Commit changes to jupyter-book

_config.yml

@@ -1,33 +1,32 @@
 # Book settings
 # Learn more at https://jupyterbook.org/customize/config.html
 
-title: Collection of notes on {ml.nn-zero2hero}
-author: Kithmin Wickremasinghe
-logo: media/logo.png
-exclude_patterns: [.DS_Store, "**.ipynb_checkpoints", "**.pytest_cache", "tools"]
-
-# Launch on Google Colab button
-launch_buttons:
-  notebook_interface: "classic"
-  colab_url: "https://colab.research.google.com"
-
-# only build files that appear in toc
-only_build_toc_files: true
+title: My sample book
+author: The Jupyter Book Community
+logo: logo.png
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: off
+  execute_notebooks: force
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
 
-# Information about where it exists on the web
+# 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/kithminrw/ml-nn-zero2hero/  # Online location
-  branch: main  # Which branch of the repository should be used when creating links (optional)
-
+  url: https://github.com/executablebooks/jupyter-book  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: master  # 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: true
   use_repository_button: true
-  use_multitoc_numbering: false
-  google_analytics_id: G-DVQ7NZ8CYZ

_toc.yml

@@ -1,46 +1,9 @@
 # Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
 
 format: jb-book
-root: intro.md
+root: intro
 chapters:
-- file: notebooks/01/01.md
-  sections:
-  - file: notebooks/01/NB_1_1.ipynb
-
-- file: notebooks/02/02.md
-  sections:
-  - file: notebooks/02/NB_2_1.ipynb
-
-- file: notebooks/03/03.md
-  sections:
-  - file: notebooks/03/NB_3_1.ipynb
-
-- file: notebooks/04/04.md
-  sections:
-  - file: notebooks/04/NB_4_1.ipynb
-
-- file: notebooks/05/05.md
-  sections: 
-  - file: notebooks/05/NB_5_1.ipynb
-
-- file: notebooks/06/06.md
-  sections:
-  - file: notebooks/06/NB_6_1.ipynb
-
-- file: notebooks/07/07.md
-  sections:
-  - file: notebooks/07/NB_7_1.ipynb
-
-- file: notebooks/08/08.md
-  sections:
-  - file: notebooks/08/NB_8_1.ipynb
-
-- file: notebooks/09/09.md
-  sections:
-  - file: notebooks/09/NB_9_1.ipynb
-
-- file: notebooks/10/10.md
-  sections:
-  - file: notebooks/10/NB_10_1.ipynb
-
-- file: genindex.md 
+- file: markdown
+- file: notebooks
+- file: markdown-notebooks

intro.md

@@ -1,54 +1,11 @@
-# Hands-On Mathematical Optimization with Python
+# Welcome to your Jupyter Book
 
-Welcome to this repository of companion notebooks for the book *Hands-On Mathematical Optimization with Python*, which will be published by Cambridge University press in 2024. This book introduces the concepts and tools of mathematical optimization with examples from a range of disciplines. The goals of these companion notebooks are to:
+This is a small sample book to give you a feel for how book content is
+structured.
+It shows off a few of the major file types, as well as some sample content.
+It does not go in-depth into any particular topic - check out [the Jupyter Book documentation](https://jupyterbook.org) for more information.
 
-* Provide a foundation for hands-on learning of mathematical optimization,
-* Demonstrate the tools and concepts of optimization with practical examples,
-* Help readers to develop the practical skills needed to build models and solving problem using state-of-the-art modeling languages and solvers.
-
-## Getting started
-
-The notebooks in this repository make extensive use of [Pyomo](https://en.wikipedia.org/wiki/Pyomo) which is a complete and versatile mathematical optimization package for the Python ecosystem. Pyomo provides a means to build models for optimization using the concepts of decision variables, constraints, and objectives from mathematical optimization, then transform and generate solutions using open source or commercial solvers.
-
-All notebooks in this repository can be opened and run in Google Colab. A launch icon appearing at the top of a page (look for the rocket) indicates the notebook can be opened as an executable document. Selecting Colab will reopen the notebook in Google Colab. Cells inside the notebooks will perform any necessary installations of Pyomo and solvers needed to execute the code within the notebook.
-
-Start your journey with the [first chapter](/notebooks/01/01.00.md)!
-
-## Help us!
-
-We seek your feedback! If you encounter an issue or have suggestions on how to make these examples better, please open an issue using the link at the top of every page (look for the Github cat icon). 
-
-## About Us
-
-We are a group of researchers and educators who came together with a common purpose of developing materials for use in our classroom teaching. Hopefully, these materials will find use in other classrooms and, most importantly, by those seeking entry into the world of building optimization models for data-rich applications.
-
-* Krzysztof Postek, Boston Consulting Group (formerly TU Delft)
-* Alessandro Zocca, VU Amsterdam
-* Joaquim Gromicho, ORTEC and the University of Amsterdam
-* Jeffrey Kantor, University of Notre Dame
-
-## Citation
-
-If you wish to cite this work, please use
-
-```
-@book{PZGK2024book,
-  author = {Postek, Krzysztof and Zocca, Alessandro and Gromicho, Joaquim and Kantor, Jeffrey},
-  title = {{Hands-On Mathematical Optimization with Python}},
-  year = {2024},
-  publisher = {Cambridge University Press}
-}
-```
-
-and
+Check out the content pages bundled with this sample book to see more.
 
+```{tableofcontents}
 ```
-@online{PZGK2024online,
-  author = {Postek, Krzysztof and Zocca, Alessandro and Gromicho, Joaquim and Kantor, Jeffrey},
-  title = {Companion Jupyter Book for {``Hands-On Mathematical Optimization with Python’’}},
-  year = {2024},
-  publisher = {GitHub},
-  howpublished = {\url{https://github.com/mobook/MO-book}},
-  note = {Textbook to be published by Cambridge University Press},
-}
-```

markdown-notebooks.md

@@ -0,0 +1,53 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.11.5
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+---
+
+# Notebooks with MyST Markdown
+
+Jupyter Book also lets you write text-based notebooks using MyST Markdown.
+See [the Notebooks with MyST Markdown documentation](https://jupyterbook.org/file-types/myst-notebooks.html) for more detailed instructions.
+This page shows off a notebook written in MyST Markdown.
+
+## An example cell
+
+With MyST Markdown, you can define code cells with a directive like so:
+
+```{code-cell}
+print(2 + 2)
+```
+
+When your book is built, the contents of any `{code-cell}` blocks will be
+executed with your default Jupyter kernel, and their outputs will be displayed
+in-line with the rest of your content.
+
+```{seealso}
+Jupyter Book uses [Jupytext](https://jupytext.readthedocs.io/en/latest/) to convert text-based files to notebooks, and can support [many other text-based notebook files](https://jupyterbook.org/file-types/jupytext.html).
+```
+
+## Create a notebook with MyST Markdown
+
+MyST Markdown notebooks are defined by two things:
+
+1. YAML metadata that is needed to understand if / how it should convert text files to notebooks (including information about the kernel needed).
+   See the YAML at the top of this page for example.
+2. The presence of `{code-cell}` directives, which will be executed with your book.
+
+That's all that is needed to get started!
+
+## Quickly add YAML metadata for MyST Notebooks
+
+If you have a markdown file and you'd like to quickly add YAML metadata to it, so that Jupyter Book will treat it as a MyST Markdown Notebook, run the following command:
+
+```
+jupyter-book myst init path/to/markdownfile.md
+```

markdown.md

@@ -0,0 +1,55 @@
+# Markdown Files
+
+Whether you write your book's content in Jupyter Notebooks (`.ipynb`) or
+in regular markdown files (`.md`), you'll write in the same flavor of markdown
+called **MyST Markdown**.
+This is a simple file to help you get started and show off some syntax.
+
+## What is MyST?
+
+MyST stands for "Markedly Structured Text". It
+is a slight variation on a flavor of markdown called "CommonMark" markdown,
+with small syntax extensions to allow you to write **roles** and **directives**
+in the Sphinx ecosystem.
+
+For more about MyST, see [the MyST Markdown Overview](https://jupyterbook.org/content/myst.html).
+
+## Sample Roles and Directives
+
+Roles and directives are two of the most powerful tools in Jupyter Book. They
+are like functions, but written in a markup language. They both
+serve a similar purpose, but **roles are written in one line**, whereas
+**directives span many lines**. They both accept different kinds of inputs,
+and what they do with those inputs depends on the specific role or directive
+that is being called.
+
+Here is a "note" directive:
+
+```{note}
+Here is a note
+```
+
+It will be rendered in a special box when you build your book.
+
+Here is an inline directive to refer to a document: {doc}`markdown-notebooks`.
+
+
+## Citations
+
+You can also cite references that are stored in a `bibtex` file. For example,
+the following syntax: `` {cite}`holdgraf_evidence_2014` `` will render like
+this: {cite}`holdgraf_evidence_2014`.
+
+Moreover, you can insert a bibliography into your page with this syntax:
+The `{bibliography}` directive must be used for all the `{cite}` roles to
+render properly.
+For example, if the references for your book are stored in `references.bib`,
+then the bibliography is inserted with:
+
+```{bibliography}
+```
+
+## Learn more
+
+This is just a simple starter to get you started.
+You can learn a lot more at [jupyterbook.org](https://jupyterbook.org).