CTIR / ressources

A curated, hand-picked hub of computational biomedical research resources for CTIR — Computational Trauma and Tissue Injury Research (GitHub org: CTTIR). Built with Quarto, deployed at https://cttir.github.io/ressources/.

What this is

• A single source of truth for "where do I find a good R package / dataset / paper for X" within the CTIR scope.
• Editorially reviewed, not auto-aggregated. Every entry was selected on purpose.
• Static site: no analytics, no cookies, no tracking.

Building locally

Prerequisites:

• Quarto 1.5.57 (pinned in .quarto-version)
• R 4.4+ with jsonlite, knitr, rmarkdown

quarto render
quarto preview

Refreshing the CTIR package inventory

The list on ressources/cttir-packages.qmd is generated from _data/cttir-repos.json, which is fetched from the live GitHub API. To refresh it (CI also enforces a 30-day freshness limit):

Rscript scripts/fetch-cttir-repos.R
git add _data/cttir-repos.json
git commit -m "refresh CTIR package inventory"

CI gates

Every PR runs:

1. render-check — quarto render must succeed; warnings fail the job.
2. todo-marker-check — fails if any TODO_IMPRESSUM or TODO_FILL_BEFORE_DEPLOY marker remains. This is intentional: the site cannot deploy with placeholder legal metadata or unverified citations.
3. link-check — every external link must resolve. Allowlist exceptions go in .lycheeignore with a comment explaining why.
4. doi-verify — every DOI in references.bib must resolve via https://doi.org/<doi>.
5. blocklist-check — commercial / paywalled URLs forbidden in ressources/*.qmd (see _data/blocklist.txt).
6. inventory-freshness — _data/cttir-repos.json must be ≤ 30 days old in git history.

Deployment

Pages serves from the gh-pages branch, populated by quarto-actions/publish@v2 on push to main. Configure once, in repo Settings → Pages → Source: Deploy from a branch → gh-pages → / (root).

Custom domain is unconfigured. To add one later: drop a CNAME file at the repo root containing the domain, configure DNS, and Pages will pick it up.

Repository layout

See PLAN.md for the directory tour, deferred-items list, and design decisions.

License

• Code (scripts, configuration, the build itself) — MIT.
• Editorial content (text in *.qmd files) — CC BY-SA 4.0.