workspace-course-topics

Orchestrator: MyST Assembly

Phase: Skills
Time: ~45 minutes

Purpose

Create a multi-notebook MyST document that weaves together an intro, prior literature, the original notebook, and subsequent literature — with proper citations and a unified table of contents.

Prerequisites

.bib files from PaperPile (references.bib) and LitMaps (subsequent-literature.bib)
prior-literature.md working document (from Assignment 030)
subsequent-literature-analysis.md working document (from Assignment 040)
Environment set up via bash scripts/setup_env.sh (which installs MyST CLI, jupytext, myst-parser, and the Cursor extension)

Target structure

Four notebooks in TOC order, plus two .bib files:

Order	Notebook	Content	.bib source
1	`[name]_intro.ipynb`	Paper identity, original authors, student contributor	—
2	`[name]_prior-literature.ipynb`	Prior lit summary with MyST citations	`references.bib`
3	`[name].ipynb`	Original notebook (modified with citations, NOT converted)	`references.bib`
4	`[name]_subsequent-literature.ipynb`	Subsequent lit summary with MyST citations	`subsequent-literature.bib`

Workflow sequence

1. Verify MyST tools

Quick check that all MyST tools are installed. If setup_env.sh ran successfully, this should take under a minute.

Deliverable: myst --version works; MyST-Markdown extension visible in Cursor

2. Create intro notebook

Create [name]_intro.ipynb with paper metadata: title, authors, year, original ballpark authors, and student contributor name.

Deliverable: [name]_intro.ipynb created

3. Create prior-literature notebook

Create [name]_prior-literature.ipynb from your prior-literature.md working document. Insert MyST citations ({cite:t} / {cite:p}) that resolve against references.bib.

Deliverable: [name]_prior-literature.ipynb with citations

4. Create subsequent-literature notebook

Create [name]_subsequent-literature.ipynb from your analysis. Insert MyST citations that resolve against subsequent-literature.bib.

Deliverable: [name]_subsequent-literature.ipynb with citations

5. MyST assembly and configuration

Add MyST citations to the original notebook. Create myst.yml with TOC (four notebooks) and bibliography (two .bib files).

Deliverable: myst.yml configured; original notebook has MyST citations

6. Verify build

Run myst build from the paper folder and confirm:

Build completes without errors
Citations resolve (no “undefined citation” warnings)
HTML output shows rendered bibliography

Checkpoint

Before proceeding, verify:

Four notebooks exist in the paper folder
myst.yml lists all four notebooks in the TOC
references.bib and subsequent-literature.bib are in the paper folder
myst build completes without errors
Citations render correctly in the build output

Next orchestrator

Contribution