Add codespell support with configuration and typo fixes

[yarikoptic]

Add codespell configuration, CI check, and fix existing typos.

More about codespell: https://github.com/codespell-project/codespell — a spell-checker for source code that has been introduced to well over a hundred open-source projects with generally positive feedback.

The added CI workflow has permissions: contents: read, so it is a safe addition.

Here I did use claude code with my codespell'ing SKILL since otherwise it would be hard-to-impossible to weed out the typos. I did review the diff, it is quite big but really reviewable. It would be great if not postponed for long time since given the spread -- PR could rot quite quickly. I would be happy to address issues if any observed/reported to make UBERON typos freee

Details on the changes

Changes

Configuration & Infrastructure

• .codespellrc — comprehensive config that:

  • Skips generated release artifacts derived from src/ontology/uberon-edit.obo (top-level uberon.obo, uberon-base.owl, uberon-with-isa.obo, uberon-taxmod-*.obo, musculoskeletal.*, homology*, project.owl, reasoner_axioms.owl, rules.owl, ssso-merged-uberon.owl, depictions.owl, external-disjoints.owl).
  • Skips subsets/, src/ontology/imports/, src/ontology/taxmods/, src/ontology/diffs/, src/ontology/languages/ (all derived), plus source-ontologies/, resources/, ext-mappings/, mappings/, modules/, reports/, attic/, bulk_ntr_workflow/, experimental/ (external / auto-generated content), and docs/resources/ (binary graffle assets).
  • Skips src/scripts/ubermacros.el (~196k-line auto-generated Emacs macros indexing NCBITaxon species names — Latin binomials trip codespell).
  • Skips LICENSE (fixed legal wording).
  • Uses ignore-regex to protect URLs, camelCase/PascalCase identifiers, and cross-reference values after a PREFIX: (e.g. BAMS:MEnt) so external IDs are never "corrected".
  • Uses ignore-words-list (with per-word comments) for legitimate anatomical, Latin, medical, and abbreviation vocabulary that codespell flags as typos (e.g. mater, processus, vas, regio, collum, discus, cyclin, transferrin, formate, infarction, ans, als, sart, covert, panting, stye, preformed, pervious, horizontale, disjointness, etc.).

• .github/workflows/codespell.yml — GitHub Actions workflow using the official codespell-project/actions-codespell action, pinned by SHA, permissions: contents: read, triggered on push and PR to master.

Typo Fixes

Ambiguous typos fixed manually (each reviewed in context):

• component fo the ODK → to, considere to be → considered to be (docs & references)
• wall fo trunk → wall of trunk, foor → foot (×2), fot phalanx → foot, eigth toe → eighth, partion → portion, throught → through (×3), retricts → restricts, identiy → identity, tha → that (×3), referes → refers, extermal → external, inernal → internal, bein → vein (obsoletion comment), con- sists → consists (line-break artifact) — all in src/ontology/uberon-edit.obo.
• Formen → Foramen in def: line for ectepicondylar foramen (codespell's single suggestion here was Foremen, which is wrong for the anatomy domain).

Non-ambiguous typos auto-fixed with codespell -w via datalad run for reproducible provenance. About 200 fixes across src/ontology/uberon-edit.obo, docs, reference/, and scripts. Common patterns: mucuous → mucous, analagous → analogous, accomodate → accommodate, opthalmic → ophthalmic, prinicipal → principal, Hoever → However, seperate → separate, thier → their, protruberances → protuberances, etc.

False-positive reverts — reviewing the codespell -w diff surfaced 5 semantic false positives, all reverted in a follow-up commit and protected in the config so a future run cannot re-introduce them:

• crus horizontal striae diagonalis → crus horizontale (Latin adjective preserved).
• xref: BAMS:meant → xref: BAMS:MEnt (external cross-reference identifier).
• cemetery gland → cementary gland (documented RELATED synonym).
• duct remains previous → remains pervious (medical term: allowing passage).
• develop- meant → development (line-break artifact of development).

Historical Context

This repo has ~166 prior commits mentioning typo, spelling, or misspell — automated spell-checking will catch these before merge going forward.

Testing

✅ Codespell passes with zero errors on this branch (with the configured skip / ignore rules).

Notes for reviewers

• The datalad run commit records the exact uvx codespell -w invocation in git metadata for full provenance; the changes it introduced were then reviewed and 5 false positives were manually reverted in the next commit.
• src/ontology/uberon-edit.obo was reserialised with robot convert -i src/ontology/uberon-edit.obo -f obo -o src/ontology/uberon-edit.obo (robot 1.9.10) as the final commit, per the project's editor SOP. The reserialisation only reordered synonym: lines alphabetically within their parent Term stanzas (16 lines moved across 9 hunks); no text content changed and codespell still passes with zero errors afterwards.
• The .codespellrc is heavily commented so future contributors can decide per-entry whether to keep or remove each skip / ignore entry as the corpus evolves.

---

🤖 Generated with Claude Code (Opus 4.7, 1M context) in an interactive session with @yarikoptic.

PS I removed that @ai4c-agent in signature since I did not use whatever that is . Let me know if I need to return it

[cmungall]

Thanks @yarikoptic! Still shilling for codespell hope you get a commission for all this 😉😉😉 ❤️ ❤️ ❤️

I believe some of these fixes are for derived docs eg from ODK. I think it's better to exclude some of these. The most valuable fixed are in the ontology source file. I'm unsure of the implications of a direct merge eg if we open ourselves to spurious PR blocks eg if we update ODK....?

[yarikoptic]

Still shilling for codespell hope you get a commission for all this 😉😉😉 ❤️ ❤️ ❤️

;) thanks for the ❤️s -- appreciated. Besides taming my now existent typosalergy, my evil underlying purpose is to run 'litmus testing' of "open" projects regarding contributions ;) some times responses do surprise me!

also, with all the automation it is nearly as simple for me (or simpler since it right away creates a fork) to do it instead of plain git clone ;)

I believe some of these fixes are for derived docs eg from ODK. I think it's better to exclude some of these.

I would be happy to exclude whatever to be excluded. To not torture CI without need, I will wait for answers to your questions and any particular instructions on which ones to exclude since seems not having any particular 'auto-generated' marker in them like some others do

❯ git diff origin/master.. | lsdiff | grep generated
❯ git diff origin/master.. | lsdiff | sed -e 's,^[ab]/,,g' | xargs grep -i 'Auto-*generated'
.codespellrc:#   - src/scripts/ubermacros.el (auto-generated ~196k-line NCBITaxon index)

# overall:
❯ git grep -li 'Auto-*generated' | wc -l
85

for me to approach them systematically

[matentzn]

Thank you @yarikoptic - As always, much appreciated.

[matentzn]

not sure, could be

[yarikoptic]

@matentzn THANKS! I force pushed cleaned up changes.

[matentzn]

Thank you @yarikoptic! I hope you will also do uberon-edit.obo and ODK next :P These are the biggest impact!

[yarikoptic]

sure, next after this one is merged will be the uberon-edit.obo ;)

note: 3 failing CI checks due to me submitting from a fork -- I do not think there is anything for me to address there but may be some one would be interested to resubmit from a branch within for better/fuller review etc.

edit: or should I add more or restructure reference to the agentic assistance?