Notebooks written entirely in Markdown¶

It is possible to store Jupyter notebooks in plain Markdown. This allows you to define a notebook structure entirely using MyST Markdown. For more information about MyST Markdown, see MyST Markdown overview.

Notebooks with Markdown can be read in, executed, and cached by Jupyter Book (see Execute and cache your pages for information on how to cache pages). This allows you to store all of your notebook content in a text format that is much nicer for version control software, while still having all the functionality of a Jupyter notebook.

:::{note} MyST notebooks uses [MyST-NB to convert between ipynb and text files][myst-nb:index]. See its documentation for more information. :::

To see an example of a MyST notebook, you can look at many of the pages of this documentation. For example, see ../interactive/hiding.md and ../content/layout.md.

Create a MyST notebook with Jupytext¶

The easiest way to create a MyST notebook is to use Jupytext, a tool that allows for two-way conversion between .ipynb and a variety of text files.

You can convert an .ipynb file to a MyST notebook with the following command:

jupytext mynotebook.ipynb --to myst

A resulting mynotebook.md file will be created. This can then be used as a page in your book.

:::{important} For full compatibility with myst-parser, it is necessary to use jupytext>=1.6.0. :::

Jupytext can also automatically synchronize an .ipynb file with your Markdown. To do so, use a Jupyter interface such as Jupyter Lab or the classic notebook interface and follow the Jupytext instructions for paired notebooks.

Convert a Markdown file into Jupytext MyST Markdown¶

Jupyter Book has a small CLI to provide common functionality for manipulating and creating MyST Markdown files that synchronize with Jupytext. To add Jupytext syntax to a Markdown file (that will tell Jupytext it is a MyST Markdown file), run the following command:

jupyter-book myst init mymarkdownfile.md --kernel kernelname

If you do not specify --kernel, then the default kernel will be used if there is only one available. If there are multiple kernels available, you must specify one manually.

Structure of MyST notebooks¶

Let’s take a look at the structure that Jupytext creates, which you may also use to create a MyST notebook from scratch. First, let’s take a look at a simple MyST notebook:

---
jupytext:
  formats: md:myst
  text_representation:
    extension: .md
    format_name: myst
kernelspec:
  display_name: Python 3
  language: python
  name: python3
---

# My simple notebook

Some **intro Markdown**!

```{code-cell} ipython3
:tags: [mytag]

print("A python cell")
```

## A section

And some more Markdown...

There are three main sections to notice:

Frontmatter YAML¶

MyST notebooks need special frontmatter YAML to tell Jupytext that they can be converted to .ipynb files. The frontmatter YAML block

---
jupytext:
  formats: md:myst
  text_representation:
    extension: .md
    format_name: myst
kernelspec:
  display_name: Python 3
  language: python
  name: python3
---

tells Jupytext that the file is in myst format, and that its code should be run with a Python 3 kernel.

Code cells¶

Code blocks in MyST notebooks are defined with the following MyST directive:

```{code-cell}
your-code
```

You can optionally add extra metadata to the code cell, which will be converted into cell metadata in the .ipynb file. For example, you can add tags to your code cell like so:

```{code-cell}
:tags: [tag1, tag2, tag3]
your-code
```

You may also explicitly pass the kernel name after {code-cell} to make it clear which kernel you are running. For example:

```{code-cell} python3
your-code
```

However, remember that there is only one kernel allowed per page.

Markdown content¶

Everything in-between your code cells is parsed as Markdown content using the MyST Markdown parser. See MyST Markdown overview for more information about MyST Markdown.

To explicitly split up Markdown content into two Markdown cells, use the following pattern:

Content in one Markdown cell

+++

Content in another Markdown cell

You may also attach metadata to the cell by adding a Python dictionary after the +++. For example, to add tags to the second cell above:

Content in one Markdown cell

+++ {"tags": ["tag1", "tag2", "tag3"]}

Content in another Markdown cell

Warning

Please note that cell breaks and metadata specified in MyST files via the +++ syntax only propagate to their .ipynb counterpart. When generating the book’s HTML, Markdown cell information is discarded to avoid conflicting hierarchies in the structure of the document. In other words, only code cell tags have an effect on the generated HTML.

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