execute

Development

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

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How to use this skill

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Prompt to paste

I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/blob/HEAD/skills/29-quarcs-lab-project20XXy/dot-claude/skills/execute/SKILL.md

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First, summarize what it does, its dependencies, license status if identifiable, and any risks. Show the exact files you propose to add under .agents/skills/execute/. Do not write files or run scripts until I approve.

After I approve, install the complete skill folder, including required referenced files, into that project location. Verify it is discoverable, then tell me its actual invocation name and how to use it. Do not claim it is installed until you have verified it.

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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.

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