🔧 Add codespell configuration and fix existing typos

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Codespell
+        uses: codespell-project/actions-codespell@8f01853be192eb0f849a5c7d721450e7a467c579  # v2.2

.pre-commit-config.yaml

@@ -18,3 +18,11 @@ repos:
         language: script
         stages: [commit-msg]
         entry: scripts/check-gitmoji.sh
+
+  - repo: https://github.com/codespell-project/codespell
+    # Configuration for codespell is in pyproject.toml
+    rev: v2.4.2
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli; python_version<'3.11'

include/utilities.h

@@ -10,7 +10,7 @@
 namespace py = pybind11;
 
 /**
- * @brief print sequnce
+ * @brief print sequence
  *
  * @tparam sequence
  * @param seq

include/warps.h

@@ -315,7 +315,7 @@ py::array_t<T, py::array::f_style> compute_jacobian_determinant(py::array_t<T, p
     typename DisplacementFieldJacobianDeterminantFilterType::Pointer jacobian_filter =
         DisplacementFieldJacobianDeterminantFilterType::New();
 
-    // Pass displacment fields into jacobian filters
+    // Pass displacement fields into jacobian filters
     jacobian_filter->SetInput(field);
     jacobian_filter->SetUseImageSpacingOff();
 

pyproject.toml

@@ -136,3 +136,15 @@ archs = ["auto"]
 archs = ["universal2"]
 repair-wheel-command = "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
 before-build = ["pip install delocate>=0.13.0"]
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = './.git*,*/.git-meta/*,*.pdf,*.lock,*include/romeo/*,*include/itk/*,*/build/*,*/.venv/*'
+check-hidden = true
+# ignore-words-list rationale:
+#   te,tes    - MR-physics abbreviations (echo time / echo times); see CLAUDE.md
+#   nd        - DICOM ImageType flag in BIDS test fixtures
+#   datas     - PyInstaller Analysis() parameter name (packaging/pyinstaller/)
+#   framei    - loop variable "frame i" in tests/test_distortion.py
+#   thirdparty - refers to ITK's ThirdParty/Eigen3 module in CMakeLists.txt comment
+ignore-words-list = 'te,tes,nd,datas,framei,thirdparty'

warpkit/concurrency.py

@@ -93,7 +93,7 @@ def run_executor(
     for future in as_completed(futures):
         # get the index of the future
         idx = futures[future]
-        # pass thre result of the future to the post_fn
+        # pass the result of the future to the post_fn
         if post_fn is not None:
             post_fn(idx, future.result())
 

warpkit/unwrap.py

@@ -408,7 +408,7 @@ def unwrap_phase(
             npt.NDArray[np.bool_], binary_dilation(combined_mask, strel, iterations=2)
         )
 
-        # get a dilated verision of the mask
+        # get a dilated version of the mask
         combined_mask_dilated = cast(
             npt.NDArray[np.bool_],
             binary_dilation(combined_mask, strel, iterations=automask_dilation),
@@ -533,7 +533,7 @@ def check_temporal_consistency_corr(
     # get the correlation between the current frame and all other frames
     corr = corr2_coeff(current_frame_data, unwrapped_echo_1[brain_mask, :]).ravel()
 
-    # threhold the RD
+    # threshold the RD
     tmask = corr > threshold
 
     # get indices of mask
@@ -653,7 +653,7 @@ def compute_offset(
     # compute closest multiple of 2pi to the difference
     int_map = np.round(y_diff / (2 * np.pi)).astype(int)
 
-    # compute the most often occuring multiple
+    # compute the most often occurring multiple
     best_offset = mode(int_map, axis=0, keepdims=False).mode
     best_offset = cast(int, best_offset)
 

warpkit/utilities.py

@@ -286,7 +286,7 @@ def field_maps_to_displacement_maps(
     Returns
     -------
     nib.Nifti1Image
-        Displacment maps in mm
+        Displacement maps in mm
     """
     voxel_size = _signed_pe_voxel_size(field_maps, phase_encoding_direction)