sync-notebooks

name	sync-notebooks
description	This skill should be used when the user asks to "sync notebooks", "sync jupytext", "update notebooks", "pair notebooks", or mentions syncing .ipynb and .md files. Also use when the user edits a notebook markdown file and needs to regenerate the .ipynb. Syncs Jupytext paired notebook (.ipynb) and MyST Markdown (.md) files.

Sync Notebooks

The project has 4 paired notebooks:

Notebook	Paired .md	Language
c01_view_from_space.ipynb	c01_view_from_space.md	Python
c02_regional_convergence_sc.ipynb	c02_regional_convergence_sc.md	R
c03_spatial_dependence_lisa.ipynb	c03_spatial_dependence_lisa.md	Python
c04_spillover_modeling_6nn.ipynb	c04_spillover_modeling_6nn.md	Stata

Sync all notebooks

uv run jupytext --sync notebooks/c01_view_from_space.ipynb
uv run jupytext --sync notebooks/c02_regional_convergence_sc.ipynb
uv run jupytext --sync notebooks/c03_spatial_dependence_lisa.ipynb
uv run jupytext --sync notebooks/c04_spillover_modeling_6nn.ipynb

Sync a specific notebook

If the user specifies a notebook (by name or number like "c01", "c03"), sync only that one.

Guidelines

• Always use uv run jupytext --sync (not plain jupytext)
• The .md files use MyST Markdown format
• Cell outputs are stored only in .ipynb; .md files contain just code and markdown
• Prefer editing the .md file, then syncing to regenerate the .ipynb
• After syncing, consider running bash scripts/clean-render.sh if the notebooks feed into the manuscript