Pairing Jupyter notebooks and MyST-NB

What you’ll do

This guide will keep a Jupyter notebook synced or paired between .ipynb and .md.

What you’ll learn

  • The difference between Jupyter’s json format and MyST-NB’s markdown format

  • The benefits and drawbacks of json and markdown

  • How to keep .ipynb and .md files in sync

What you’ll need


Background

The NumPy tutorials are reviewed and executed as MyST-NB notebooks. Content is easier to review in this markdown format. You can keep your .ipynb in sync with the content on NumPy tutorials. The NumPy tutorials use Jupytext to convert your .ipynb file to MyST Markdown format.

Jupyter notebooks are stored on your disk in a json format. The json format is very powerful and allows you to store almost any input and output that Python libraries can create. The drawback is that it is hard to see and compare changes made in the notebook file when reviewing pull requests, because this means the reviewers are looking only at the raw json files.

MyST-NB notebooks are stored on your disk in a markdown format. The markdown format is a lightweight markup language. Its key design goal is readability. The drawback is that markdown can only store the inputs of your code. Each time you open the notebook, you must execute the inputs to see the output.

Note: You should use common mark markdown cells. Jupyter only renders common mark markdown, but MyST-NB supports a variety of restructured text directives. These Sphinx markdown directives will render when NumPy tutorials are built into a static website, but they will show up as raw code when you open in Jupyter locally or on Binder.

Consider these two versions of the same Simple notebook example. You have three things in the notebooks:

  1. A markdown cell that explains the code This code calculates 2+2 and prints the output.

  2. A code cell that shows the code

    x = 2 + 2
    print('x = ', x)
    
  3. The output of the code cell

    x = 4
    

Simple notebook example
This code calculates 2+2 and prints the output.

x = 2 + 2
print("x = ", x)
x =  4

Here are the two Simple notebook example raw inputs side-by-side:

json .ipynb MyST-NB .md
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This code calculates 2+2 and prints the output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "x =  4\n"
     ]
    }
   ],
   "source": [
    "x = 2 + 2\n",
    "print('x = ', x)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.8.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}
---
jupytext:
  formats: ipynb,md:myst
  text_representation:
    extension: .md
    format_name: myst
    format_version: 0.12
    jupytext_version: 1.6.0
kernelspec:
  display_name: Python 3
  language: python
  name: python3
---

This code calculates 2+2 and prints the output

```{code-cell} ipython3
x = 2 + 2
print('x = ', x)
```

The MyST-NB .md is much shorter, but it does not save the output 4.

Pair your notebook files .ipynb and .md

When you submit a Jupyter notebook to NumPy tutorials, we (the reviewers) will convert it to a MyST-NB format. You can also submit the MyST-NB .md in your pull request. To keep the .ipynb and .md in sync–or paired–you need Jupytext.

Install jupytext using:

pip install jupytext

or

conda install jupytext -c conda-forge

Once installed, start your jupyter lab or jupyter notebook session in the browser. When launching jupyter lab it will ask you to rebuild to include the Jupytext extension.

You can pair the two formats in the classic Jupyter, Jupyter Lab, or the command line:

1. Classic Jupyter Jupytext pairing

Animation showing pairing with Jupyter classic

2. JupyterLab Jupytext pairing

Animation showing pairing with JupyterLab

3. Command line Jupytext pairing

jupytext --set-formats ipynb,myst notebook.ipynb

Then, update either the MyST markdown or notebook file:

jupytext --sync notebook.ipynb

Note: With Jupytext installed, the classic Jupyter interface will automatically open MyST files as notebooks. In JupyterLab, you can right-click and choose “Open With -> Notebook” to open as a notebook. The outputs of your code cells are only saved in the .ipynb file.

Wrapping up

In this tutorial, you saw the json .ipynb and MyST-NB .md raw code to create Jupyter notebooks. You can use both formats to create tutorials. Now you can work in either a simple text editor like VIM or emacs or continue building notebooks in your browser. Jupytext can handle pairing to keep your work in sync.