phenopacket-schema
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Add documentation link checking and fix broken links
Summary
This PR addresses issue #313 by implementing comprehensive link checking for documentation and fixing several broken links.
Changes Made
-
Added GitHub workflow for automated link checking using
sphinx-build -b linkcheck -
Fixed malformed VRS URL in variant.rst (removed duplicate
https://) - Fixed obsolete GitHub organization reference in version2.rst
- Updated sphinx configuration to use modern CSS API and set language to 'en'
- Configured linkcheck to run on push/PR to docs, weekly schedule, and manual dispatch
Link Check Results
The link checker identifies ~109 broken/redirected links across the documentation, including:
- Multiple broken HPO links (hpo.jax.org/app/browse/term/*)
- Broken protocol buffer documentation anchors
- SSL certificate issues with some external sites
- Various redirects that could be updated
Test Plan
- [x] Sphinx linkcheck runs successfully and identifies broken links
- [x] Fixed links now work correctly
- [x] GitHub workflow validates properly
- [x] Documentation builds without errors
The workflow will now automatically check for broken links on documentation changes and run weekly to catch external link breakage.
🤖 Generated with Claude Code