🔧 Add codespell configuration and fix existing typos

[yarikoptic]

Add codespell spell-checking to warpkit.

Summary

• Wire codespell into CI (.github/workflows/codespell.yml) and pre-commit.
• Tune the config in [tool.codespell] (pyproject.toml) so the domain vocabulary (MR-physics terms, PyInstaller API, DICOM/BIDS metadata, vendored ROMEO port) does not produce false positives.
• Fix the 7 real typos that codespell surfaced (all in comments/docstrings — no user-facing strings, identifiers, or public API touched).

Result: codespell passes with zero errors on the tree.

Config choices

Skip patterns and ignore-words-list rationale

Skip — all ./-anchored so they match the paths codespell walks when invoked as codespell .:

• ./include/romeo/*, ./include/itk/* — vendored code (do not modify upstream)
• ./build/*, ./.venv/* — build / venv artifacts
• ./.git, ./.git-meta, ./.gitignore, ./.gitattributes — VCS metadata (.git-meta/ is a per-developer scratch dir for draft commit messages, which naturally contain typos-under-discussion)
• *.pdf, *.lock — binary / generated

ignore-words-list (documented in-file with rationale):

word	reason
te, tes	MR-physics abbreviations for echo time / echo times (see CLAUDE.md)
nd	DICOM ImageType flag ("Normalized Distortion-corrected") in BIDS fixtures
datas	PyInstaller Analysis() parameter name in packaging/pyinstaller/
framei	frame_i loop variable in tests/test_distortion.py
thirdparty	Refers to ITK's ThirdParty/Eigen3 module in a CMakeLists.txt comment

Typos fixed (comments/docstrings only)

file	before	after	note
include/utilities.h	sequnce	sequence	@brief comment
include/warps.h	displacment	displacement	// Pass displacement fields ... comment
warpkit/concurrency.py	thre	the	"pass the result of the future" — ambiguous per codespell, clear from context
warpkit/unwrap.py	verision	version	"dilated version of the mask" — ambiguous per codespell, clear from context
warpkit/unwrap.py	threhold	threshold	"threshold the RD" comment
warpkit/unwrap.py	occuring	occurring	"most often occurring multiple" comment
warpkit/utilities.py	Displacment	Displacement	docstring return-value description

All fixes reviewed line-by-line: none touch identifiers, API surface, string literals, or regex patterns.

Extended-dictionary pass (for future auditors)

codespell --builtin clear,rare,usage,code,names was run as a follow-up audit. All remaining hits are false positives (real domain terms) and are left untouched:

• sinc (include/warps.h) — the sinc interpolator
• arange (tests) — np.arange
• iff (tests) — mathematical "if and only if"
• ba (warpkit/utilities.py) — SciPy iirfilter(output="ba") convention
• master in tests/test_romeo.py and tests/data/test_data/*.json — legitimate references to ROMEO.jl's master branch and Siemens scanner sequence metadata, respectively

Not adding these to ignore-words-list since CI uses only the default clear,rare dictionaries where none are flagged.

Historical context

The project has had prior manual typo-fix commits (:memo: fix typo in import in README, :memo: fix README typo) — automated checking replaces the ad-hoc process.

Testing

• uvx codespell — passes with exit 0
• uvx pre-commit run --files <changed> — ruff-check, ruff-format, codespell all pass (pyright reports missing-import errors due to my local env not having the compiled extension + Python deps; unrelated to these changes, which only touch comments/docstrings)

CI safety

The workflow uses permissions: contents: read and pins codespell-project/actions-codespell to a full commit SHA (v2.2).

[Copilot]

Pull request overview

Adds automated spell-checking to the warpkit repository via codespell, and fixes a small set of existing typos (all in comments/docstrings), improving code hygiene without changing runtime behavior.

Changes:

• Add codespell configuration under [tool.codespell] in pyproject.toml.
• Wire codespell into both GitHub Actions (new workflow) and pre-commit.
• Fix several spelling mistakes in comments/docstrings across Python and C++ headers.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Adds [tool.codespell] config (skip patterns, ignore word list, check-hidden).
.github/workflows/codespell.yml	Introduces a CI job that runs codespell on pushes/PRs to main.
.pre-commit-config.yaml	Adds the codespell pre-commit hook (with tomli for Python < 3.11).
warpkit/concurrency.py	Fixes a comment typo.
warpkit/unwrap.py	Fixes several comment typos.
warpkit/utilities.py	Fixes a docstring typo in the return description.
include/warps.h	Fixes a comment typo.
include/utilities.h	Fixes a Doxygen @brief typo.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.25%. Comparing base (827a8ba) to head (8c27407).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #34   +/-   ##
=======================================
  Coverage   96.25%   96.25%           
=======================================
  Files          18       18           
  Lines        1280     1280           
=======================================
  Hits         1232     1232           
  Misses         48       48           

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[vanandrew]

Typo fixes all look right. I checked the config too — removing ignore-words-list does give back the 38 hits, and the pinned SHA matches v2.2.

One problem with the skip globs, comment inline.

[vanandrew]

lgtm