Update config files and deplyment scripts

This update makes sure that jupyterbook v1 is used to build
the webpage. The current files do not work well with jupyterbook v2.

Author: jdrugo

.github/workflows/publish-book.yml

@@ -5,27 +5,47 @@ on:
 
 #   workflow_dispatch:
   push:
-    branches:
-    - jupyterbook
+    branches: [main]
 #     # If your git repository has the Jupyter Book within some-subfolder next to
 #     # unrelated files, you can make this run only if a file within that specific
 #     # folder has been modified.
 #     #
 #     # paths:
 #     # - some-subfolder/**
 
+env:
+  # `BASE_URL` determines, relative to the root of the domain, the URL that your site is served from.
+  # E.g., if your site lives at `https://mydomain.org/myproject`, set `BASE_URL=/myproject`.
+  # If, instead, your site lives at the root of the domain, at `https://mydomain.org`, set `BASE_URL=''`.
+  BASE_URL: /${{ github.event.repository.name }}
+
+# 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, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: 'pages'
+  cancel-in-progress: false
+
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:
   deploy-book:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
-    # Install dependencies
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v1
+    # Install dependencies to process page files
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v6
       with:
-        python-version: 3.8
+        python-version: '3.13'
 
     - name: Install dependencies
       run: |
@@ -34,15 +54,35 @@ jobs:
     - name: Process files
       run: |
         python ci/process_files.py
-        
+
+    # setup pages, build book, and deploy
+    - name: Setup Pages
+      uses: actions/configure-pages@v3
+#    - uses: actions/setup-node@v4
+#      with:
+#        node-version: 18.x
+#    - name: Install Jupyter Book (via myst)
+#      run: npm install -g jupyter-book
+    - name: Build HTML Assets
+      run: jupyter-book build .
+
+#      run: jupyter-book build --html
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: './_build/html'
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4
+
     # Build the book
-    - name: Build the book
-      run: |
-        jupyter-book build .
+#    - name: Build the book
+#      run: |
+#        jupyter-book build .
 
     # Push the book's HTML to github-pages
-    - name: GitHub Pages action
-      uses: peaceiris/[email protected]
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./_build/html
+#    - name: GitHub Pages action
+#      uses: peaceiris/[email protected]
+#      with:
+#        github_token: ${{ secrets.GITHUB_TOKEN }}
+#        publish_dir: ./_build/html

_config.yml

@@ -7,7 +7,7 @@
 # Book settings
 title                       : Mathematical Tools for Neuroscientists # The title of the book. Will be placed in the left navbar.
 author                      : Ella Batty  # The author of the book
-copyright                   : "2022"  # Copyright year to be placed in the footer
+copyright                   : "2026"  # Copyright year to be placed in the footer
 #logo                        : images/NeuroImage.png  # A path to the book logo
 only_build_toc_files        : true
 
@@ -17,7 +17,7 @@ only_build_toc_files        : true
 execute:
   execute_notebooks         : force # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off")
   cache                     : ""    # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/`
-  exclude_patterns          : ""    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
+  exclude_patterns          : []    # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time)
   timeout                   : 500    # The maximum time (in seconds) each notebook cell is allowed to run.
   run_in_temp               : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),
                                     # otherwise the notebook's parent directory will be the cwd.

requirements.txt

@@ -1,5 +1,5 @@
 numpy
 scipy
 matplotlib
-jupyter-book
+jupyter-book<2.0
 ipywidgets