Add codespell support with configuration and fixes by yarikoptic · Pull Request #13 · ucscGenomeBrowser/cellBrowser

yarikoptic · 2026-06-04T18:36:07Z

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").

The GitHub Actions CI workflow has permissions set only to read, so it is safe.

Changes

Configuration & Infrastructure

Added .codespellrc with skip patterns for vendored JavaScript libraries
(*/ext/*, */node_modules/*), gene-annotation reference data
(*/cellbrowserData/*, */cbWeb/genes/*), sample data (*/sampleData/*),
generated artifacts (versioneer.py, */_version.py, */build/*,
docs/_build/*, docs/build/*), the vendored EZID CLI from CDL
(*/ucsc/ezid.py), local .git-meta/ worktrees, and binary/data
filetypes (PDF/SVG/PNG/JPG/CSS/min.*, TSV/CSV/JSON/JSON.gz, fonts, h5ad,
rds, .tags, .sizes).
Created .github/workflows/codespell.yml to check spelling on push and PRs
to develop. Uses codespell-project/actions-codespell@v2 pinned by SHA.
permissions: contents: read only.

Domain-Specific Whitelist

ore — JavaScript regex variable name (ore = /^0/) in the natural-sort
code in cellBrowser.js. Documented inline in .codespellrc.

Typo Fixes

Ambiguous typos fixed manually (5 fixes with context review):

interative → interactive (README.rst:43)
fo → of (docs/howto.rst:23 — "RDS file fo your dataset")
installion → installation (docs/scanpy.rst:14)
recusively → recursively (cellbrowser.py:6798, in a commented-out block)
strin → string (cbData.js:236, in a comment)

False positives protected with inline codespell:ignore pragmas:

nd (the "not determined" abbreviation in two emptyVals /
likeEmptyString lists) — cellbrowser.py:1143, cellBrowser.js:6380

Non-ambiguous typos fixed automatically via codespell -w (committed via
datalad run for reproducibility) — 50+ fixes across docs, Python, JS,
config files, and the ucsc/ scripts. Notable patterns:

coordiante(s) / coordinats → coordinate(s) (×6)
substract → subtract (×4)
indicies → indices (×4, including variable renames in
ucsc/makeDatasetList)
relase → release (×4)
configue → configure (×2)
re-use → reuse (×2)
Various one-offs: utilties, folllowing, colum, chnages, Couldnt,
Jupyther, instread, likly, implicitely, gziped, expresssion,
hideen, reponse, identifer(s), readble, endianess,
compresssion, somtimes, overriden, specfied, necesssary,
pre-selected, pallette, everthing, Attribue, antialising,
Initialiaze, numer, acccession, adapated, annoucements,
delimeter, alos, technicaly.

Historical Context

This project has had 41 prior commits mentioning typo / spelling /
spell fixes — many of them small, one-line follow-ups (git log --oneline --all --grep=typo --grep=spell --grep=spelling). Automating
this in CI catches them at PR time instead.

Testing

uvx codespell passes with zero errors after all fixes.
Python source files (cellbrowser.py, convert.py, genes.py,
hubmaker.py) still parse with ast.parse.
JS files still parse with node -c.
Function names and JS XHR/DOM properties were not touched; only their
surrounding comments and user-facing string literals.

🤖 Generated with Claude Code and love to typos free code

Co-Authored-By: Claude Code 2.1.162 / Claude Opus 4.7 <[email protected]>

Manually fix typos requiring context review (single suggestion was ambiguous to codespell): - interative -> interactive (README.rst:43) - fo -> of (docs/howto.rst:23) - installion -> installation (docs/scanpy.rst:14) - recusively -> recursively (cellbrowser.py:6798, in a comment) - strin -> string (cbData.js:236, in a comment) Protect false positives via inline `codespell:ignore` pragmas: - "nd" string literal in emptyVals lists (cellbrowser.py:1143, cellBrowser.js:6380) — this is an empty-value abbreviation ("not determined"), not the start of "and" / "2nd". Add JavaScript regex variable name `ore` (/^0/ in the natural-sort code in cellBrowser.js) to ignore-words-list with an explanatory comment. Skip ucsc/ezid.py from codespell entirely — it is the vendored EZID CLI client from CDL (California Digital Library) and contains intentional CLI-usage notation like `c[reate][!]` that codespell misreads as a "reate" typo. Co-Authored-By: Claude Code 2.1.162 / Claude Opus 4.7 <[email protected]>

Fixed typos: - re-use -> reuse (docs/bulk.rst, cellBrowser.js) - utilties -> utilities (docs/combine.rst) - folllowing -> following (docs/dataDesc.rst) - configue -> configure (docs/howto.rst, 2x) - coordinats -> coordinates (docs/howto.rst) - relase -> release (docs/howto.rst x2, genes.py x2) - colum -> column (cellbrowser.py) - chnages -> changes (cellbrowser.py) - Couldnt -> Couldn't (cellbrowser.py) - Jupyther -> Jupyter (cellbrowser.py) - instread -> instead (cellbrowser.py) - likly -> likely (cellbrowser.py) - implicitely -> implicitly (cellbrowser.py) - gziped -> gzipped (convert.py) - expresssion -> expression (hubmaker.py) - hideen -> hidden (hubmaker.py) - reponse -> response (cbData.js) - identifers -> identifiers (cbData.js, hub.conf) - substract -> subtract (cbData.js x4) - readble -> readable (cbData.js) - endianess -> endianness (cbData.js) - compresssion -> compression (cbData.js) - somtimes -> sometimes (cbData.js) - overriden -> overridden (cellBrowser.js) - specfied -> specified (cellBrowser.js) - necesssary -> necessary (cellBrowser.js) - pre-selected -> preselected (cellBrowser.js) - pallette -> palette (cellBrowser.js) - everthing -> everything (cellBrowser.js) - Attribue -> Attribute (maxPlot.js) - coordiante(s) -> coordinate(s) (maxPlot.js x5) - antialising -> antialiasing (maxPlot.js) - Initialiaze -> Initialize (maxPlot.js) - numer -> number (cellbrowser.conf) - acccession -> accession (desc.conf) - identifer -> identifier (hub.conf) - adapated -> adapted (ucsc/addTags x2) - annoucements -> announcements (ucsc/generateAnnouncement) - delimeter -> delimiter (ucsc/makeCbHub) - indicies -> indices (ucsc/makeDatasetList x4) - alos -> also (ucsc/tabulate_facets.pl) - technicaly -> technically (ucsc/tabulate_facets.pl) Co-Authored-By: Claude Code 2.1.162 / Claude Opus 4.7 <[email protected]> === Do not change lines below === { "chain": [], "cmd": "uvx codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^

gemini-code-assist

Code Review

This pull request introduces a .codespellrc configuration file and fixes numerous spelling mistakes and typos across the codebase, including documentation, configuration files, and source code in JavaScript, Python, and Perl. The review feedback suggests updating deprecated logging.warn calls to logging.warning in cellbrowser.py to adhere to modern Python standards.

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gemini-code-assist · 2026-06-04T18:37:40Z

    ##Check for cluster markers
    if (markerField not in adata.uns or clusterField is not None) and not skipMarkers:
-        logging.warn("Couldnt find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "
+        logging.warn("Couldn't find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "


The logging.warn method has been deprecated since Python 3.0 in favor of logging.warning. Since this line is already being modified, please update it to use logging.warning to adhere to modern Python standards and avoid future deprecation issues.

Suggested change

logging.warn("Couldn't find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "

logging.warning("Couldn't find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "

gemini-code-assist · 2026-06-04T18:37:40Z


    except ValueError:
-        logging.warn("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likly this happens when the field names in the h5ad and the meta file overlap")
+        logging.warn("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likely this happens when the field names in the h5ad and the meta file overlap")


The logging.warn method has been deprecated since Python 3.0 in favor of logging.warning. Since this line is already being modified, please update it to use logging.warning to adhere to modern Python standards and avoid future deprecation issues.

Suggested change

logging.warn("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likely this happens when the field names in the h5ad and the meta file overlap")

logging.warning("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likely this happens when the field names in the h5ad and the meta file overlap")

yarikoptic and others added 4 commits June 4, 2026 09:56

Add rudimentary codespell config

c906f21

Co-Authored-By: Claude Code 2.1.162 / Claude Opus 4.7 <[email protected]>

Add CI workflow to codespell develop on push and PRs

b0d0b97

Co-Authored-By: Claude Code 2.1.162 / Claude Opus 4.7 <[email protected]>

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Add codespell support with configuration and fixes#13

Add codespell support with configuration and fixes#13
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	logging.warn("Couldn't find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "
	logging.warning("Couldn't find list of cluster marker genes in the h5ad file in adata.uns with the key '%s'. "

	logging.warn("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likely this happens when the field names in the h5ad and the meta file overlap")
	logging.warning("Could not merge h5ad and meta data, skipping h5ad meta and using only provided meta. Most likely this happens when the field names in the h5ad and the meta file overlap")

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yarikoptic commented Jun 4, 2026

Changes

Configuration & Infrastructure

Domain-Specific Whitelist

Typo Fixes

Historical Context

Testing

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