# Execute

> Executes all registered notebooks, strips noisy cell metadata, and syncs Jupytext pairs. Use when asked to re-run notebooks or refresh outputs.

- Skill: `brycewang-stanford/execute` (Agent Skill)
- Install (CLI): `npx skillmds@latest add brycewang-stanford/execute`
- Raw SKILL.md: https://api.skillmd.com/api/skills/brycewang-stanford/execute/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: brycewang-stanford (https://skillmd.com/u/brycewang-stanford)
- Updated: 2026-09-08
- Page: https://skillmd.com/skills/brycewang-stanford/execute

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# 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:
   ```bash
   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:
   ```bash
   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.