Add codespell support with configuration and fixes#589
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- Skip external vocabulary data files (fuji_server/data/*.{yaml,json},
linked_vocabs/) — these are third-party identifier and ontology data.
- Skip test VCR cassettes and the PHP simpleclient (external content).
- Skip Jupyter notebooks (base64 images cause false positives).
- Add ignore-regex for URLs (DOIs/links can contain "typos" that must
not be fixed).
- Add ignore-words-list entries for domain terms:
- connexion — Python library name
- lod — Linked Open Data
- ore — Object Reuse and Exchange (OAI-ORE)
- Fix stale comment in pre-commit config (codespell config lives in
pyproject.toml, not .pre-commit-config.yaml) and add tomli fallback
dependency for Python <3.11.
Co-Authored-By: Claude Code 2.1.114 / Claude Opus 4.7 <noreply@anthropic.com>
Fixed typos where codespell offers multiple suggestions, selecting the correct fix based on surrounding context: - Selectin -> Selecting (metrics_configuration.md:38 heading) - shat -> that (docs/source/conf.py:324 comment) - stati -> statuses (metadata_harvester.py:111 comment) - doesnt -> doesn't (metadata_harvester.py:1268 comment) - "fo rthe" -> "for the" (body.py, openapi.yaml — misplaced space) - taked -> tagged (test_preprocessor.py:17 docstring — not in codespell's dictionary; actual word is "tagged", not "took/taken") - identifer -> identifiers (fuji_server/data/README.md:9 — refers to the identifiers.org service) Co-Authored-By: Claude Code 2.1.114 / Claude Opus 4.7 <noreply@anthropic.com>
=== Do not change lines below ===
{
"chain": [],
"cmd": "uvx codespell -w",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
yarikoptic
commented
Apr 20, 2026
| :type core_metadata_status: str | ||
| """ | ||
| allowed_values = ["insufficent metadata", "partial metadata", "all metadata"] | ||
| allowed_values = ["insufficient metadata", "partial metadata", "all metadata"] |
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Add codespell configuration and fix existing typos.
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 the improveit-dashboard note).
CI workflow has
permissionsset only toreadso also should be safe.Changes
Configuration & Infrastructure
[tool.codespell]configuration topyproject.toml..github/workflows/codespell.yml)to check spelling on push and PRs to
master.codespellhook to.pre-commit-config.yaml(with
tomlifallback for Python <3.11).third-party / auto-generated content:
fuji_server/data/*.yaml,fuji_server/data/*.json,fuji_server/data/linked_vocabs/— external identifier andontology data (identifiers.org, bioregistry, bioportal, etc.).
tests/*/cassettes/— VCR recordings.simpleclient/— auto-generated PHP client.*.ipynb— base64-encoded images cause false positives.https?://\S+) so DOIs and linksare never "fixed" (e.g.
doi.org/.../j.patter.2021.100370).Domain-Specific Whitelist (
ignore-words-list)connexion— Python library name (https://github.com/spec-first/connexion).lod— Linked Open Data.ore— Object Reuse and Exchange (OAI-ORE), used throughout fuji_server.Typo Fixes
Ambiguous typos fixed manually (7 fixes with context review,
fb5135f):
Selectin→Selecting(metrics_configuration.mdheading)shat→that(docs/source/conf.pycomment)stati→statuses(metadata_harvester.pycomment)doesnt→doesn't(metadata_harvester.pycomment)"fo rthe"→"for the"(misplaced space inbody.py,openapi.yaml)taked→tagged(tests/helper/test_preprocessor.py— not incodespell's dictionary; actual intended word is "tagged")
identifer→identifiers(fuji_server/data/README.md—refers to the identifiers.org service)
Non-ambiguous typos fixed automatically via
datalad run codespell -w(single-suggestion fixes,5f43837). Common fixes include:
explicitely→explicitly,ressources→resources,Sucessfully/sucessfully/Succesfully→Successfully/successfully,inaccesible→inaccessible,peristent→persistent,accesibility→accessibility,folows→follows,seperate→separate,souce→source,paramter→parameter,Returm→Return,metadat/matadata→metadata,variuos→various,namepace→namespace,exent→extent,opional→optional,reposiroty→repository,occured→occurred,insufficent→insufficient,publically→publicly,stanard→standard,identied→identified.Potential functional fix
fuji_server/models/core_metadata_output.py:79contained anallowed_valuesvalidator list that used"insufficent metadata"(typo),while the producing evaluator
(
fair_evaluator_minimal_metadata.py:219) already uses"insufficient metadata"(correct). This means the validator wouldhave raised
ValueErrorfor the normal code path. Fix propagates thecorrect spelling to the enum here and in
openapi.yaml.Historical Context
Master has ~21 prior commits mentioning typo / spelling fixes,
confirming the value of automated spell-checking going forward.
Testing
🤖 Generated with Claude Code and love to typos free code