execute
Executes all registered notebooks, strips noisy cell metadata, and syncs Jupytext pairs. Use when asked to re-run notebooks or refresh outputs.
Profile →npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill execute --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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.
- Steps
- Error handling
uv run jupyter execute --inplace notebooks/<name>.ipynb uv run jupytext --sync notebooks/<name>.md
What does the execute skill do?
Executes all registered notebooks, strips noisy cell metadata, and syncs Jupytext pairs. Use when asked to re-run notebooks or refresh outputs.
How do I install it?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill execute --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From brycewang-stanford/Auto-Empirical-Research-Skills, a repository with 3,244 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.