Quickstart: Run a FoodSpec Protocol in 10 Minutes

CLI

foodspec-run-protocol \
  --input data/oils.csv \
  --protocol examples/protocols/EdibleOil_Classification_v1.yml \
  --output-dir runs

Outputs: runs/<protocol>_<input>/ containing report.txt, figures, tables, metadata.

Tips

• Validate before running; fix blocking errors first.
• Keep protocols versioned; record seeds and CV design in outputs.

Notes

• Protocols are YAML/JSON in examples/protocols/.
• Common overrides: --seed, --cv-folds, --normalization-mode, --baseline-method, --spike-removal/--no-spike-removal.
• HDF5 stores instrument metadata, preprocessing history, provenance.