This repo hosts the Jupyter book of mine for the analysis of (community) metabolic models.

For Enterprise version: GitHub Pages now gives you the option to limit access, making the site visible only to users with access to the repository that published the Page. With access control, you can use GitHub Pages to publish and share internal documentation and knowledge across your enterprise. For the free plan, it seems you need to have your repo public.

Examples of Jbooks.

Building a Jupyter Book broadly consists of these steps:

• Create your book’s content. You structure your book with a collection of folders, files, and configuration. See Anatomy of a Jupyter Book. There are three things that you need in order to build a Jupyter Book, each of which was just created by running jupyter-book create:

  • A configuration file (_config.yml)

  Here’s an example of a simple _config.yml file:

  # In _config.yml
  title: My sample book
  author: The Jupyter Book Community
  logo: logo.png
  # Execute can be important: https://jupyterbook.org/en/stable/content/execute.html
  execute:
  execute_notebooks: force
  
  # Add a bibtex file so that we can create citations
  bibtex_bibfiles:
  - references.bib

  • A table of contents file (_toc.yml)

  Example:

  # In _toc.yml
  format: jb-book
  root: intro
  chapters:
  - file: markdown
  - file: notebooks
  - file: markdown-notebooks

  • Your book’s content

• Build your book. Using Jupyter Book’s command-line interface you can convert your pages into either an HTML or a PDF book. See Build your book. In our case, the mybookname will be the root of the repo, thus we run:

jupyter-book build .

• Publish your book online. Once your book is built, you can share it with others. Most common is to build HTML, and host it as a public website. See Publish your book online.

Never edit the gh-pages directly!

As mentioned in the requirements.txt file, we need to make sure jupyter-book is available locally. If not, to get it:

pip install -U jupyter-book

Then, for our book, we need the sphinx libraries:

pip install sphinx 
pip install sphinx-proof
pip install pydata-sphinx-theme

Also, the ghp-import library will be needed.

pip install ghp-import

Then, once your notebooks are ready to go, just execute the deplosy.sh script.

bash deploy.sh

To add a reference, you need to first add the .bit item to the references.bib file within the notebooks folder and to mention it in a notebook you need to follow the following syntax. Assuming your .bib item is

@article{dwork2014,
  title={The algorithmic foundations of differential privacy},
  author={Dwork, Cynthia and Roth, Aaron and others},
  journal={Foundations and Trends{\textregistered} in Theoretical Computer Science},
  volume={9},
  number={3--4},
  pages={211--407},
  year={2014},
  publisher={Now Publishers, Inc.}
}

You would need to have on your notebook:

{cite}`dwork2014`

You may have a markdown cell directly with a latex block like:

\begin{align}
N \times  v = 0 = N \times v^+  - N \times v^- = 
\left[ N \ {-N} \right] 
\begin{bmatrix}
    v^+  \\
    v^-
\end{bmatrix} \qquad
\end{align}

that will be numbered.

We use definitions, observations etc. from sphinx-proof.