diff --git a/.circleci/version.py b/.circleci/version.py
index cbaaacb31b..207a6b4fef 100644
--- a/.circleci/version.py
+++ b/.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__)
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index fe21fefa26..c262426f78 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,3 +1,9 @@
+# Thu May 15 11:41:29 2025 -0400 - markiewicz@stanford.edu - chore: Manual ruff fixes [ignore-rev]
+d0da75c1e4d6345ea1cc2b337668f6774288195e
+# Thu May 15 11:11:38 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+497670f170f87cdcfb32cc525f5bf0668f96129a
+# Thu May 15 09:34:34 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
+dc3706038661984718da079e24a863842407a837
 # Thu May 15 09:29:29 2025 -0400 - markiewicz@stanford.edu - run: ruff format [ignore-rev]
 d97ae316c0bdf71084a0732760ceed5221033fc2
 # Thu May 15 09:26:57 2025 -0400 - markiewicz@stanford.edu - run: ruff check --fix [ignore-rev]
diff --git a/.maint/update_authors.py b/.maint/update_authors.py
index 48fe34eed0..a5a6a3d93c 100644
--- a/.maint/update_authors.py
+++ b/.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(['{0: >2}. {1}'.format(i + 1, a) for i, a in enumerate(affiliations)])
+        '\n\nAffiliations:\n{}'.format(
+            '\n'.join([f'{i + 1: >2}. {a}' for i, a in enumerate(affiliations)])
+        )
     )
 
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ce9679c707..9fa3868f94 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,12 +12,9 @@ repos:
       - id: end-of-file-fixer
       - id: fix-byte-order-marker
       - id: trailing-whitespace
-  # Enable when no significant PRs are in progress
-  # - repo: https://github.com/psf/black
-  #   rev: 23.1.0
-  #   hooks:
-  #     - id: black
-  # - repo: https://github.com/pycqa/isort
-  #   rev: 5.12.0
-  #   hooks:
-  #     - id: isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.10
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
diff --git a/docs/tools/apigen.py b/docs/tools/apigen.py
index f602f45fa8..30e4b4789f 100644
--- a/docs/tools/apigen.py
+++ b/docs/tools/apigen.py
@@ -27,7 +27,7 @@
 DEBUG = True
 
 
-class ApiDocWriter(object):
+class ApiDocWriter:
     """Class for automatic detection and parsing of API docs
     to Sphinx-parsable reST format"""
 
@@ -185,9 +185,8 @@ def _parse_module(self, uri):
             # nothing that we could handle here.
             return ([], [])
 
-        f = open(filename, 'rt')
-        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):
@@ -217,14 +216,10 @@ 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 +273,7 @@ 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 = ''
@@ -345,20 +340,12 @@ 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:
             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``
@@ -426,7 +413,7 @@ 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 = []
 
@@ -438,11 +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, 'wt')
-
-            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
@@ -497,14 +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, 'wt')
-        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('   %s\n' % os.path.join(relpath, f))
-        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')
diff --git a/docs/tools/buildmodref.py b/docs/tools/buildmodref.py
index e0a7c41059..2e81222b95 100755
--- a/docs/tools/buildmodref.py
+++ b/docs/tools/buildmodref.py
@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 """Script to auto-generate API docs."""
 
-from __future__ import division, print_function
-
 # stdlib imports
 import sys
 
@@ -16,7 +14,7 @@
 
 
 def abort(error):
-    print('*WARNING* API documentation not generated: %s' % error)
+    print(f'*WARNING* API documentation not generated: {error}')
     exit()
 
 
@@ -43,13 +41,13 @@ 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.*$',
         r'\.version.*$',
     ]
     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__':
diff --git a/pyproject.toml b/pyproject.toml
index 040fab4974..72e0e5949c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -182,8 +182,12 @@ line-length = 99
 select = [
   "F",
   "E",
+  "C",
   "W",
+  "B",
   "I",
+  "SIM",
+  "UP",
 ]
 ignore = [
   "E203",
@@ -198,6 +202,9 @@ inline-quotes = "single"
 [tool.ruff.lint.extend-per-file-ignores]
 "*/__init__.py" = ["F401"]
 "docs/conf.py" = ["E265"]
+"*/test_*.py" = [
+  "B018",  # Unassigned expressions are fine
+]
 
 [tool.ruff.format]
 quote-style = "single"
diff --git a/sdcflows/cli/main.py b/sdcflows/cli/main.py
index d96751dd2c..9336903f31 100644
--- a/sdcflows/cli/main.py
+++ b/sdcflows/cli/main.py
@@ -25,7 +25,6 @@
 
 def main(argv=None):
     """Entry point for SDCFlows' CLI."""
-    import atexit
     import gc
     import os
     import sys
@@ -34,8 +33,6 @@ def main(argv=None):
     from sdcflows import config
     from sdcflows.cli.parser import parse_args
 
-    atexit.register(config.restore_env)
-
     # Run parser
     parse_args(argv)
 
diff --git a/sdcflows/cli/parser.py b/sdcflows/cli/parser.py
index 184f375717..ed89836d1f 100644
--- a/sdcflows/cli/parser.py
+++ b/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:
diff --git a/sdcflows/config.py b/sdcflows/config.py
index e2e851184d..98a660c7dd 100644
--- a/sdcflows/config.py
+++ b/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
 
@@ -200,7 +202,7 @@
 _memory_gb = None
 try:
     if 'linux' in sys.platform:
-        with open('/proc/meminfo', 'r') as f_in:
+        with open('/proc/meminfo') as f_in:
             _meminfo_lines = f_in.readlines()
             _mem_total_line = [line for line in _meminfo_lines if 'MemTotal' in line][0]
             _mem_total = float(_mem_total_line.split()[1])
@@ -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):
@@ -647,13 +647,3 @@ def _process_initializer(config_file: Path):
 
     # Set the maximal number of threads per process
     os.environ['OMP_NUM_THREADS'] = f'{config.nipype.omp_nthreads}'
-
-
-def restore_env():
-    """Restore the original environment."""
-
-    for k in os.environ.keys():
-        del os.environ[k]
-
-    for k, v in environment._pre_sdcflows.items():
-        os.environ[k] = v
diff --git a/sdcflows/fieldmaps.py b/sdcflows/fieldmaps.py
index 5f9262f44b..b05e7f7822 100644
--- a/sdcflows/fieldmaps.py
+++ b/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:
@@ -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
@@ -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:
diff --git a/sdcflows/interfaces/bspline.py b/sdcflows/interfaces/bspline.py
index ecf394823e..bdf88ba1c1 100644
--- a/sdcflows/interfaces/bspline.py
+++ b/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)
diff --git a/sdcflows/interfaces/reportlets.py b/sdcflows/interfaces/reportlets.py
index 3f7b05f39e..bccd855f1b 100644
--- a/sdcflows/interfaces/reportlets.py
+++ b/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
diff --git a/sdcflows/interfaces/utils.py b/sdcflows/interfaces/utils.py
index f315623de0..80a5be0b6d 100644
--- a/sdcflows/interfaces/utils.py
+++ b/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))
diff --git a/sdcflows/tests/test_fieldmaps.py b/sdcflows/tests/test_fieldmaps.py
index 5032c68dcf..383376b988 100644
--- a/sdcflows/tests/test_fieldmaps.py
+++ b/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(
diff --git a/sdcflows/tests/test_transform.py b/sdcflows/tests/test_transform.py
index 05b54f4712..cb2d01bb3e 100644
--- a/sdcflows/tests/test_transform.py
+++ b/sdcflows/tests/test_transform.py
@@ -197,7 +197,7 @@ def test_apply_transform(tmpdir, outdir, datadir, pe0, hmc, fmap):
     error_margin = 0.5
     if fmap is False:  # If no fieldmap, this is equivalent to only HMC
         realigned = LinearTransformsMapping(hmc_xfms, reference=in_file).apply(in_file)
-        error = np.sqrt(((corrected.dataobj - realigned.dataobj) ** 2))
+        error = np.sqrt((corrected.dataobj - realigned.dataobj) ** 2)
 
         if outdir:
             # Do not include the first volume in the average to enhance differences
@@ -226,7 +226,7 @@ def test_apply_transform(tmpdir, outdir, datadir, pe0, hmc, fmap):
             )
     else:
         realigned = nb.load(in_file)
-        error = np.nan_to_num(np.sqrt(((corrected.dataobj - realigned.dataobj) ** 2)), nan=0)
+        error = np.nan_to_num(np.sqrt((corrected.dataobj - realigned.dataobj) ** 2), nan=0)
         error_margin = 200  # test oracle is pretty bad here - needs revision.
 
         if outdir:
@@ -290,7 +290,7 @@ def test_apply_transform(tmpdir, outdir, datadir, pe0, hmc, fmap):
             out_report=str(outdir / f'sub-pilot_ses-15_acq-b0_dir-{pe0}_desc-hmcdiff_dwi.svg'),
         ).run()
 
-        error = np.sqrt(((corrected.dataobj - corrected_nohmc.dataobj) ** 2))
+        error = np.sqrt((corrected.dataobj - corrected_nohmc.dataobj) ** 2)
         realigned.__class__(
             error,
             realigned.affine,
diff --git a/sdcflows/transform.py b/sdcflows/transform.py
index 3388789ac3..d3ad85dd1d 100644
--- a/sdcflows/transform.py
+++ b/sdcflows/transform.py
@@ -49,9 +49,10 @@
 
 import asyncio
 import os
+from collections.abc import Sequence
 from functools import partial
 from pathlib import Path
-from typing import Callable, Sequence, Tuple
+from typing import Callable
 from warnings import warn
 
 import attr
@@ -71,7 +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,
@@ -120,7 +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,
@@ -136,7 +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,
@@ -463,7 +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)
@@ -490,18 +492,12 @@ def apply(
             ro_time *= n_volumes
 
         pe_info = []
-        for volid in range(n_volumes):
-            pe_axis = 'ijk'.index(pe_dir[volid][0])
-            axis_flip = axcodes[pe_axis] in ('LPI')
-            pe_flip = pe_dir[volid].endswith('-')
-
-            pe_info.append(
-                (
-                    pe_axis,
-                    # Displacements are reversed if either is true (after ensuring positive cosines)
-                    -ro_time[volid] if (axis_flip ^ pe_flip) else ro_time[volid],
-                )
-            )
+        for vol_pe_dir, vol_ro_time in zip(pe_dir, ro_time):
+            pe_axis = 'ijk'.index(vol_pe_dir[0])
+            # Displacements are reversed if either is true (after ensuring positive cosines)
+            flip = (axcodes[pe_axis] in 'LPI') ^ vol_pe_dir.endswith('-')
+
+            pe_info.append((pe_axis, -vol_ro_time if flip else vol_ro_time))
 
         # Reference image's voxel coordinates (in voxel units)
         voxcoords = (
@@ -524,7 +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
@@ -738,7 +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 = []
diff --git a/sdcflows/utils/bimap.py b/sdcflows/utils/bimap.py
index 5a8ed03759..bb360daea3 100644
--- a/sdcflows/utils/bimap.py
+++ b/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")
@@ -174,11 +174,11 @@ def __contains__(self, key):
 
     def add(self, value):
         """Insert a new value in the bidict, generating an automatic key."""
-        _used = set(
+        _used = {
             int(i.groups()[0])
             for i in [_autokey_pat.match(k) for k in self.keys() if k.startswith('auto_')]
             if i is not None
-        )
+        }
         for i in range(len(_used) + 1):
             if i not in _used:
                 newkey = f'auto_{i:05d}'
@@ -222,11 +222,11 @@ class EstimatorRegistry(bidict):
     @property
     def sources(self):
         """Return a flattened list of fieldmap sources."""
-        return sorted(set([el for group in self.values() for el in group]))
+        return sorted({el for group in self.values() for el in group})
 
     def get_key(self, value):
         """Get the key(s) containing a particular value."""
         if value not in self.sources:
-            return tuple()
+            return ()
 
         return tuple(sorted(k for k, v in self.items() if value in v))
diff --git a/sdcflows/utils/phasemanip.py b/sdcflows/utils/phasemanip.py
index 2ee029ab92..c32c8c8d3f 100644
--- a/sdcflows/utils/phasemanip.py
+++ b/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)
diff --git a/sdcflows/utils/wrangler.py b/sdcflows/utils/wrangler.py
index acbcbe6ff9..235697bbff 100644
--- a/sdcflows/utils/wrangler.py
+++ b/sdcflows/utils/wrangler.py
@@ -29,7 +29,7 @@
 from functools import reduce
 from itertools import product
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
 
 from bids.layout import BIDSFile, BIDSLayout
 from bids.utils import listify
@@ -59,7 +59,7 @@ def _resolve_intent(intent: str, layout: BIDSLayout, subject: str) -> str | None
     return intent
 
 
-def _filter_metadata(metadata: Dict[str, Any], subject: str) -> Dict[str, Any]:
+def _filter_metadata(metadata: dict[str, Any], subject: str) -> dict[str, Any]:
     intents = metadata.get('IntendedFor')
     if intents:
         updated = [_normalize_intent(intent, subject) for intent in listify(intents)]
@@ -71,12 +71,12 @@ def find_estimators(
     *,
     layout: BIDSLayout,
     subject: str,
-    sessions: Optional[List[str]] = None,
-    fmapless: Union[bool, set] = True,
+    sessions: list[str] | None = None,
+    fmapless: bool | set = True,
     force_fmapless: bool = False,
-    logger: Optional[logging.Logger] = None,
-    bids_filters: Optional[dict] = None,
-    anat_suffix: Union[str, List[str]] = 'T1w',
+    logger: logging.Logger | None = None,
+    bids_filters: dict | None = None,
+    anat_suffix: str | list[str] = 'T1w',
 ) -> list:
     """
     Apply basic heuristics to automatically find available data for fieldmap estimation.
@@ -346,7 +346,7 @@ def find_estimators(
     estimators = []
 
     # Step 1. Use B0FieldIdentifier metadata
-    b0_ids = tuple()
+    b0_ids = ()
     with suppress(BIDSEntityError):
         # flatten lists from json (tupled in pybids for hashing), then unique
         b0_ids = reduce(
@@ -445,7 +445,7 @@ def find_estimators(
 
         # At this point, only single-PE _epi files WITH ``IntendedFor`` can
         # be automatically processed.
-        has_intended = tuple()
+        has_intended = ()
         with suppress(ValueError):
             has_intended = layout.get(
                 **{
@@ -545,10 +545,10 @@ def find_anatomical_estimators(
     anat_file: BIDSFile,
     layout: BIDSLayout,
     subject: str,
-    sessions: List[str],
-    base_entities: Dict[str, Any],
-    suffixes: List[str],
-) -> List[List[fm.FieldmapFile]]:
+    sessions: list[str],
+    base_entities: dict[str, Any],
+    suffixes: list[str],
+) -> list[list[fm.FieldmapFile]]:
     r"""Find anatomical estimators
 
     Given an anatomical reference image, create lists of files for estimating
@@ -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)
 
@@ -644,7 +644,7 @@ def _log_debug_estimation(
 
 
 def _log_debug_estimator_fail(
-    logger: logging.Logger, b0_id: str, files: List[BIDSFile], bids_root: str, message: str
+    logger: logging.Logger, b0_id: str, files: list[BIDSFile], bids_root: str, message: str
 ) -> None:
     """A helper function to log failures to build an estimator when running with verbosity."""
     logger.debug(
diff --git a/sdcflows/viz/utils.py b/sdcflows/viz/utils.py
index 2da06282bc..422cb1add6 100644
--- a/sdcflows/viz/utils.py
+++ b/sdcflows/viz/utils.py
@@ -89,8 +89,8 @@ def plot_registration(
 
         # Find and replace the figure_1 id.
         xml_data = etree.fromstring(svg)
-        find_text = etree.ETXPath("//{%s}g[@id='figure_1']" % SVGNS)
-        find_text(xml_data)[0].set('id', '%s-%s-%s' % (div_id, mode, uuid4()))
+        find_text = etree.ETXPath(f"//{{{SVGNS}}}g[@id='figure_1']")
+        find_text(xml_data)[0].set('id', f'{div_id}-{mode}-{uuid4()}')
 
         svg_fig = SVGFigure()
         svg_fig.root = xml_data
diff --git a/sdcflows/workflows/apply/registration.py b/sdcflows/workflows/apply/registration.py
index b9fb1b2775..f8b89a6593 100644
--- a/sdcflows/workflows/apply/registration.py
+++ b/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.'
+            'the `write_coeff` parameter will be removed in a future release.',
+            stacklevel=2,
         )
 
     return workflow
diff --git a/sdcflows/workflows/base.py b/sdcflows/workflows/base.py
index 788fd8b77f..b026f53a89 100644
--- a/sdcflows/workflows/base.py
+++ b/sdcflows/workflows/base.py
@@ -115,9 +115,9 @@ def init_fmap_preproc_wf(
                             in_file=f.path,
                             use_estimate=use_metadata_estimates,
                         )
-                    except ValueError:
+                    except ValueError as e:
                         msg = f'Missing readout timing information for <{f.path}>.'
-                        raise RuntimeError(msg)
+                        raise RuntimeError(msg) from e
 
         est_wf = estimator.get_workflow(
             use_metadata_estimates=use_metadata_estimates,
diff --git a/sdcflows/workflows/fit/base.py b/sdcflows/workflows/fit/base.py
index 7ad2f086be..d3264702be 100644
--- a/sdcflows/workflows/fit/base.py
+++ b/sdcflows/workflows/fit/base.py
@@ -49,7 +49,7 @@ def init_sdcflows_wf():
             logger=config.loggers.cli,
         )
 
-    for subject, sub_estimators in estimators_record.items():
+    for sub_estimators in estimators_record.values():
         for estim in sub_estimators:
             estim_wf = estim.get_workflow(
                 omp_nthreads=config.nipype.omp_nthreads,
diff --git a/sdcflows/workflows/fit/pepolar.py b/sdcflows/workflows/fit/pepolar.py
index 25ae08e827..c64a694c89 100644
--- a/sdcflows/workflows/fit/pepolar.py
+++ b/sdcflows/workflows/fit/pepolar.py
@@ -293,9 +293,8 @@ def init_3dQwarp_wf(omp_nthreads=1, debug=False, name='pepolar_estimate_wf'):
     from ...utils.misc import last as _last
 
     workflow = Workflow(name=name)
-    workflow.__desc__ = f"""{_PEPOLAR_DESC} \
-with `3dQwarp` (@afni; AFNI {''.join(['%02d' % v for v in afni.Info().version() or []])}).
-"""
+    afni_ver = ''.join(f'{v:02d}' for v in afni.Info().version() or [])
+    workflow.__desc__ = f'{_PEPOLAR_DESC} with `3dQwarp` (@afni; AFNI {afni_ver}).'
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['in_data', 'metadata']), name='inputnode')
 
diff --git a/sdcflows/workflows/outputs.py b/sdcflows/workflows/outputs.py
index aeac11f92d..ce5aa09997 100644
--- a/sdcflows/workflows/outputs.py
+++ b/sdcflows/workflows/outputs.py
@@ -337,4 +337,4 @@ def _selectintent(metadata):
     """
     from bids.utils import listify
 
-    return sorted(set([el for m in listify(metadata) for el in listify(m.get('IntendedFor', []))]))
+    return sorted({el for m in listify(metadata) for el in listify(m.get('IntendedFor', []))})
diff --git a/tox.ini b/tox.ini
index 77d4df3b13..031a66f45d 100644
--- a/tox.ini
+++ b/tox.ini
@@ -71,9 +71,6 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
   PYTHON_GIL
-deps =
-  # Waiting on a release
-  py313: traits @ git+https://github.com/enthought/traits.git@10954eb
 extras = tests
 setenv =
   pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple