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REPRODUCIBILITY_REPORT.md

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Permea Core Public Reproducibility Report

Run summary

  • Run name: permea_core_public_reproducibility_bundle
  • Generated at: example-generated
  • Status: PASS

Generated surfaces

Validation summary

  • unified artifact validation: python3 scripts/validate_permea_artifacts.py
  • reproducibility bundle validation: python3 scripts/permea_validate.py
  • focused reproducibility tests: python3 -m pytest tests/test_reproducibility_bundle.py

Artifact lineage

  1. README: README.md (present)
  2. Quickstart: QUICKSTART.md (present)
  3. Reproducibility guide: REPRODUCIBILITY.md (present)
  4. Evaluation guide: EVALUATION.md (present)
  5. Generated evidence surface: docs/examples/generated/README.md (present)
  6. Evaluation packet: docs/examples/generated/EVALUATION_PACKET.md (present)
  7. Demo packet: docs/examples/generated/DEMO_PACKET.md (present)
  8. Artifact index: docs/examples/generated/ARTIFACT_INDEX.md (present)
  9. Evidence matrix: docs/examples/generated/EVIDENCE_MATRIX.md (present)
  10. Reproducibility report: docs/examples/generated/REPRODUCIBILITY_REPORT.md (present)
  11. Dry-run report: docs/examples/generated/dry_runs/example_benchmark_dry_run.md (present)
  12. Benchmark cards: docs/examples/generated/benchmark_cards (present)
  13. Dataset cards: docs/examples/generated/dataset_cards (present)
  14. Acquisition manifests: docs/examples/generated/acquisition_manifests (present)
  15. Evidence cards: docs/examples/generated/evidence_cards (present)
  16. Output packages: docs/examples/generated/output_packages (present)
  17. Run manifests: docs/examples/generated/run_manifests (present)

Reproducibility status

The bundle is reproducible when the listed artifacts are present and the reproduction and validation commands exit successfully.

Explicit Non-Claims

  • no dataset downloaded
  • no acquisition executed
  • no redistribution rights confirmed
  • no wet-lab validation by Permea
  • no clinical-effectiveness claim
  • no model performance claim
  • no state-of-the-art claim
  • no solved-delivery claim

Limitations

  • This bundle regenerates deterministic public metadata artifacts from repository files only.
  • It does not download datasets, execute acquisition, call external services, run ML, or score candidates.
  • It validates artifact presence, structure, links, and stated boundaries; it does not validate biological performance.
  • Researchers and developers should treat generated examples as infrastructure surfaces, not experimental evidence.

Next Evidence Steps

  • Run the reproduction command after cloning or changing generator code.
  • Run the validation command before proposing changes to generated artifact surfaces.
  • Extend the artifact system by adding generator, validation, tests, and bounded claim language together.