Merge pull request #1 from psobolewskiPhD/setup_jupyter_book

Setup jupyter book

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 -r 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

.gitignore

@@ -163,4 +163,10 @@ cython_debug/
 # Image files
 *.svs
 *.zarr
-*.bfmemo
+*.bfmemo
+
+# jupyter-book build output
+_build/
+
+# macOS file
+.DS_Store

_config.yml

@@ -0,0 +1,40 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Scaling-up deep learning inference to large-scale bioimage data
+author: Fernando Cervantes
+copyright: 2025
+# logo: logo.png
+
+# Only build files in the table of contents.
+only_build_toc_files: true
+
+
+# Don't execute the code cells in the book when building it
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: off
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+# bibtex_bibfiles:
+#  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/fercer/scaling-up-with-dask-tutorial/tree/main  # Online location of your book
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: false
+  use_repository_button: true
+
+parse:
+  myst_enable_extensions:
+    - html_image

_toc.yml

@@ -0,0 +1,8 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: README
+chapters:
+- file: notebooks/Zarr_and_Dask_for_large-scale_imaging-Part-1.ipynb
+- file: notebooks/Zarr_and_Dask_for_large-scale_imaging-Part-2.ipynb