CLAUDE.md

Website for UCLID (University of Cincinnati Lab for Interfacial Dynamics, PI Kishan Bellur): https://kishanbellur.github.io. It’s a Jekyll site on the academicpages / Minimal Mistakes theme, plus two custom classroom apps (LecturePulse and SAM). Contributor how-tos (talks, publications, people, posts) are in README.md. Read it first and keep it in sync when workflows change.

Build & deploy

GitHub Pages builds master automatically on push. There is no CI and no test suite. Pushing to master publishes to the live site, so confirm before you push.
Local preview: bundle exec jekyll serve --config _config.yml,_config.dev.yml → http://localhost:4000. Restart after editing _config.yml.
Gemfile uses the github-pages gem, so GitHub builds in safe mode. Custom _plugins/ do not run on GitHub. _plugins/ruby_compat.rb exists only so local builds work on newer Ruby (it restores Object#tainted?).
Gemfile.lock is gitignored. If bundle install breaks, delete it and try again.
assets/js/main.min.js is the theme bundle (built with npm run build:js from the root package.json). The classroom-app JS files in assets/js/ are loaded directly and are not part of that bundle.

Content model

Collections (_config.yml): teaching, publications, research, talks, people. Standalone pages are in _pages/, and each sets its own permalink.
_talks/ and _publications/ are generated. Edit markdown_generator/talks.tsv / pubs.bib, then run python3 talks.py / python3 pubsFromBib.py from markdown_generator/. After changing talks, also run python3 talkmap.py from the repo root. Needs pandas, pybtex (and getorg + geopy for the talkmap).
People: _pages/people.md groups members with where: "position", "..." on these exact strings: Principal Investigator, PhD Student, MS Student, BS Student, PhD Alum, MS Alum, BS Alum. Any other position value leaves the person off the page. Within each group, people are sorted by the order front-matter field; anyone without order goes last.
Top nav: _data/navigation.yml.
Posts dated in the future don’t render (future: false). _posts/2199-01-01-future-post.md is a theme placeholder.

Classroom apps

Each app’s markup and page-specific CSS are inline in a _pages/*.md file, with logic in assets/js/. Firebase config is inline in the pages. All of them use Firebase project lecture-feedback-e758b.

App	Page (permalink)	JS	Backend
LecturePulse (student)	`_pages/student-check-in.md` (`/lecturepulse/`)	`student-check-in.js`	Firebase Realtime DB
LecturePulse (instructor)	`_pages/lecture-pulse.md` (`/lecturepulse-admin/`)	`lecture-pulse.js`	Firebase Realtime DB, client-side access code
SAM (student)	`_pages/sam.md` (`/sam/`)	`sam.js`	Cloudflare Worker, gated by class code
SAM (instructor)	`_pages/sam-admin.md` (`/sam-admin/`)	`sam-admin.js` (ES module)	Worker, gated by Firebase Google sign-in

The file names don’t match the permalinks, because the apps were renamed (student check-in → LecturePulse, Study Buddy → SAM). Links on _pages/teaching.html use the permalinks. lecture-pulse-test.html at the root is a standalone prototype.

SAM backend: study-buddy-worker/

Cloudflare Worker + D1 (study-buddy-db, one lectures table, see schema.sql), which calls the Gemini API. It’s excluded from the Jekyll build.
Routes (src/index.js): POST /api/ask (class code), POST /api/ingest, GET /api/lectures, and DELETE /api/lectures/:id. The last three are admin-only (src/auth.js verifies the Firebase ID token against the ADMIN_EMAIL secret).
src/relevance.js does keyword-overlap filtering of lectures. There are no embeddings.
wrangler.toml holds non-secret vars (GEMINI_MODEL, FIREBASE_PROJECT_ID, ALLOWED_ORIGIN). The secrets GEMINI_API_KEY, ADMIN_EMAIL, and CLASS_ACCESS_CODE are set with wrangler secret put. Never commit them.
Dev/deploy: npm install, npx wrangler dev, npx wrangler deploy (run from study-buddy-worker/). Deploying is a separate step from pushing the site.
The Worker URL is hardcoded as window.SAM_API_BASE in both sam.md and sam-admin.md.
CORS only allows https://kishanbellur.github.io, so SAM won’t work from a local Jekyll preview.
The directory, Worker, and D1 database keep the old “study-buddy” names so the deployed URL doesn’t change. Everything user-facing is called SAM. Full setup steps are in study-buddy-worker/README.md.

Conventions / gotchas

Most files come from the upstream theme (_layouts/, _includes/, _sass/, CHANGELOG.md, CONTRIBUTING.md, and demo pages like _pages/markdown.md and archive-layout-with-content.md). Avoid changing them unless the task requires it.
Contributors are lab students editing by hand. Keep changes simple and add a changelog line at the bottom of README.md for content updates.
.DS_Store is gitignored. Don’t add it back.