Update configuration files for Jupyter Book v 2.x deployment and project settings

Author: aaronjnewman

.github/workflows/deploy.yml

@@ -0,0 +1,48 @@
+# This file was created automatically with `jupyter-book init --gh-pages` 🪄 💚
+# Ensure your GitHub Pages settings for this repository are set to deploy with **GitHub Actions**.
+
+name: Jupyter Book (via myst) GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main]
+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
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - 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 --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

_config.yml

@@ -1,33 +1,58 @@
 # Book settings
-title       : Neural Data Science in Python
-author      : Aaron J Newman
-copyright   : 2020-23. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported License
-logo        : images/NESC3505_icon.png
+title: Neural Data Science in Python
+author: Aaron J Newman
+copyright: "2020-23. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Unported License"
+logo: images/NESC3505_icon.png
 
-latex:
-  latex_documents:
-    targetname: book.tex
+# Force all builds to be HTML only
+exclude_patterns: [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"]
 
+# Parse and render settings
+parse:
+  myst_enable_extensions:
+    - colon_fence
+    - dollarmath
+    - linkify
+    - substitution
+    - tasklist
+  myst_url_schemes: [mailto, http, https]
+
+# Bibliography settings  
 bibtex_bibfiles:
-    - references.bib
+  - references.bib
 
+# Repository settings
 repository:
-  url                       : "https://github.com/neural-data-science/NESC_3505_textbook"
+  url: https://github.com/neural-data-science/NESC_3505_textbook
+  path_to_book: ""
+  branch: master
 
+# HTML settings
 html:
-  favicon                   : "images/NESC3505_favicon.png"  # A path to a favicon image
-  navbar_footer_text        : 'Powered by <a href="https://jupyterbook.org">Jupyter Book</a>'  # Will be displayed underneath the left navbar.
-  google_analytics_id       : G-1SNTM6T50K # A GA id that can be used to track book views.
-  home_page_in_navbar       : true  # Whether to include your home page in the left Navigation Bar
-  use_edit_page_button      : false  # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in
-  baseurl                   : "http://neuraldatascience.io"  # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/
-  use_repository_button     : true
-  use_issues_button         : true
+  favicon: images/NESC3505_favicon.png
+  use_edit_page_button: false
+  use_repository_button: true
+  use_issues_button: true
+  home_page_in_navbar: true
+  baseurl: http://neuraldatascience.io
+  google_analytics_id: G-1SNTM6T50K
+  extra_footer: |
+    <p>Powered by <a href="https://jupyterbook.org">Jupyter Book</a></p>
 
+# Execution settings
 execute:
   execute_notebooks: auto
   allow_errors: true
   timeout: -1
 
+# Only build files in the TOC
 only_build_toc_files: true
+
+# Sphinx settings
+sphinx:
+  config:
+    html_theme_options:
+      repository_url: https://github.com/neural-data-science/NESC_3505_textbook
+      use_repository_button: true
+      use_issues_button: true
 

myst.yml.backup

@@ -0,0 +1,26 @@
+version: 1
+project:
+  title: Neural Data Science in Python
+  description: An open educational resource for neural data science
+  authors:
+    - name: Aaron J Newman
+  keywords:
+    - neuroscience
+    - data science
+    - python
+  github: https://github.com/neural-data-science/NESC_3505_textbook
+  license:
+    content: CC-BY-NC-SA-4.0
+  bibliography:
+    - references.bib
+  
+site:
+  template: book-theme
+  title: Neural Data Science in Python
+  options:
+    logo: images/NESC3505_icon.png
+    favicon: images/NESC3505_favicon.png
+  nav: []
+  actions:
+    - title: GitHub
+      url: https://github.com/neural-data-science/NESC_3505_textbook