Project-driven simulations: persistent library, runs with provenance, notebook-first analysis

.github/workflows/deploy.yaml

@@ -12,24 +12,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-      - name: Install JupyterLite dependencies
-        run: |
-          python -m pip install -r jupyterlite/requirements.txt
-      - name: Build JupyterLite site
-        run: |
-          jupyter lite build --contents jupyterlite/content --output-dir public/jupyter
       - name: Use Node.js 20.x
         uses: actions/setup-node@v4
         with:
           node-version: "20.x"
-      - name: Patch JupyterLite service worker (COOP/COEP for the Notebook iframe)
-        run: node scripts/patch-jupyterlite-sw.mjs
+      # npm install must come before the JupyterLite build: `make jupyter`
+      # copies node_modules/lammps.js/dist into public/jupyter/lammps.
+      # (make jupyter also applies the COOP/COEP service-worker patch via
+      # scripts/jupyter_coi_patch.py, superseding main's standalone
+      # patch-jupyterlite-sw.mjs step.)
       - name: Install Packages
         run: npm install
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Build JupyterLite site
+        run: make jupyter
       - name: Run Typecheck
         run: npm run typecheck
       - name: Run Tests

.gitignore

@@ -2,11 +2,15 @@ node_modules
 cpp/lammps
 cpp/obj
 /dist
-# JupyterLite build output (built in CI, or locally via `jupyter lite build`)
+# JupyterLite build output (built in CI, or locally via `make jupyter`)
 /public/jupyter
 .jupyterlite.doit.db
+/.venv-jupyterlite
 .DS_Store
 cpp/lammps.mjs
 cpp/lammps.wasm
 cpp/lammps.worker.js
-build/
+build/
+/.cache/
+/playwright-report/
+/test-results/

.prettierignore

@@ -5,4 +5,15 @@ cpp
 jupyterlite
 public
 src/wasm
-.github/dependabot.yml
+.github/dependabot.yml
+# Build/tool output (CI runs `make jupyter` before prettier: the venv and
+# the built site must never be formatted — formatting the 500 MB venv hung
+# the CI prettier step for 35+ minutes)
+.venv-jupyterlite
+dist
+pypi
+test-results
+playwright-report
+.claude
+# Separate service with its own tooling (ruff); never formatted from here
+backend

Makefile

@@ -34,6 +34,25 @@ frontend-lint: ## Run frontend linter (prettier)
 frontend-lint-fix: ## Fix frontend linting issues
 	cd . && npx prettier --write .
 
+## JUPYTER
+
+JUPYTER_VENV := .venv-jupyterlite
+
+jupyter: ## Build the JupyterLite site into public/jupyter (piplite wheels, lammps.js client, COI patch)
+	test -d node_modules/lammps.js/dist || { echo "error: node_modules/lammps.js/dist is missing — run 'make frontend-install' (npm install) first" >&2; exit 1; }
+	test -x $(JUPYTER_VENV)/bin/pip || python3 -m venv $(JUPYTER_VENV)
+	$(JUPYTER_VENV)/bin/pip install --quiet -r jupyterlite/requirements.txt build
+	rm -rf public/jupyter .jupyterlite.doit.db
+	# Wheels in <repo>/pypi/ (lammps-js, lammps-logfile) are auto-indexed
+	# into the piplite index because the lite dir is the repo root.
+	$(JUPYTER_VENV)/bin/jupyter lite build --contents jupyterlite/content --output-dir public/jupyter
+	# Notebooks import the engine from {site}/lammps/client.js; ship the whole
+	# built package so its relative imports (worker, wasm modules) resolve.
+	mkdir -p public/jupyter/lammps
+	cp -R node_modules/lammps.js/dist/. public/jupyter/lammps/
+	# Cross-origin isolation on static hosting (ADR-002 §5).
+	$(JUPYTER_VENV)/bin/python scripts/jupyter_coi_patch.py public/jupyter
+
 ## BACKEND
 
 backend-install: ## Install backend dependencies