Execute

Skill brycewang-stanford/Auto-Empirical-Research-Skills/skills/29-quarcs-lab-project20XXy/dot-claude/skills/execute

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

Install

npx -y skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill execute

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One thing to look at

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SKILL.md

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Execute All Notebooks

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

Steps

Read _quarto.yml and extract all notebook paths from manuscript.notebooks
For each notebook, execute it:
```
uv run jupyter execute --inplace notebooks/<name>.ipynb
```
Record execution time and success/failure for each notebook.
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).

Sync all Jupytext .md pairs:

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

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.

What ships with it

Read from the repository