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Freeze check

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

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Install
npx -y skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill freeze-check

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Checks whether registered notebooks have current, stale, or missing outputs. Use before rendering or to verify freshness.

SKILL.md

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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
โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€
notebook-01.ipynb     Yes           2026-02-28 14:30     Current
notebook-02.ipynb     Yes           2026-03-01 09:15     Stale
notebook-03.ipynb     No            2026-02-25 11:00     Unexecuted

  5. If any notebooks are stale or unexecuted, flag them and offer to run /project:execute to re-execute all notebooks.

  6. If all notebooks are current, report "All notebooks are up to date."

Error handling

  • If _quarto.yml has no notebooks registered, report "No notebooks found in _quarto.yml" and stop.
  • If a registered notebook file does not exist on disk, flag it as missing.

Keep looking

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