[codex] Enable docs generation through pre-commit#8
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Expose nf-docs as a reusable pre-commit hook so downstream Nextflow pipeline repositories can regenerate documentation before commits. The manifest runs the existing CLI against the repository root and leaves command customization to hook args, which keeps the hook small and aligned with the package entry point. Constraint: pre-commit passes changed filenames by default, but nf-docs operates on a pipeline directory, so the hook disables filename passing. Rejected: Add a second hook wrapper command | unnecessary API surface when nf-docs generate already supports the needed arguments. Confidence: high Scope-risk: narrow Directive: Keep the hook manifest as a thin wrapper around nf-docs generate unless pre-commit users need behavior the CLI cannot express. Tested: pre-commit validate-manifest .pre-commit-hooks.yaml Tested: pre-commit validate-config .pre-commit-config.yaml Tested: pre-commit run --files README.md docs/running.md tests/test_pre_commit_hooks.py .pre-commit-hooks.yaml Tested: pytest Tested: ruff check src/ tests/ Tested: ruff format --check src/ tests/ Tested: ty check src/ Not-tested: End-to-end hook execution inside an external Nextflow pipeline repository
ewels
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May 20, 2026
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ewels
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Great idea!
Tested locally, works well. I updated the docs slightly to prefer Prek over pre-commit, but no other changes.
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Warning
Vibe coded slop before I go on holiday #noragrets
Summary
Adds a reusable
.pre-commit-hooks.yamlentry so downstream Nextflow pipeline repositories can use this repo directly as a pre-commit hook to regenerate nf-docs output.What changed
nf-docspre-commit hook manifest that runsnf-docs generate . --format htmland disables filename passing.ty check src/passes cleanly.Validation
pre-commit validate-manifest .pre-commit-hooks.yamlpre-commit validate-config .pre-commit-config.yamlpre-commit run --files README.md docs/running.md tests/test_pre_commit_hooks.py .pre-commit-hooks.yamlpytestruff check src/ tests/ruff format --check src/ tests/ty check src/Notes
The hook default assumes the consuming repository's pipeline lives at
.and writes HTML docs todocs/. Repositories with a different layout can overrideargsin their.pre-commit-config.yaml.