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MyST in JupyterLab","maintainers":[{"name":"rowanc1","email":"rowanc1@gmail.com"},{"name":"agoose77","email":"goosey15@gmail.com"},{"name":"ebp-bot","email":"rowan@curvenote.com"}],"readme":"# JupyterLab MyST Extension\n\n[![Made with MyST][myst-badge]][myst-link]\n[![GitHub Actions Status][actions-badge]][actions-link]\n[![Launch on Binder][binder-badge]][binder-link]\n[![PyPI][pypi-badge]][pypi-link]\n\nRender markdown cells using [MyST Markdown](https://mystmd.org/), including support for rich frontmatter, interactive references, admonitions, figure numbering, tabs, proofs, exercises, glossaries, cards, and grids!\n\n![](./images/walkthrough.gif)\n\n> **Note**: If you are looking for the version of this repository based on jupyterlab-markup,\n> see the [`v0 branch`](https://github.com/executablebooks/jupyterlab-myst/tree/v0).\n\n> **Info**\n> This extension is composed of a Python package named `jupyterlab_myst`\n> for the server extension and a NPM package named `jupyterlab-myst`\n> for the frontend extension.\n\n## Requirements\n\n- JupyterLab >= 4.0.0\n\n## Install\n\nTo install the extension, execute:\n\n```bash\npip install jupyterlab_myst\n```\n\n## Features\n\n`jupyterlab-myst` is a fully featured markdown renderer for technical documents, [get started with MyST Markdown](https://mystmd.org/guide/quickstart-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.\n\nIn the code cell:\n\n```python\nimport numpy as np\narray = np.arange(4)\n```\n\nIn the markdown cell:\n\n```markdown\nLet's consider the following array: {eval}`array`.\n\nWe can compute the total: {eval}`array.sum()` and the maximum value is {eval}`array.max()`.\n```\n\nThis will evaluate inline, and show:\n\n```text\nLet's consider the following array: array([0, 1, 2, 3]).\n\nWe can compute the total: 6 and the maximum value is 3.\n```\n\nYou can also use this with `ipywidgets`, and have inline interactive text:\n\n![](./images/cookies.gif)\n\nOr with `matplotlib` to show inline spark-lines:\n\n![](./images/stock-price.gif)\n\nYou can also edit task lists directly in the rendered markdown.\n\n![](./images/tasklists-in-jupyterlab.gif)\n\n## Usage\n\n[MyST][myst-quickstart] 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.\n\n### Execution 🚀\n\nTo 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:\n\n```bash\njupyter labextension disable jupyterlab-myst:executor\n```\n\n### Trust 🔎\n\nJupyter Notebooks implement a [trust-based security model](https://jupyter-server.readthedocs.io/en/stable/operators/security.html). 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.\nExecuting the notebook will cause each cell to be considered trusted.\n\nTo facilitate this extension of the trust model, the `jupyterlab_myst` server extension replaces the `NotebookNotary` from `nbformat` with `MySTNotebookNotary`. This can be disabled with\n\n```bash\njupyter server extension disable jupyterlab-myst\n```\n\nBy 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.\n\n## Uninstall\n\nTo remove the extension, execute:\n\n```bash\npip uninstall jupyterlab_myst\n```\n\n## Troubleshoot\n\nIf you are seeing the frontend extension, but it is not working, check\nthat the server extension is enabled:\n\n```bash\njupyter server extension list\n```\n\nIf the server extension is installed and enabled, but you are not seeing\nthe frontend extension, check the frontend extension is installed:\n\n```bash\njupyter labextension list\n```\n\n## Contributing\n\n> [!IMPORTANT]\n> jupyterlab-myst uses `jsonnet` to render `package.jsonnet` into `package.json`\n\n### Development install\n\nNote: You will need NodeJS to build the extension package.\n\n```bash\n# Clone the repo to your local environment\n# Change directory to the jupyterlab_myst directory\n# Install package in development mode\npip install -e \".[test]\"\n# Link your development version of the extension with JupyterLab\njupyter-builder develop . --overwrite\n# Server extension must be manually installed in develop mode\njupyter server extension enable jupyterlab_myst\n# Rebuild extension Typescript source after making changes\nnpm run build\n```\n\nYou 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.\n\n```bash\n# Watch the source directory in one terminal, automatically rebuilding when needed\nnpm run watch\n# Run JupyterLab in another terminal\njupyter lab\n```\n\nWith 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).\n\nBy default, the `npm run 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:\n\n```bash\njupyter lab build --minimize=False\n```\n\n### Development uninstall\n\n```bash\n# Server extension must be manually disabled in develop mode\njupyter server extension disable jupyterlab_myst\npip uninstall jupyterlab_myst\n```\n\nIn development mode, you will also need to remove the symlink created by `jupyter labextension develop`\ncommand. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`\nfolder is located. Then you can remove the symlink named `jupyterlab-myst` within that folder.\n\n### Testing the extension\n\n#### Server tests\n\nThis extension is using [Pytest](https://docs.pytest.org/) for Python code testing.\n\nInstall test dependencies (needed only once):\n\n```sh\npip install -e \".[test]\"\n# Each time you install the Python package, you need to restore the front-end extension link\njupyter-builder develop . --overwrite\n```\n\nTo execute them, run:\n\n```sh\npytest -vv -r ap --cov jupyterlab_myst\n```\n\n#### Frontend tests\n\nThis extension is using [Jest](https://jestjs.io/) for JavaScript code testing.\n\nTo execute them, execute:\n\n```sh\nnpm install\nnpm test\n```\n\n#### Integration tests\n\nThis extension uses [Playwright](https://playwright.dev/docs/intro) for the integration tests (aka user level tests).\nMore precisely, the JupyterLab helper [Galata](https://github.com/jupyterlab/jupyterlab/tree/master/galata) is used to handle testing the extension in JupyterLab.\n\nMore information are provided within the [ui-tests](./ui-tests/README.md) README.\n\n### Packaging the extension\n\nSee [RELEASE](RELEASE.md)\n\n[myst-badge]: https://img.shields.io/badge/made%20with-myst-orange\n[myst-link]: https://mystmd.org\n[myst-quickstart]: https://mystmd.org/guide/quickstart-myst-markdown\n[actions-badge]: https://github.com/executablebooks/jupyterlab-myst/workflows/Build/badge.svg\n[actions-link]: https://github.com/executablebooks/jupyterlab-myst/actions/workflows/build.yml\n[binder-badge]: https://mybinder.org/badge_logo.svg\n[binder-link]: https://mybinder.org/v2/gh/executablebooks/jupyterlab-myst/main?urlpath=lab\n[pypi-badge]: https://img.shields.io/pypi/v/jupyterlab-myst.svg\n[pypi-link]: https://pypi.org/project/jupyterlab-myst\n","readmeFilename":"README.md"}