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Dossier Generation

dossier_generate.py creates a deterministic lightweight baseline ferm-doe-dossier/ from a campaign manifest and CSV run ledger.

For the normal orchestrator, issue-tracker, remote-compute, or cloud success path, use compile_ferm_doe_dossier.py plus dossier_check.py and ferm_doe_contract_self_check.py. The lightweight generator is useful for legacy smoke tests and quick summaries. It does not produce the full contract proof artifacts.

Demo Command

python3 skills/biosymphony-ferm-doe/scripts/compile_ferm_doe_dossier.py \
  --manifest examples/xylanase-wxz1-2012/campaign_manifest.json \
  --out ferm-doe-dossier \
  --run-budget 8

python3 skills/biosymphony-ferm-doe/scripts/dossier_check.py ferm-doe-dossier
python3 skills/biosymphony-ferm-doe/scripts/ferm_doe_contract_self_check.py ferm-doe-dossier

Legacy lightweight command:

python3 skills/biosymphony-ferm-doe/scripts/dossier_generate.py \
  --manifest examples/xylanase-wxz1-2012/campaign_manifest.json \
  --ledger examples/xylanase-wxz1-2012/inputs/historical_run_ledger.csv \
  --output ferm-doe-dossier

If --ledger is omitted, the script uses the first ledger-like CSV input listed in the manifest.

Outputs

The lightweight output directory contains:

  • data_trust_report.md
  • factor_space_audit.md
  • model_summary.md
  • provenance.md
  • readiness_verdict.md

The generator reports run count, objective response, best observed run, best observed response, trust status, and readiness status. It does not fit a predictive model or produce lab-execution recommendations.

Determinism

The Markdown output avoids timestamps and environment-specific randomness. Re-running the command with the same manifest, ledger, and output path should produce identical file content.