Add codespell support with configuration and fixes#4
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Add ignore-words-list with domain-specific terms codespell flags as typos: - fpr: False Positive Rate variable from sklearn roc_curve output - abou: part of contributor name "Sacha Abou Rachid" in acknowledgements - sortings: SpikeInterface domain term (plural of "sorting" — a spike sort result; also used as variable name `both_sortings`) Also add comment above ignore-regex documenting that it skips base64-encoded images embedded in Jupyter notebooks. Co-Authored-By: Claude Code 2.1.142 / Claude Opus 4.7 <noreply@anthropic.com>
Codespell offered multiple suggestions for these typos; chose based on
surrounding text:
- "Accuray" -> "Accuracy" (not "Actuary") in printed training output
Locations: src/unitrefine/train.py:307, src/unitrefine/README.md:78
Context: "Balanced Accuray:" stat label in model training results.
- "labeld" -> "labeled" (not "labelled") in src/unitrefine/README.md:91
Context: "(labeld model_1_retrained_02, etc)" — surrounding doc uses
US English ("labeling", "labels"), so matched that spelling.
Co-Authored-By: Claude Code 2.1.142 / Claude Opus 4.7 <noreply@anthropic.com>
Applied codespell -w for typos with a single suggestion: - UnitRefine/models/sua_mua_classifier/train_manual_curation.py: calcualted -> calculated - UnitRefine/plots/SHAP_plots.ipynb: minuts -> minutes - UnitRefine/scripts/model_based_curation.py: parmeters -> parameters (x3), defualt -> default (x2) - UnitRefine/scripts/train_manual_curation.py: calcualted -> calculated - UnitRefine/tutorial/train_model/train_model_using_csv_metrics_files.ipynb: atleast -> at least - UnitRefine/tutorial/train_model/train_model_using_sorting_analyzer.ipynb: atleast -> at least - src/unitrefine/README.md: classifer -> classifier, efficency -> efficiency Co-Authored-By: Claude Code 2.1.142 / Claude Opus 4.7 <noreply@anthropic.com>
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Add codespell configuration, CI workflow, and fix existing typos.
More about codespell: https://github.com/codespell-project/codespell
I've introduced codespell to over a hundred projects already, mostly with positive feedback (see the
improveit-dashboardexample).The CI workflow has
permissionsset toreadonly, so it's safe.Changes
Configuration & infrastructure
[tool.codespell]section topyproject.tomlwith skip list, hidden-file scanning, and a regex to skip base64-encoded images embedded in Jupyter notebooks..github/workflows/codespell.ymlto run codespell on push and PRs targetingmain.Domain-specific whitelist
Added legitimate terms flagged by codespell to
ignore-words-list:fpr— False Positive Rate variable fromsklearn.metrics.roc_curve(e.g.fpr, tpr, thresholds = roc_curve(...))abou— part of contributor name "Sacha Abou Rachid" in the README acknowledgementssortings— SpikeInterface domain term (plural of "sorting" = a spike sort result; also used as the variableboth_sortings)Ambiguous typos fixed manually (context-aware)
Accuray→Accuracy(notActuary) insrc/unitrefine/train.py:307andsrc/unitrefine/README.md:78— printed"Balanced Accuray:"stat label in training output.labeld→labeled(notlabelled) insrc/unitrefine/README.md:91— surrounding doc uses US English ("labeling", "labels").Non-ambiguous typos fixed via
codespell -wcalcualted→calculated(×2:UnitRefine/models/sua_mua_classifier/train_manual_curation.py,UnitRefine/scripts/train_manual_curation.py)minuts→minutes(UnitRefine/plots/SHAP_plots.ipynb)parmeters→parameters(×3 inUnitRefine/scripts/model_based_curation.py)defualt→default(×2 inUnitRefine/scripts/model_based_curation.py— indefault:parameter documentation)atleast→at least(×2 inUnitRefine/tutorial/train_model/train_model_using_csv_metrics_files.ipynband..._using_sorting_analyzer.ipynb)classifer→classifier(src/unitrefine/README.md)efficency→efficiency(src/unitrefine/README.md)Historical context
The repository already has a
fixed typos in tutorialscommit (7db121f) — manual typo fixes have been needed before, so adding automated checking should help going forward.Testing
✅
codespellpasses with zero errors on a fresh checkout after these changes.🤖 Generated with Claude Code and love to typos free code