freeze-check

npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill freeze-check --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Check Notebook Execution Freshness Verify that all registered notebooks have been executed and their outputs are current. ## Steps 1. Read `_quarto.yml` and extract all notebook paths from `manuscript.notebooks`. 2. For each registered notebook, check: - **Has outputs:** Open the `.ipynb` JSON and check if any code cells have non-empty `outputs` arrays - **Last modified:** File modification timestamp of the `.ipynb` - **Outputs age:** Check `execution` metadata timestamps in cell metadata (if present) to determine when outputs were last generated - **Freeze cache:** Check if `_freeze/notebooks/<name>/` directory exists and contains cached output 3. Determine freshness status for each notebook: - **Current:** has outputs and the `.ipynb` has not been modified since outputs were generated - **Stale:** has outputs but the `.ipynb` source cells have been modified more recently than the outputs - **Unexecuted:** no outputs in any code cell - **Freeze only:** no cell outputs but a `_freeze/` cache exists (Quarto will use the cache) 4. Report a summary table: ``` Notebook Has Outputs Last Modified Status ───────────────────────────────────────────────────────────────── notebook-01.ipynb