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data-audit

Scans notebooks for data file references and verifies each file exists on disk. Use when checking for broken data paths.

Published by brycewang-stanford ↗brycewang-stanford/Auto-Empirical-Research-Skills

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data-audit

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Use data-audit to audit notebook data-file references and return resolved, broken, and unreferenced files with a totals summary.

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    SKILL.md

    name: data-auditdescription: Scans notebooks for data file references and verifies each file exists on disk. Use when checking for broken data paths.allowed-tools: Bash, Read, Glob, Grep

    Audit Data References

    Scan all notebooks for data file references and verify they exist on disk.

    Steps

    1. Scan all .ipynb files in notebooks/ for data loading patterns:

      • Python: pd.read_csv(...), pd.read_stata(...), pd.read_excel(...), pd.read_parquet(...), open(...), np.loadtxt(...)
      • R: read.csv(...), read_csv(...), read.dta(...), haven::read_dta(...), readxl::read_excel(...), load(...)
      • Stata: use "...", import delimited "...", import excel "...", insheet using "..."
      • Also check the .md Jupytext pairs for the same patterns

    2. Extract every referenced file path and normalize it:

      • Resolve relative paths from the notebook's directory (notebooks/)
      • Resolve paths using DATA_DIR, RAW_DATA_DIR from config.py / config.R

    3. Check that each referenced file exists in data/rawData/ or data/

    4. Scan data/rawData/ and data/ for all data files present on disk

    5. Report three categories:

      Resolved — referenced and found:

      • File path, which notebook references it, line/cell number

      Broken — referenced but not found:

      • File path as written in code, which notebook, suggested fix (closest matching file, or note that it may need to be downloaded)

      Undocumented — on disk but never referenced by any notebook:

      • File path in data/rawData/ or data/ that no notebook loads

    6. Print a summary: total references, resolved, broken, undocumented files

    Error handling

    • If no notebooks exist, report "No notebooks found" and stop.
    • If data/rawData/ does not exist, warn but continue checking data/.