execute

name	execute
description	Executes all registered notebooks via Quarto render. Use when asked to re-run notebooks or refresh outputs.
disable-model-invocation	true
allowed-tools	Bash, Read, Write, Edit, Glob, Grep
version	1.0.0
workflow_stage	analysis
tags	["execution","notebooks","Quarto"]

Execute All Notebooks

Render all registered notebooks to refresh their outputs.

Steps

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

   quarto render notebooks/<name>.qmd
   

   Record execution time and success/failure for each notebook.
3. Report a summary table:
   • Notebook name
   • Status (success / failure)
   • Execution time
   • Any errors or warnings

Error handling

• If a notebook fails to render, 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.