Update ruff, typos and codespell config and fix errors (#313)

pre-commit-ci[bot] · schuenke · web-flow · commit 7917e782ecfb · 2025-10-14T08:29:23.000+02:00
* [pre-commit] pre-commit autoupdate

* push typos and ruff version

* fix RUF043 errors

* fix B905 and RUF059 errors

* fix codespell pre-commit config

---------

Co-authored-by: Patrick Schuenke &lt;patrick.schuenke@nvision-imaging.com&gt;
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -16,25 +16,26 @@ repos:
       - id: mixed-line-ending
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.14.0
     hooks:
       - id: ruff # linter
         args: [--fix]
       - id: ruff-format # formatter
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.35.6
+    rev: v1.38.1
     hooks:
       - id: typos
+        args: [] # empty, to remove write-changes from the default arguments.
         exclude: ^examples/|paper.md
   
   - repo: https://github.com/codespell-project/codespell
     # Configuration for codespell is in pyproject.toml
     rev: v2.4.1
     hooks:
     - id: codespell
-    additional_dependencies:
-    - tomli; python_version<'3.11'
+      additional_dependencies:
+        - tomli; python_version<'3.11'
 
 ci:
   autofix_commit_msg: |
diff --git a/pyproject.toml b/pyproject.toml
@@ -36,12 +36,7 @@ test = [
   "pytest-cov<6.1",
   "pytest-xdist",
 ]
-docs = [
-  "sphinx",
-  "jinja2",
-  "furo",
-  "recommonmark",
-]
+docs = ["sphinx", "jinja2", "furo", "recommonmark"]
 
 [project.urls]
 Homepage = "https://github.com/imr-framework/pypulseq"
@@ -128,7 +123,6 @@ skip-magic-trailing-comma = false
 
 [tool.typos.default]
 locale = "en-us"
-exclude = ["examples/**"]
 
 # PyTest section
 [tool.pytest.ini_options]
diff --git a/src/pypulseq/SAR/SAR_calc.py b/src/pypulseq/SAR/SAR_calc.py
@@ -280,13 +280,13 @@ def calc_SAR(file: Union[str, Path, Sequence]) -> None:
     SARhg_lim, tsec = _SAR_interp(SAR_hg, t)
     (
         SAR_wbg_tensec,
-        SAR_wbg_sixmin,
+        _SAR_wbg_sixmin,
         SAR_hg_tensec,
-        SAR_hg_sixmin,
-        SAR_wbg_sixmin_peak,
-        SAR_hg_sixmin_peak,
-        SAR_wbg_tensec_peak,
-        SAR_hg_tensec_peak,
+        _SAR_hg_sixmin,
+        _SAR_wbg_sixmin_peak,
+        _SAR_hg_sixmin_peak,
+        _SAR_wbg_tensec_peak,
+        _SAR_hg_tensec_peak,
     ) = _SAR_lims_check(SARwbg_lim, SARhg_lim, tsec)
 
     # Plot 10 sec average SAR
diff --git a/src/pypulseq/Sequence/block.py b/src/pypulseq/Sequence/block.py
@@ -297,7 +297,7 @@ def get_block(self, block_index: int) -> SimpleNamespace:
     block = SimpleNamespace()
     attrs = ['block_duration', 'rf', 'gx', 'gy', 'gz', 'adc', 'label']
     values = [None] * len(attrs)
-    for att, val in zip(attrs, values):
+    for att, val in zip(attrs, values, strict=False):
         setattr(block, att, val)
     event_ind = self.block_events[block_index]
 
diff --git a/src/pypulseq/Sequence/calc_grad_spectrum.py b/src/pypulseq/Sequence/calc_grad_spectrum.py
@@ -156,7 +156,7 @@ def calculate_gradient_spectrum(
                 plt.axvline(res['frequency'] - res['bandwidth'] / 2, color='k', linestyle='--')
                 plt.axvline(res['frequency'] + res['bandwidth'] / 2, color='k', linestyle='--')
         else:
-            for s, c in zip(spectrograms, ['X', 'Y', 'Z']):
+            for s, c in zip(spectrograms, ['X', 'Y', 'Z'], strict=False):
                 plt.figure()
                 plt.title(f'Spectrum {c}')
                 plt.xlabel('Time (s)')
diff --git a/src/pypulseq/Sequence/ext_test_report.py b/src/pypulseq/Sequence/ext_test_report.py
@@ -28,7 +28,7 @@ def ext_test_report(self) -> str:
     # Calculate TE, TR
     duration, num_blocks, event_count = self.duration()
 
-    k_traj_adc, k_traj, t_excitation, t_refocusing, t_adc = self.calculate_kspace()
+    k_traj_adc, _, t_excitation, _, t_adc = self.calculate_kspace()
     t_excitation = np.asarray(t_excitation)
 
     k_abs_adc = np.sqrt(np.sum(np.square(k_traj_adc), axis=0))
diff --git a/src/pypulseq/Sequence/sequence.py b/src/pypulseq/Sequence/sequence.py
@@ -1001,7 +1001,7 @@ def plot(
                         _t = [t_factor * t] * len(lbl_vals)
                         # Plot each label individually to retrieve each corresponding Line2D object
                         p = itertools.chain.from_iterable(
-                            [sp11.plot(__t, _lbl_vals, '.') for __t, _lbl_vals in zip(_t, lbl_vals)]
+                            [sp11.plot(__t, _lbl_vals, '.') for __t, _lbl_vals in zip(_t, lbl_vals, strict=False)]
                         )
                         if len(label_legend_to_plot) != 0:
                             sp11.legend(list(p), label_legend_to_plot, loc='upper left')
@@ -1596,7 +1596,7 @@ def waveforms(self, append_RF: bool = False, time_range: Union[List[float], None
             # element of the next shape.
             shape_pieces[j] = [shape_pieces[j][0]] + [
                 cur if prev[0, -1] + eps < cur[0, 0] else cur[:, 1:]
-                for prev, cur in zip(shape_pieces[j][:-1], shape_pieces[j][1:])
+                for prev, cur in zip(shape_pieces[j][:-1], shape_pieces[j][1:], strict=False)
             ]
 
             wave_data.append(np.concatenate(shape_pieces[j], axis=1))
@@ -1820,7 +1820,7 @@ def write(
         # Check whether all gradients in the last block are ramped down properly
         last_block_id = next(reversed(self.block_events))
         last_block = self.get_block(last_block_id)
-        for channel, event in zip(('x', 'y', 'z'), (last_block.gx, last_block.gy, last_block.gz)):
+        for channel, event in zip(('x', 'y', 'z'), (last_block.gx, last_block.gy, last_block.gz), strict=False):
             if (
                 event is not None
                 and event.type == 'grad'
diff --git a/src/pypulseq/event_lib.py b/src/pypulseq/event_lib.py
@@ -280,7 +280,7 @@ def round_data(data: Tuple[float], digits: Tuple[int]) -> Tuple[float]:
             """
             return tuple(
                 round(d, dig - math.ceil(math.log10(abs(d) + 1e-12)) if dig > 0 else -dig)
-                for d, dig in zip(data, digits)
+                for d, dig in zip(data, digits, strict=False)
             )
 
         def round_data_numpy(data: np.ndarray, digits: int) -> np.ndarray:
diff --git a/src/pypulseq/make_sigpy_pulse.py b/src/pypulseq/make_sigpy_pulse.py
@@ -121,7 +121,7 @@ def sigpy_n_seq(
         )
 
     if pulse_cfg.pulse_type == 'slr':
-        [signal, t, pulse] = make_slr(
+        [signal, t, _] = make_slr(
             flip_angle=flip_angle,
             time_bw_product=time_bw_product,
             duration=duration,
@@ -130,7 +130,7 @@ def sigpy_n_seq(
             disp=plot,
         )
     if pulse_cfg.pulse_type == 'sms':
-        [signal, t, pulse] = make_sms(
+        [signal, t, _] = make_sms(
             flip_angle=flip_angle,
             time_bw_product=time_bw_product,
             duration=duration,
diff --git a/src/pypulseq/utils/safe_pns_prediction.py b/src/pypulseq/utils/safe_pns_prediction.py
@@ -405,7 +405,7 @@ def safe_example():
     # safe_hw_verify(hw)
 
     # Predict PNS levels
-    pns, res = safe_gwf_to_pns(gwf, rf, dt, hw, 1)
+    pns, _ = safe_gwf_to_pns(gwf, rf, dt, hw, 1)
 
     # Plot some results
     safe_plot(pns, dt)
diff --git a/src/pypulseq/utils/siemens/asc_to_hw.py b/src/pypulseq/utils/siemens/asc_to_hw.py
@@ -25,7 +25,7 @@ def asc_to_acoustic_resonances(asc: dict) -> List[dict]:
         freqs = asc['asGPAParameters'][0]['sGCParameters']['aflAcousticResonanceFrequency']
         bw = asc['asGPAParameters'][0]['sGCParameters']['aflAcousticResonanceBandwidth']
 
-    return [{'frequency': f, 'bandwidth': b} for f, b in zip(freqs.values(), bw.values()) if f != 0]
+    return [{'frequency': f, 'bandwidth': b} for f, b in zip(freqs.values(), bw.values(), strict=False) if f != 0]
 
 
 def asc_to_hw(asc: dict, cardiac_model: bool = False) -> SimpleNamespace:
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -34,7 +34,7 @@ def compare(file1, file2):
         contents1 = Path(file1).read_text().splitlines()[7:-2]
         contents2 = Path(file2).read_text().splitlines()[7:-2]
 
-        for line1, line2 in zip(contents1, contents2):
+        for line1, line2 in zip(contents1, contents2, strict=False):
             assert line1 == line2
 
     return compare
diff --git a/tests/test_check_timing.py b/tests/test_check_timing.py
@@ -69,7 +69,7 @@ def test_check_timing():
     seq.add_block(gx)  # Block 9: NEGATIVE_DELAY
 
     # Check timing errors
-    ok, error_report = seq.check_timing()
+    _, error_report = seq.check_timing()
 
     # Check whether the timing error report is as expected
     assert blocks_not_in_error_report(error_report, [1, 3, 6]), 'No timing errors expected on blocks 1, 3, and 6'
diff --git a/tests/test_make_adiabatic_pulse.py b/tests/test_make_adiabatic_pulse.py
@@ -23,13 +23,13 @@ def test_pulse_select():
         assert rf_obj.use == use_label
 
     # Check the appropriate errors are raised if we specify nonsense
-    with pytest.raises(ValueError, match='Invalid type parameter. Must be one of '):
+    with pytest.raises(ValueError, match=r'Invalid type parameter\. Must be one of '):
         make_adiabatic_pulse(pulse_type='not a pulse type')
 
-    with pytest.raises(ValueError, match='Invalid type parameter. Must be one of '):
+    with pytest.raises(ValueError, match=r'Invalid type parameter\. Must be one of '):
         make_adiabatic_pulse(pulse_type='')
 
-    with pytest.raises(ValueError, match='Invalid use parameter. Must be one of '):
+    with pytest.raises(ValueError, match=r'Invalid use parameter\. Must be one of '):
         make_adiabatic_pulse(pulse_type='hypsec', use='not a use')
 
     # Default use case
diff --git a/tests/test_sequence.py b/tests/test_sequence.py
@@ -38,7 +38,7 @@ def __eq__(self, actual):
             if len(self.expected) != len(actual):
                 return False
 
-            for e, a in zip(self.expected, actual):
+            for e, a in zip(self.expected, actual, strict=False):
                 if a != Approx(e, rel=self.rel, abs=self.abs, nan_ok=self.nan_ok):
                     return False
             return True
@@ -65,7 +65,7 @@ def _repr_compare(self, actual):
             if len(self.expected) != len(actual):
                 return [f'Actual and expected lengths do not match: {len(actual)} != {len(self.expected)}']
             r = []
-            for i, (e, a) in enumerate(zip(self.expected, actual)):
+            for i, (e, a) in enumerate(zip(self.expected, actual, strict=False)):
                 approx_obj = Approx(e, rel=self.rel, abs=self.abs, nan_ok=self.nan_ok)
                 if a != approx_obj:
                     r += [f'Index {i} does not match:']
@@ -319,7 +319,7 @@ def test_writeread(self, seq_func, tmp_path, compare_seq_file):
             assert block_compare == Approx(block_orig, abs=1e-5, rel=1e-5), f'Block {block_counter} does not match'
 
         # Test for approximate equality of all gradient waveforms
-        for a, b, channel in zip(seq2.get_gradients(), seq.get_gradients(), ['x', 'y', 'z']):
+        for a, b, channel in zip(seq2.get_gradients(), seq.get_gradients(), ['x', 'y', 'z'], strict=False):
             if a is None and b is None:
                 continue
             assert a is not None and b is not None
@@ -377,7 +377,7 @@ def test_recreate(self, seq_func):  # noqa: ARG002
             )
 
         # Test for approximate equality of all gradient waveforms
-        for a, b, channel in zip(seq2.get_gradients(), seq.get_gradients(), ['x', 'y', 'z']):
+        for a, b, channel in zip(seq2.get_gradients(), seq.get_gradients(), ['x', 'y', 'z'], strict=False):
             if a is None and b is None:
                 continue
             assert a is not None and b is not None
diff --git a/tests/test_sigpy.py b/tests/test_sigpy.py
@@ -14,7 +14,7 @@ def test_sigpy_import():
         # Attempt to import and ensure no issues
         pass
     else:
-        with pytest.raises(ModuleNotFoundError, match='SigPy is not installed.'):
+        with pytest.raises(ModuleNotFoundError, match='SigPy is not installed'):
             raise ModuleNotFoundError('SigPy is not installed.')
 
 

Original file line number	Diff line number	Diff line change
`@@ -280,7 +280,7 @@ def round_data(data: Tuple[float], digits: Tuple[int]) -> Tuple[float]:`
`280`	`280`	`"""`
`281`	`281`	`return tuple(`
`282`	`282`	`round(d, dig - math.ceil(math.log10(abs(d) + 1e-12)) if dig > 0 else -dig)`
`283`		`- for d, dig in zip(data, digits)`
	`283`	`+ for d, dig in zip(data, digits, strict=False)`
`284`	`284`	`)`
`285`	`285`
`286`	`286`	`def round_data_numpy(data: np.ndarray, digits: int) -> np.ndarray:`