Supporting documentation for the family catalog.
The catalog reads authored *-review.yaml and *-review.md files under
interpro/<database>/<entry>/. It merges structured and prose reviews for the
same entry. Metadata and research reports alone do not create catalog rows.
PANTHER functional coherence and Pfam-associated InterPro mapping viability are
separate assessments and are displayed separately.
Rendering
The source page selects the catalog through template: family_index in its YAML
frontmatter. The filename is arbitrary; sources must be under projects/, or the
renderer must receive an explicit projects_dir. Unknown template names fail with
an error.
uv run ai-gene-review render-projects projects/FAMILIES.md -o pages/projects
PR previews
Published source links default to the repository's main branch. To preview files
that exist only on a PR branch, pass --source-ref while rendering to a
separate output directory:
uv run ai-gene-review render-projects projects/FAMILIES.md --source-ref cmungall/gr-pages -o /tmp/family-preview
The revision can be a branch or commit. It affects GitHub source links; links to
other rendered site pages still require the corresponding site tree. Keep the
default main links in committed production pages.
The CLI also accepts AI_GENE_REVIEW_SOURCE_REF as a fallback; an explicit
--source-ref takes precedence. Python render functions accept source_ref
directly and do not read the environment. The selected revision applies to
catalog links, related source links, and the footer.