name: execute description: Executes all registered notebooks, strips noisy cell metadata, and syncs Jupytext pairs. Use when asked to re-run notebooks or refresh outputs. disable-model-invocation: true allowed-tools: Bash, Read, Write, Edit, Glob, Grep

Execute All Notebooks

Execute all registered notebooks, strip noisy metadata, and sync Jupytext pairs.

Steps

1. Read _quarto.yml and extract all notebook paths from manuscript.notebooks
2. For each notebook, execute it:

   uv run jupyter execute --inplace notebooks/<name>.ipynb
   

   Record execution time and success/failure for each notebook.
3. After all notebooks execute, strip noisy cell metadata from every .ipynb file. Open each .ipynb as JSON and remove these keys from every cell's metadata object:
   • execution (timestamps added by jupyter execute)
   • _sphinx_cell_id (MyST/Sphinx artifact)
   • vscode (VS Code editor state) Save the cleaned JSON back to the file (preserve formatting with 1-space indent).
4. Sync all Jupytext .md pairs:

   uv run jupytext --sync notebooks/<name>.md
   

5. Report a summary table:
   • Notebook name
   • Status (success / failure)
   • Execution time
   • Any errors or warnings

Error handling

• If a notebook fails to execute, continue with the remaining notebooks. Report the error at the end.
• If _quarto.yml has no notebooks registered, report "No notebooks found in _quarto.yml" and stop.