feat: AI Agents & Foundation Models hub page (/ai-agents-foundation-models/)#39
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…ell content Add AIAgentsFoundationModels.md as the canonical thematic hub for the AI-agents / foundation-models area. It owns the Virtual Cell Initiative & Single-Cell Foundation Models section (lifted out of OtherResources.md) and cross-links the rest of the theme — the AI Agents & Foundation Models group in Software.md, the LLMs/AI Agents row and AI Tooling + AI Evaluation columns in Papers.md, the benchmark datasets in Datasets/Benchmarks.md, and the relevant Talks and Primer. OtherResources.md drops the moved section and gains a single intro cross-link. The two inbound links to the moved anchor (Primers/AI.md, Software.md State entry) are repointed at the hub. Software and Benchmarks catalogs are otherwise untouched — they remain the type-correct canonical homes and are linked, not moved.
Wire the canonical AIAgentsFoundationModels.md into the site: a route id and top-group page entry in caail-pages.ts, the file added to the prose loader's canonical sources, and a sidebar item. The fix that makes the page render correctly is the caailProseRemark guard now including the new file, so its internal .md links are rewritten and its leading H1 is stripped. Adds coverage: caail-pages.test.ts gains the new route-id mapping and a bumped page count (26 to 27); resources-toc.spec.ts asserts the hub renders the moved Virtual Cell section with rewritten links, that /other-resources/ no longer shows it, and that the page is a11y-clean.
AssayBench is a Papers.md entry surfaced in ResearchAreas/AIEvaluation.md, not a dataset in Datasets/Benchmarks.md. Drop it from the Benchmarks list (ProteinGym, LAB-Bench, BixBench remain) and attribute it to the AI Evaluation page instead.
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What
Adds a dedicated AI Agents & Foundation Models hub at
/ai-agents-foundation-models/— a thematic landing page that connects the fastest-moving corner of the library, which is currently split across several type-first canonical files.Why
CAAIL organizes canonical content by resource type (tools →
Software.md, datasets →Datasets/, initiatives →OtherResources.md, research →Papers.md). The AI-agents / foundation-models theme is therefore deliberately spread out and only discoverable by hopping between pages. Rather than fight that organization, this adds a hub (same genre asPrimers/) that aggregates the theme while leaving each resource in its type-correct home.What moved vs. what stayed
## Virtual Cell Initiative & Single-Cell Foundation Modelssection is lifted out ofOtherResources.mdinto the newAIAgentsFoundationModels.md, which now owns it (the natural "initiatives & ecosystem" content for the hub). The two inbound links to its old anchor (Primers/AI.md, theSoftware.mdState entry) are repointed.## AI Agents & Foundation Modelsgroup inSoftware.mdand theDatasets/Benchmarks.mdevaluation datasets remain the type-correct canonical homes. Benchmarks is intentionally not folded in — it's broader than this theme (GPQA, MMLU-Pro, SWE-bench, MassSpecGym, ProteinGym are general/domain benchmarks).Site wiring
New route via the canonical-prose loader: route id + top-group entry in
caail-pages.ts, the file added to the loader'sCANONICAL_SOURCES.files, a sidebar item, and thecaailProseRemarkguard updated to include the new file (so its internal.mdlinks are rewritten and its leading# H1is stripped). No Papers matrix,counts.json, ormetrics.jsonchanges — moving anOtherResourcessection shifts no homepage tally.Verification
pnpm --dir site build→ exit 0, 39 pages (incl./ai-agents-foundation-models/), no loader "missing from disk" warning.pnpm --dir site test→ 296 unit tests pass (page count updated 26 → 27, new id mapping covered).pnpm --dir site test:e2e→ 11 Playwright + axe tests pass, including 3 new ones: the hub renders the moved Virtual Cell section with rewritten links,/other-resources/no longer shows it, and the page is a11y-clean.<h1>and no raw.mdlink leaks.Note for reviewers (pre-existing, not fixed here)
Taxonomy.mdis in the loader'sCANONICAL_SOURCES.files/CAAIL_PAGESbut is absent from the samecaailProseRemarkguard — the exact gap this PR fixes for the new file. That suggests/taxonomy/currently renders a duplicate H1 and un-rewritten.mdlinks. Left out of scope; worth a follow-up.