Merge pull request #1 from TheJacksonLaboratory/add-pages

Added un-solved notebooks and actions to the github workflow

Author: fercer

.github/workflows/build_pages.yml

@@ -0,0 +1,75 @@
+name: deploy-book
+
+# Run this when the master or main branch changes
+on:
+  push:
+    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/**
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+    contents: read
+    pages: write
+    id-token: write
+
+# Allow one concurrent deployment, cancelling any in-progress deployments
+# This is useful if you are making a lot of changes to the book
+# and don't want to wait for the previous deployment to finish
+concurrency:
+    group: "pages"
+    cancel-in-progress: true
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+
+    # Install dependencies
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        pip install jupyter-book
+
+    # (optional) Cache your executed notebooks between runs
+    # if you have config:
+    # execute:
+    #   execute_notebooks: cache
+    # - name: cache executed notebooks
+    #   uses: actions/cache@v3
+    #   with:
+    #     path: _build/.jupyter_cache
+    #     key: jupyter-book-cache-${{ hashFiles('requirements.txt') }}
+
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build .
+
+    # Upload the book's HTML as an artifact
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: "_build/html"
+
+    # Deploy the book's HTML to GitHub Pages
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4

_config.yml

@@ -3,7 +3,7 @@
 
 title: Scaling-up deep learning inference to large-scale bioimage data
 author: Fernando Cervantes
-copyright: 2025
+copyright: The Jackson Laboratory 2025
 # logo: logo.png
 
 # Only build files in the table of contents.

_toc.yml

@@ -8,12 +8,18 @@ parts:
     chapters:
     - file: Outline.md
     - file: Installation.md
-  # - caption: Notebooks
-  #   chapters:
-  #   - file: notebooks/Zarr_and_Dask_for_large-scale_image_analysis-Lesson-1.ipynb
-  #     title: Lesson 1
-  #   - file: notebooks/Zarr_and_Dask_for_large-scale_imaging-Part-2.ipynb
-  #     title: Lesson 2
+
+  - caption: Notebooks
+    chapters:
+    - file: notebooks/Zarr_and_Dask_for_large-scale_image_analysis-Lesson-1.ipynb
+      title: Lesson 1
+    - file: notebooks/Zarr_and_Dask_for_large-scale_image_analysis-Lesson-2.ipynb
+      title: Lesson 2
+    - file: notebooks/Zarr_and_Dask_for_large-scale_image_analysis-Lesson-3.ipynb
+      title: Lesson 3
+    - file: notebooks/Zarr_and_Dask_for_large-scale_image_analysis-Lesson-4.ipynb
+      title: Lesson 4
+
   - caption: Solved notebooks
     chapters:
     - file: notebooks/Solved_Zarr_and_Dask_for_large-scale_image_analysis-Lesson-1.ipynb