fix: Issues identified by ruff

Author: effigies

.circleci/version.py

@@ -2,4 +2,5 @@
 
 import sdcflows
 
-print(sdcflows.__version__, end='', file=open('/tmp/.docker-version.txt', 'w'))
+with open('/tmp/.docker-version.txt', 'w') as f:
+    f.write(sdcflows.__version__)

docs/tools/apigen.py

@@ -185,9 +185,8 @@ def _parse_module(self, uri):
             # nothing that we could handle here.
             return ([], [])
 
-        f = open(filename)
-        functions, classes = self._parse_lines(f)
-        f.close()
+        with open(filename) as f:
+            functions, classes = self._parse_lines(f)
         return functions, classes
 
     def _parse_module_with_import(self, uri):
@@ -220,9 +219,7 @@ def _parse_module_with_import(self, uri):
             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, FunctionType))
-            ):
+            if hasattr(obj, 'func_name') or isinstance(obj, (BuiltinFunctionType, FunctionType)):
                 functions.append(obj_str)
             else:
                 try:
@@ -348,15 +345,7 @@ def _survives_exclude(self, matchstr, match_type):
         L = len(self.package_name)
         if matchstr[:L] == self.package_name:
             matchstr = matchstr[L:]
-        for pat in patterns:
-            try:
-                pat.search
-            except AttributeError:
-                pat = re.compile(pat)
-            if pat.search(matchstr):
-                return False
-
-        return True
+        return not any(re.search(pat, matchstr) for pat in patterns)
 
     def discover_modules(self):
         r"""Return module sequence discovered from ``self.package_name``
@@ -436,11 +425,8 @@ def write_modules_api(self, modules, outdir):
                 document_body.append(body)
 
             out_module = ulm + self.rst_extension
-            outfile = os.path.join(outdir, out_module)
-            fileobj = open(outfile, 'w')
-
-            fileobj.writelines(document_head + document_body)
-            fileobj.close()
+            with open(os.path.join(outdir, out_module), 'w') as fileobj:
+                fileobj.writelines(document_head + document_body)
             written_modules.append(out_module)
 
         self.written_modules = written_modules
@@ -495,14 +481,13 @@ def write_index(self, outdir, froot='gen', relative_to=None):
             relpath = (outdir + os.path.sep).replace(relative_to + os.path.sep, '')
         else:
             relpath = outdir
-        idx = open(path, 'w')
-        w = idx.write
-        w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
-
-        title = 'API Reference'
-        w(title + '\n')
-        w('=' * len(title) + '\n\n')
-        w('.. toctree::\n\n')
-        for f in self.written_modules:
-            w(f'   {os.path.join(relpath, f)}\n')
-        idx.close()
+        with open(path, 'w') as idx:
+            w = idx.write
+            w('.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n')
+
+            title = 'API Reference'
+            w(title + '\n')
+            w('=' * len(title) + '\n\n')
+            w('.. toctree::\n\n')
+            for f in self.written_modules:
+                w(f'   {os.path.join(relpath, f)}\n')

docs/tools/buildmodref.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 """Script to auto-generate API docs."""
 
-
 # stdlib imports
 import sys
 
@@ -48,7 +47,7 @@ def writeapi(package, outdir, source_version, other_defines=True):
     ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)
-    print('%d files written' % len(docwriter.written_modules))
+    print(f'{len(docwriter.written_modules)} files written')
 
 
 if __name__ == '__main__':

sdcflows/fieldmaps.py

@@ -376,7 +376,7 @@ def __attrs_post_init__(self):
                     raise ValueError(
                         'A fieldmap or phase-difference estimation type was found, '
                         f'but an anatomical reference ({magnitude} file) is missing.'
-                    )
+                    ) from None
 
             # Check presence and try to find (if necessary) the second magnitude file
             if self.method == EstimatorType.PHASEDIFF and 'magnitude2' not in suffix_set:
@@ -390,7 +390,7 @@ def __attrs_post_init__(self):
                         raise ValueError(
                             'A phase-difference estimation (phase1/2) type was found, '
                             'but an anatomical reference (magnitude2 file) is missing.'
-                        )
+                        ) from None
 
         # Fieldmap option 2: PEPOLAR (and fieldmap-less or ANAT)
         # IMPORTANT NOTE: fieldmap-less approaches can be considered PEPOLAR with RO = 0.0s

sdcflows/tests/test_fieldmaps.py

@@ -125,7 +125,7 @@ def test_FieldmapEstimation(dsA_dir, inputfiles, method, nsources):
 
     # Exercise workflow creation
     wf = fe.get_workflow()
-    wf == fe.get_workflow()
+    assert wf == fe.get_workflow()
 
 
 @pytest.mark.parametrize(

sdcflows/transform.py

@@ -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.', stacklevel=2
+                '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.', stacklevel=1
+                'are implemented for its quality assurance.',
+                stacklevel=1,
             )
 
         # Resample

sdcflows/utils/bimap.py

@@ -135,11 +135,11 @@ def __setitem__(self, key, value):
         try:
             hash(value)
         except TypeError as exc:
-            raise TypeError(f"value '{value}' of {exc}")
+            raise TypeError(f"value '{value}' of {exc}") from None
         try:
             hash(key)
         except TypeError as exc:
-            raise TypeError(f"key '{key}' of {exc}")
+            raise TypeError(f"key '{key}' of {exc}") from None
 
         if self.__contains__(key):
             raise KeyError(f"'{key}' is already {'a value' * (key in self._inverse)} in mapping")

sdcflows/utils/phasemanip.py

@@ -135,13 +135,15 @@ def delta_te(in_values):
             te2 = float(in_values.get('EchoTimeDifference'))
             return abs(te2)
         except TypeError:
-            raise ValueError('Phase/phase-difference fieldmaps: no echo-times information.')
+            raise ValueError(
+                'Phase/phase-difference fieldmaps: no echo-times information.'
+            ) from None
         except ValueError:
-            raise ValueError(f'Could not interpret metadata <EchoTimeDifference={te2}>.')
+            raise ValueError(f'Could not interpret metadata <EchoTimeDifference={te2}>.') from None
     try:
         te2 = float(te2 or 'unknown')
         te1 = float(te1 or 'unknown')
     except ValueError:
-        raise ValueError(f'Could not interpret metadata <EchoTime(1,2)={(te1, te2)}>.')
+        raise ValueError(f'Could not interpret metadata <EchoTime(1,2)={(te1, te2)}>.') from None
 
     return abs(te2 - te1)

sdcflows/utils/wrangler.py

@@ -606,7 +606,7 @@ def find_anatomical_estimators(
                 meta.update({'TotalReadoutTime': get_trt(meta, candidate.path)})
             epi_targets.append(fm.FieldmapFile(candidate, metadata=meta))
 
-        def sort_key(fmap):
+        def sort_key(fmap, suffixes=suffixes):
             # Return sbref before DWI/BOLD and shortest echo first
             return suffixes.index(fmap.suffix), fmap.metadata.get('EchoTime', 1)
 

sdcflows/workflows/apply/registration.py

@@ -164,7 +164,8 @@ def init_coeff2epi_wf(
     if write_coeff:
         warn(
             'SDCFlows does not tinker with the coefficients file anymore, '
-            'the `write_coeff` parameter will be removed in a future release.', stacklevel=2
+            'the `write_coeff` parameter will be removed in a future release.',
+            stacklevel=2,
         )
 
     return workflow