Add docs_pages lint test - #4475
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erikrikarddaniel wants to merge 3 commits into
Open
erikrikarddaniel wants to merge 3 commits into
erikrikarddaniel wants to merge 3 commits into
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The nf-core website generates a page for a markdown file in docs/ only if it is docs/usage.md or docs/output.md, or lives under docs/usage/ or docs/output/. A page placed anywhere else renders correctly on GitHub, where it is written and reviewed, and 404s on the website, with nothing to say so. Warns rather than fails, since a pipeline may keep a working document in docs/ on purpose; those can be listed under docs_pages in .nf-core.yml. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LydWahEnWZexTULEub5bfX
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LydWahEnWZexTULEub5bfX
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The suffix filter was untested in both directions, so it could have been wrong either way without a test noticing. Dropping the docs/ existence guard: glob on a missing directory already returns nothing, so the early return never did anything. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LydWahEnWZexTULEub5bfX
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PR checklist
CHANGELOG.mdis updateddocsis updatedDescription
Closes #4474.
The website renders a page in
docs/only forusage.md,output.md, or files underdocs/usage/anddocs/output/. A page anywhere else renders on GitHub, where docs get reviewed, and 404s on the website, with nothing warning the author. nf-core/metatdenovo shippeddocs/large_datasets.mdthat way and it was unreachable for its entire life (nf-core/metatdenovo#493).This adds a
docs_pageslint test that names the move that would fix it:A warning, not a failure: about twenty of the 144 active pipelines keep internal working documents in
docs/. Those are silenced per file in.nf-core.yml:docs/README.md,docs/CONTRIBUTING.mdanddocs/images/are skipped without configuration, and existingdocs/usage/anddocs/output/pages pass unchanged.The check keys on the rule as documented rather than the website's substring match on the path, so
docs/my_usage_notes.mdis flagged even though the site publishes it today by coincidence. Seven new tests, including that case.Companion PR: nf-core/website#4409 corrects the specification, which currently promises these pages are rendered. nf-core/website#4408 has the survey behind the numbers above.
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