Add codespell support with configuration and fixes

[yarikoptic]

Add codespell configuration, CI workflow, and fix a handful of typos in
authored prose/code.

More about codespell: https://github.com/codespell-project/codespell

I personally introduced it to over a hundred of projects already mostly
with a positive feedback (see
"improveit-dashboard"
for a write-up). The CI workflow has permissions: contents: read, so it
is safe.

Why scope matters here

This is an ontology project, so most files are either built artifacts or
contain biological/anatomical/genetic terminology inherited from upstream
sources — they are not prose authored in this repo and should not be
"corrected". codespell flagged ~75k matches when run without any skips,
the overwhelming majority of which are legitimate domain terms (Inh for
inhibitory neurons, cyclin, selectin, transferrin, nestin,
contactin, mater as in "pia mater" / "dura mater", anatomical
abbreviations like VILL, ONL, etc.).

So .codespellrc skips:

• bdso*.{owl,obo,json} — built release artifacts
• src/ontology/{mirror,imports,components,tmp} — mirrored / imported /
  generated ontologies
• src/{templates,markers,dendrograms,metadata} and
  src/test/test_data — data tables
• imports/, scratch/, *.ipynb, *.tsv, *.csv, *.obo, *.owl,
  *.json
• src/test/marker_tools_test.py — references Inh L1-2 VIP … cluster
  names verbatim

…and whitelists:

• inh — "Inhibitory" neuron abbreviation (used pervasively across
  cell-type ontologies, e.g. "Inh L5-6 PVALB GAPDHP60")
• ot — CLI flag --ot / args.ot ("obsolete taxonomies") in
  src/scripts/template_runner.py

This leaves codespell focused on authored prose and source code, where it
caught a small but real set of typos.

Changes

Configuration & CI

• .codespellrc with the skip / whitelist described above
• .github/workflows/codespell.yml running on push / PR against master
  (uses pinned codespell-project/actions-codespell@…v2.2, permissions
  set to read-only)
• .gitignore re-includes (!) .codespellrc and .github/workflows/
  so they are visible despite the project's **-gitignore-everything
  pattern (carried over from the existing setup commits on this branch)

Typo fixes

Ambiguous (manual, with context review):

• README.md:17 "groupings tht do not correspond …" — tht → that
  (codespell suggested the or that; context picks that)

Non-ambiguous (single suggestion, applied with uvx codespell -w):

• README.md:
  • tempaltes → templates (×3, including a URL path that now
    correctly points at the actual /src/templates/ directory instead
    of a non-existent /src/tempaltes/)
  • informtion → information
• src/sparql/README.md: perfoming → performing
• src/scripts/update_repo.sh: wont → won't
• src/ontology/Makefile: malicously → maliciously (×2),
  editted → edited — all in comments

Functional / link fix worth noting

The tempaltes → templates fix on README.md:88 repairs a broken
link: the markdown link text was [/src/tempaltes/] while the URL
targets /src/templates/. After this change, the rendered link text
matches the real on-disk directory.

Testing

uvx codespell passes with zero errors after these changes.

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🤖 Generated with Claude Code and love
to typos-free code