LICENSE
LICENSE-SAMPLES.md
README.md
pyproject.toml
src/biology_as_code/__init__.py
src/biology_as_code/carrier.py
src/biology_as_code/evidence.py
src/biology_as_code/laws.py
src/biology_as_code/py.typed
src/biology_as_code.egg-info/PKG-INFO
src/biology_as_code.egg-info/SOURCES.txt
src/biology_as_code.egg-info/dependency_links.txt
src/biology_as_code.egg-info/requires.txt
src/biology_as_code.egg-info/top_level.txt
src/biology_as_code/agents/__init__.py
src/biology_as_code/agents/assay/__init__.py
src/biology_as_code/agents/assay/__main__.py
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src/biology_as_code/agents/assay/handler.py
src/biology_as_code/agents/assay/ids.py
src/biology_as_code/agents/assay/multi_claim.py
src/biology_as_code/agents/assay/ontology_stub.py
src/biology_as_code/agents/assay/organ_systems.py
src/biology_as_code/agents/assay/pipeline.py
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src/biology_as_code/agents/assay/score.py
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src/biology_as_code/agents/assay/fixtures/golden.py
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src/biology_as_code/audit/auditor.py
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src/biology_as_code/contrib/from_assay.py
src/biology_as_code/contrib/validator.py
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src/biology_as_code/digestion/conditions.py
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src/biology_as_code/engine/signals.py
src/biology_as_code/engine/systems.py
src/biology_as_code/engine/data/LAW026_PMID_FILTER.md
src/biology_as_code/engine/data/LAW026_PROMOTION_DECISION.md
src/biology_as_code/engine/data/all_laws_system_bound.json
src/biology_as_code/engine/data/ascorbate_dual_chain.json
src/biology_as_code/engine/data/atomic_stage.schema.json
src/biology_as_code/engine/data/base_unit_colon_fermentation.skeleton.json
src/biology_as_code/engine/data/base_unit_lumen_iron.filled.json
src/biology_as_code/engine/data/evidence_candidates_LAW026.json
src/biology_as_code/engine/data/food_quality_claims.json
src/biology_as_code/engine/data/path_colon_scfa.atomic.json
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src/biology_as_code/machines/data/schemas/food-subsets/FOOD-SUBSETS.md
src/biology_as_code/machines/data/schemas/food-subsets/FoodSubsetTags.schema.json
src/biology_as_code/machines/data/schemas/food-subsets/meal-acquisition.catalog.json
src/biology_as_code/machines/data/schemas/food-subsets/oil-lipid.catalog.json
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src/biology_as_code/simulation/hormonal_energy.py
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src/biology_as_code/simulation/respiratory_quotient.py
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src/biology_as_code/systems/__init__.py
src/biology_as_code/systems/__main__.py
src/biology_as_code/systems/adapters.py
src/biology_as_code/systems/anatomy.py
src/biology_as_code/systems/coverage.py
src/biology_as_code/systems/edges.py
src/biology_as_code/systems/linter.py
src/biology_as_code/systems/meal.py
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src/biology_as_code/utils/logging.py
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src/biology_as_code/visualization/graphs.py
tests/test_absorption_bounds.py
tests/test_amino_acid_catabolism.py
tests/test_ao_law_004.py
tests/test_asl_export.py
tests/test_assay_agent.py
tests/test_assay_contrib_bridge.py
tests/test_assay_handler.py
tests/test_carrier.py
tests/test_claim_audit.py
tests/test_contribution.py
tests/test_cookbook.py
tests/test_deferred_quality.py
tests/test_digestion.py
tests/test_energy_accounting.py
tests/test_events.py
tests/test_evidence.py
tests/test_fixtures_packaged.py
tests/test_gates_can_fail.py
tests/test_graph_and_claim_model.py
tests/test_graph_json_export.py
tests/test_graph_relation_vocabulary.py
tests/test_hoststate_v2.py
tests/test_hri_artifacts.py
tests/test_ketolysis.py
tests/test_law026_policy.py
tests/test_laws.py
tests/test_machine_trace.py
tests/test_machines.py
tests/test_meal_critical_pathways.py
tests/test_micronutrient_cofactor_pathways.py
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tests/test_pathway_packs_golden.py
tests/test_public_api.py
tests/test_quiet.py
tests/test_separation_gate.py
tests/test_systems_coverage.py
tests/test_type_catalog.py
tests/test_version_manifest.py
tests/test_wave_b2_cogs.py