Oceanography Jupyter Book

Preamble

• This is the main branch README markdown file for the geo-smart oceanography repository.
  • Built from the simple template (not the more expansive template)
• This repository (automatically) publishes to this Jupyter Book website.
• A Jupyter Book is an extension of the Jupyter notebook concept and the documentation on this is at JupyterBook.org.
• Here are related badges:
  
  

Build a working Jupyter Book: Get Started

I advocate for documenting process... so here is how I began with the Geo-Smart organization 'simple skeleton' repository and built out an Oceanography JupyterBook. The important idea is that in addition to a repo there is a website compiled from that repo.

• There are two templates hosted by Geo-Smart on GitHub: A simple one and a more comprehensive version
  • Links: See 'use cases' here.
• Simple template gives directions on building a new Jupyter Book: Template README.md file
  • Click "Use This Template"
    • Name a new repo; choose the Geo-Smart organization
    • Fork the main branch (default)
    • Breadcrumbs: This README.md
  • Edit book/_config.yml to reflect the topic, again oceanography
  • Settings > Pages > Source = GitHub Actions
    • Every commit triggers a recompile of the website
  • (4) Edit environment.yml to establish a working environment
    • Template includes environment.yml: essential libraries for the Jupyter Book
      • Do not clobber this file!
        • Test the build now (see below), verify the Book
        • Add other libraries as needed
        • Open question: Myst-nb? See below on image embed
    • My test build failed
      • Top left of the GitHub console tabs: Code, Issues, Pull requests, Actions, ..., Settings
      • Earlier: > Settings > Pages > Source > enable Github Actions: Done
      • Fixing the website compile fail: > Actions tab
        • GitHub may require workflow approval: Approve
        • Trigger a build (compile): Commit a change or start it manually
        • Build fail error message: environment.yml outdated versions
          • Example: python=3.10
          • Solution: Edit environment.yml to remove =xx.yy versions
          • Example python=3.10 > python, and so for jupyter-book
          • Commit environment.yml: Book build ok
    • The section below expands environment.yml modifications
      • Read about Python environments
      • clone the repo locally
        • Sketch of setting up a local working Python environment:
          • Blank slate workstation: install miniconda
            • miniconda is lightweight and includes the conda package manager
          • **git clone https://github.com/geo-smart/newbookreponame
          • Create an environment and activate it
          • In case we forget: We include the activate command as a .bashrc echo
            • Activate this environment on each work session
            • Install libraries, develop content
              • This will introduce errors in the JupyterBook
              • ...because the environment is built from environment.yml which...
              • ...has not been updated yet. Continued below...
            • environment.yml is a derived record of installed libraries
              • From a working (activated) environment: conda env export > environment.yml
                • pip freeze is an analogous approach
              • Plan: Do not wholesale copy-paste env.yml into the GitHub repo.
              • Rather: Take a more minimalist approach; again see below

Building the JupyterBook: Content development

So far

• The Book builds / compiles with every commit
• _config.yml has been modified
• The subfolder /books/chapters is where notebooks go
• The subfolder /books/img is where static visual content (png files) reside

Questions, procedures, issues

• Each .ipynb notebook maps to a book chapter: ~/book/chapters/newchapter.ipynb.
  • Create a new chapter entry in /book/_toc.yml
    • This will look like - file: chapters/newchapter
    • Corresponding to chapters/newchapter.ipynb
• How does the Book environment develop along with increasing content?
  • First example error: No module named 'matplotlib'
    • Notice the JupyterBook builds despite errors of this sort
    • Added a matplotlib entry and an xarray entry to environment.yml fixed this error
• How much Python functionality is present in the Book?
• LaTeX?
• How much data can be bundled with the Book?

Inline images

Per the JupyterBook documentation: HTML is not recommended so I will revert to markdown inlining of images. This does not seem to work for jpegs so convert jpg to png using Python:

from PIL import Image
Image.open('revelle.jpg').save('revelle.png')

Issue The corresponding basic markdown ![text](path_to_image.png) works. A more sophisticated version seems to require Myst-nb (?) and does not seem to work natively.

To organize static content: ~/book/img/ += subfolders /rca/images/<category> and /rca/animations/<category>.