.")
+        warn("Image's and B-Spline's grids are not aligned.", stacklevel=2)
 
     target_to_grid = np.linalg.inv(ctrl_nii.affine) @ target_nii.affine
     wd = []