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MyST Notebook

"Writing in VS Code was painful. Why cannot we only focus on typing? Here I am"

Edit MyST Markdown (.md) in VS Code's notebook editor. Prose renders in place as you type, math renders inline with KaTeX, and {code-cell} blocks run through Jupyter — all in one pane, no separate preview, no build step.

Install · Features · Zotero · Shortcuts · Structure

Quick Start

Install from the VS Code Marketplace, open a MyST .md, and start writing.

1. Install MyST Notebook from the VS Code Marketplace NOT READY YET!
2. Open a .md file in a MyST / Jupyter Book project (one with a myst.yml)
3. Click Open as MyST Notebook in the editor toolbar, or right-click the tab → Reopen Editor With… → MyST Notebook

To make MyST Notebook the default for .md files: Command Palette → Configure default editor for '.md' → MyST Notebook.

Requirements: VS Code 1.85+ · Python extension (for code execution) · A Python environment (optional — editing and rendering work without one)

What's Here

Demo Gallery

Inline rendering + auto-split

Prose and math render when you leave a cell. Auto-split creates new cells as you write — no mouse, no toolbar, no modal dialogs.

Code execution

{code-cell} blocks discover your Python environment and stream output live. No Jupyter extension required.

Knowledge graph

[[wikilinks]] and {cite} references become graph edges. Navigate your book by structure, not by file tree.

Zotero Citations

MyST Notebook works with your Zotero library to insert {cite}`key` references as you write — one command to configure, then pick and cite without leaving the keyboard.

Prerequisites

1. Zotero desktop — installed and running (the picker talks to 127.0.0.1:23119, a local server that only exists while Zotero is open)
2. Better BibTeX — Zotero plugin (Tools → Plugins, search "Better BibTeX for Zotero")
3. Citation Picker for Zotero (mblode.zotero) — recommended alongside MyST Notebook; VS Code will suggest installing both together

Automated Setup

Run MyST: Configure Zotero Citations from the Command Palette in a MyST workspace. The command:

• Detects whether mblode.zotero is installed (offers to install if absent)
• Writes the correct `{cite}` CAYW URL to .vscode/settings.json
• Lets you switch between {cite} / {cite:p} / {cite:t} roles

Insert citations with Alt+Shift+Z — the Zotero picker pops up, select a reference, press Enter.

WSL2 / Windows 10 users: the automated setup will NOT work out of the box — WSL2's NAT prevents reaching Zotero's 127.0.0.1:23119. Follow the WSL2 setup guide before anything else. Windows 11 users can try mirrored networking instead (simpler, not yet verified).

Verify It Works

With Zotero running, test the endpoint:

curl -s "http://127.0.0.1:23119/better-bibtex/cayw?format=json"

Pick a reference in the Zotero popup → JSON describing your selection is returned. Then test the MyST template — run Alt+Shift+Z in a .md file → a {cite}`key` lands at your cursor.

Make Citations Resolve (Reference List)

{cite}`key` is only half the job — the key must resolve against a .bib file for a reference list to appear at build time.

1. Auto-export a .bib from Zotero: right-click your collection → Export → Better BibTeX → check "Keep updated" → save as e.g. references.bib
2. Register it in myst.yml:

   project:
     bibliography:
       - references.bib
   

3. Build with jupyter book build --html — the reference list appears per-page, only for works actually cited.

⚠️ Troubleshooting: if the picker says "could not connect to Zotero" but Zotero is running, check that zotero-citation-picker.port was saved correctly. Don't press Escape in the picker — it produces the same error message as a dead server. Always press Enter on a selection.

Keyboard Shortcuts

Writing & cells

Math & citations

Kernel management (Command Palette)

Repository Structure

myst-notebook/
├── src/
│   ├── extension.ts          # activation entry point
│   ├── mystSerializer.ts     # lossless .md ↔ notebook round-trip
│   ├── kernelSession.ts      # Jupyter kernel lifecycle
│   ├── core/                 # pure functions: split, serialize, tags, templates
│   └── graph/                # knowledge graph (foam core + webview + VS Code features)
├── renderer/                 # notebook renderer (markdown-it + KaTeX)
├── media/                    # walkthrough images
├── test-fixtures/            # sample MyST workspace for smoke tests
├── .github/workflows/        # CI (build + test) and release (vsce publish)
├── esbuild.js                # bundle script
├── package.json              # extension manifest
└── README.md

Limitations

• MyST colon-fence directives (:::{note}, :::{warning}, :::{figure}, etc.) are NOT rendered inline in the notebook editor. VS Code's notebook renderer only supports inline-level markdown, not block-level custom syntax. The directives appear as plain source text while editing — they are correctly processed by jupyter-book build at build time. Write the directive syntax as you normally would; the compiler handles the final rendering.
• Relative local image paths in figure/image directives may not resolve in the renderer sandbox. Use absolute https:// URLs or data URIs.
• CRLF line endings are out of scope for v1 (LF assumed).
• Blank-line normalization between blocks is canonicalized to one blank line on first save. Already-canonical files round-trip byte-for-byte.

Why I Built This

I write technical documents in MyST, and every existing workflow forced the same compromise: write blind in a plain editor, then run a build to see if it looked right. Preview panes split my attention; Jupyter pulled me into a browser; Quarto and JupyterBook made me stop and compile. None of them let me write the way the document actually reads.

So I built the tool I wanted — the source file is the notebook, rendered in place, no build step, no second window. If you've felt the same friction, this is for you.

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