jupyterlab-myst 1.2.0

Use MyST in JupyterLab

JupyterLab MyST Extension

Render markdown cells using MyST Markdown, including support for rich frontmatter, interactive references, admonitions, figure numbering, tabs, cards, and grids!

Note: If you are looking for the version of this repository based on jupyterlab-markup, see the v0 branch.

Requirements

• JupyterLab >= 3.0

Install

To install the extension, execute:

pip install jupyterlab_myst

Features

jupyterlab-myst is a fully featured markdown renderer for technical documents, get started with MyST Markdown. It supports the MyST {eval} inline role, which facilitates the interweaving of code outputs and prose. For example, we can use inline expressions to explore the properties of a NumPy array.

In the code cell:

import numpy as np
array = np.arange(4)

In the markdown cell:

Let's consider the following array: {eval}`array`.

We can compute the total: {eval}`array.sum()` and the maximum value is {eval}`array.max()`.

This will evaluate inline, and show:

Let's consider the following array: array([0, 1, 2, 3]).

We can compute the total: 6 and the maximum value is 3.

You can also use this with ipywidgets, and have inline interactive text:

Or with matplotlib to show inline spark-lines:

You can also edit tasklists directly in the rendered markdown.

Usage

MyST is a flavour of Markdown, which combines the fluid experience of writing Markdown with the programmable extensibility of reStructuredText. This extension for JupyterLab makes it easier to develop rich, computational narratives, technical documentation, and open scientific communication.

Restore default renderer :notebook:

By default, the MyST renderer becomes the default notebook renderer. This means that MyST notebook rendering works out-of-the-box with Jupytext and other notebook-aware extensions. Whilst this extension is in a pre-release state, there is also a "legacy mode" that integrates MyST rendering as an additional Open With option that does not replace the default notebook renderer. To enable legacy mode, disable the jupyterlab-myst:plugin plugin with:

jupyter labextension disable jupyterlab-myst:plugin

Execution :rocket:

To facilitate inline expressions, jupyterlab-myst defines a jupyterlab-myst:executor plugin. This plugin sends expression code fragments to the active kernel when the user "executes" a Markdown cell. To disable this functionality, disable the jupyterlab-myst:executor plugin with:

jupyter labextension disable jupyterlab-myst:executor

Trust :detective:

Jupyter Notebooks implement a trust-based security model. With the addition of inline expressions, Markdown cells are now considered when determining whether a given notebook is "trusted". Any Markdown cell with inline-expression metadata (with display data) is considered "untrusted". Like outputs, expression results are rendered using safe renderers if the cell is not considered trusted. Executing the notebook will cause each cell to be considered trusted.

To facilitate this extension of the trust model, the jupyterlab_myst server extension replaces the NotebookNotary from nbformat with MySTNotebookNotary. This can be disabled with

jupyter server extension disable jupyterlab-myst

By disabling this extension, it will not be possible to render unsafe expression results from inline expressions; the MySTNotebookNotary adds additional code that makes it possible to mark Markdown cells as trusted.

Uninstall

To remove the extension, execute:

pip uninstall jupyterlab_myst

Contributing

Development install

Note: You will need NodeJS to build the extension package.

The jlpm command is JupyterLab's pinned version of yarn that is installed with JupyterLab. You may use yarn or npm in lieu of jlpm below.

# Make sure jupyterlab is up to date
conda update jupyterlab
# Clone the repo to your local environment
# Change directory to the cloned jupyterlab-myst directory
# Install package in development mode
pip install -e .
# Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
# Rebuild extension Typescript source after making changes
jlpm build

You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.

# Watch the source directory in one terminal, automatically rebuilding when needed
jlpm watch
# Run JupyterLab in another terminal
jupyter lab

With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).

By default, the jlpm build command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:

jupyter lab build --minimize=False

Development uninstall

pip uninstall jupyterlab_myst

In development mode, you will also need to remove the symlink created by jupyter labextension develop command. To find its location, you can run jupyter labextension list to figure out where the labextensions folder is located. Then you can remove the symlink named jupyterlab-myst within that folder.

Testing the extension

Frontend tests

This extension is using Jest for JavaScript code testing.

To execute them, execute:

jlpm
jlpm test

Integration tests

This extension uses Playwright for the integration tests (aka user level tests). More precisely, the JupyterLab helper Galata is used to handle testing the extension in JupyterLab.

More information are provided within the ui-tests README.

Packaging the extension

See RELEASE