Fix Jupyter Book build

.github/workflows/book.yml

@@ -5,29 +5,45 @@ on:
     branches:
       - main
 
-# This job installs dependencies, build the book, and pushes it to `gh-pages`
+env:
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Set GITHUB_TOKEN permissions to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# Do NOT cancel in-progress runs (allow these production deployments to complete).
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
 jobs:
-  deploy-book:
+  deploy:
+    environment:
+        name: github-pages
+        url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-
-      # Install dependencies
+      - uses: actions/checkout@v6
+      - name: Setup Pages
+        uses: actions/configure-pages@v6
       - name: Set up Python 3.14
         uses: actions/setup-python@v6
         with:
-          python-version: "3.14"
-
+            python-version: "3.14"
       - name: Install dependencies
         run: |
-          pip install jupyter-book
-
+            python -m pip install --upgrade pip
+            pip install jupyter-book
       - name: Build the book
         run: |
-          jupyter-book build notebooks
-
-      - name: GitHub Pages action
-        uses: peaceiris/actions-gh-pages@v4.0.0
+            cd notebooks
+            jupyter-book build --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v5
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: notebooks/_build/html
+            path: "notebooks/_build/html"
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5

.gitignore

@@ -164,3 +164,5 @@ jobs/
 # pixi environments
 .pixi/*
 !.pixi/config.toml
+
+notebooks/_build

notebooks/_static/custom.css

@@ -0,0 +1,9 @@
+/* Hide "Made with MyST" branding in navbar */
+.myst-home-link {
+	display: none !important;
+}
+
+/* Hide "Made with MyST" branding in sidebar (if present) */
+.myst-made-with-myst {
+	display: none !important;
+}

notebooks/myst.yml

@@ -0,0 +1,23 @@
+version: 1
+project:
+  title: Single-cell analysis repository
+  # To display author(s)
+  # authors:
+  #   - name: Author One
+  #     email: author1@email.com
+  #     affiliation:
+  #       - Institute A
+  #   - name: Author Two
+  #     email: author2@email.com
+  # To link to GitHub repo
+  # github: GitHubID/REPO_NAME
+  toc:
+    - file: index.md
+    - title: Template notebook
+      children:
+          - file: template.ipynb
+site:
+  options:
+    folders: true
+    style: _static/custom.css
+  template: book-theme

pyproject.toml

@@ -41,6 +41,8 @@ test = [
   "pytest",
   "pytest-cov",
 ]
+docs = [ "jupyter-book>=1" ]
+agentic = [ "jcodemunch-mcp" ]
 jupyter = [
   "ipywidgets",
   "jupyterlab",