Add GitHub Pages deployment workflow

Author: Michael Vinyard

.github/workflows/docs.yml

@@ -0,0 +1,118 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  workflow_dispatch:  # Allow manual triggering
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment (but don't cancel PR builds)
+concurrency:
+  group: "pages-${{ github.event_name }}-${{ github.head_ref || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout scDiffEq
+        uses: actions/checkout@v4
+      
+      - name: Clone analysis notebooks
+        run: |
+          git clone --depth 1 https://github.com/scDiffEq/scdiffeq-analyses.git /tmp/scdiffeq-analyses
+          
+          # Create target directories
+          mkdir -p docs/source/_analyses
+          mkdir -p docs/source/_tutorials
+          
+          # Copy notebooks from manuscript figures
+          for dir in /tmp/scdiffeq-analyses/manuscript/figure_*/notebooks/; do
+            if [ -d "$dir" ]; then
+              cp -v "$dir"*.ipynb docs/source/_analyses/ 2>/dev/null || true
+            fi
+          done
+          
+          # Copy tutorial notebooks
+          cp -v /tmp/scdiffeq-analyses/tutorials/*.ipynb docs/source/_tutorials/ 2>/dev/null || true
+          
+          # List what we copied
+          echo "=== Copied analysis notebooks ==="
+          ls -la docs/source/_analyses/
+          echo "=== Copied tutorial notebooks ==="
+          ls -la docs/source/_tutorials/
+      
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+          cache: 'pip'
+      
+      - name: Free up disk space
+        run: |
+          # Remove unnecessary pre-installed software to free up space
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /usr/local/lib/android
+          sudo rm -rf /opt/ghc
+          sudo rm -rf /opt/hostedtoolcache/CodeQL
+          df -h
+      
+      - name: Install pandoc
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+      
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          # Install CPU-only PyTorch first (much smaller than CUDA version)
+          pip install torch --index-url https://download.pytorch.org/whl/cpu
+          # Install remaining dependencies
+          pip install -r docs/requirements.txt
+      
+      - name: Build documentation
+        env:
+          GITHUB_ACTIONS: true
+        run: |
+          cd docs
+          # Build docs; warnings are logged but don't fail the build
+          # (Many warnings are from type hints that don't resolve via intersphinx)
+          sphinx-build -b html source _build/html --keep-going
+      
+      # Upload preview artifact for PRs (downloadable zip)
+      - name: Upload PR preview artifact
+        if: github.event_name == 'pull_request'
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-preview-pr-${{ github.event.number }}
+          path: docs/_build/html
+          retention-days: 7
+      
+      # Upload for GitHub Pages deployment (main branch only)
+      - name: Upload Pages artifact
+        if: github.event_name != 'pull_request'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    if: github.event_name != 'pull_request'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      # NOTE: GitHub Pages must be enabled in repository settings:
+      # https://github.com/scDiffEq/scDiffEq/settings/pages
+      # Source should be set to "GitHub Actions"
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4