LICENSE
LICENSE-SAMPLES.md
README.md
pyproject.toml
src/biology_as_code/__init__.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/bridge/__init__.py
src/biology_as_code/bridge/bridge_engine.py
src/biology_as_code/core/__init__.py
src/biology_as_code/core/base.py
src/biology_as_code/core/config.py
src/biology_as_code/core/exceptions.py
src/biology_as_code/data/VERSION_MANIFEST.json
src/biology_as_code/data/__init__.py
src/biology_as_code/data/version_manifest.py
src/biology_as_code/data/fixtures/__init__.py
src/biology_as_code/data/fixtures/user-personas.json
src/biology_as_code/data/fixtures/user_personas.py
src/biology_as_code/data/fixtures/vitamins.json
src/biology_as_code/data/fixtures/meals/01_raw_01_chicken_quinoa_broccoli_bowl.json
src/biology_as_code/data/fixtures/meals/02_raw_02_salmon_sweet_potato_asparagus.json
src/biology_as_code/data/fixtures/meals/03_raw_03_spinach_feta_scramble.json
src/biology_as_code/data/fixtures/meals/04_raw_04_overnight_oats_berries_chia.json
src/biology_as_code/data/fixtures/meals/05_raw_05_greek_yogurt_berry_bowl.json
src/biology_as_code/data/fixtures/meals/06_raw_06_lentil_kale_power_salad.json
src/biology_as_code/data/fixtures/meals/07_raw_07_black_bean_rice_bowl.json
src/biology_as_code/data/fixtures/meals/08_raw_08_tofu_veggie_stirfry.json
src/biology_as_code/data/fixtures/meals/09_raw_09_shrimp_quinoa_med_bowl.json
src/biology_as_code/data/fixtures/meals/10_raw_10_turkey_sweet_potato_skillet.json
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src/biology_as_code/data/fixtures/meals/12_bc_02_quaker_pb_banana_oatmeal.json
src/biology_as_code/data/fixtures/meals/13_bc_03_ezekiel_avocado_egg_toast.json
src/biology_as_code/data/fixtures/meals/14_bc_04_kodiak_strawberry_pancakes.json
src/biology_as_code/data/fixtures/meals/15_bc_05_fage_raspberry_bowl.json
src/biology_as_code/data/fixtures/meals/16_bc_06_cheerios_banana_milk.json
src/biology_as_code/data/fixtures/meals/17_bc_07_silk_berry_protein_smoothie.json
src/biology_as_code/data/fixtures/meals/18_bc_08_good_culture_strawberry_bowl.json
src/biology_as_code/data/fixtures/meals/19_bc_09_rxbar_banana_almonds.json
src/biology_as_code/data/fixtures/meals/20_bc_10_daves_ab_banana_toast.json
src/biology_as_code/data/fixtures/meals/21_bc_11_starkist_tuna_sandwich.json
src/biology_as_code/data/fixtures/meals/22_bc_12_goya_chickpea_greek_salad.json
src/biology_as_code/data/fixtures/meals/23_bc_13_bushs_burrito_bowl.json
src/biology_as_code/data/fixtures/meals/24_bc_14_sabra_veggie_wrap.json
src/biology_as_code/data/fixtures/meals/25_bc_15_applegate_turkey_avocado_sandwich.json
src/biology_as_code/data/fixtures/meals/26_bc_16_amys_lentil_soup_triscuits.json
src/biology_as_code/data/fixtures/meals/27_bc_17_banza_pesto_chicken_bowl.json
src/biology_as_code/data/fixtures/meals/28_bc_18_bumblebee_salmon_quinoa_salad.json
src/biology_as_code/data/fixtures/meals/29_bc_19_peanut_noodles_broccoli.json
src/biology_as_code/data/fixtures/meals/30_bc_20_edamame_rice_bowl.json
src/biology_as_code/data/fixtures/meals/31_bc_21_banza_marinara_turkey.json
src/biology_as_code/data/fixtures/meals/32_bc_22_ww_spaghetti_marinara.json
src/biology_as_code/data/fixtures/meals/33_bc_23_salmon_seeds_of_change.json
src/biology_as_code/data/fixtures/meals/34_bc_24_mission_chicken_fajitas.json
src/biology_as_code/data/fixtures/meals/35_bc_25_nasoya_teriyaki_stirfry.json
src/biology_as_code/data/fixtures/meals/36_bc_26_turkey_bean_chili.json
src/biology_as_code/data/fixtures/meals/37_bc_27_drpraeger_burger_plate.json
src/biology_as_code/data/fixtures/meals/38_bc_28_alfresco_sausage_sheetpan.json
src/biology_as_code/data/fixtures/meals/39_bc_29_maya_tikka_chicken.json
src/biology_as_code/data/fixtures/meals/40_bc_30_shrimp_pesto_pasta.json
src/biology_as_code/data/fixtures/meals/41_bc_31_tuna_pasta_salad_dinner.json
src/biology_as_code/data/fixtures/meals/42_bc_32_edamame_veggie_fried_rice.json
src/biology_as_code/data/fixtures/meals/43_bc_33_kind_bar_apple.json
src/biology_as_code/data/fixtures/meals/44_bc_34_hummus_carrots_triscuits.json
src/biology_as_code/data/fixtures/meals/45_bc_35_string_cheese_orange_almonds.json
src/biology_as_code/data/fixtures/meals/46_bc_36_siggis_blueberry.json
src/biology_as_code/data/fixtures/meals/47_bc_37_skinnypop_dark_chocolate.json
src/biology_as_code/data/fixtures/meals/48_bc_38_lifeway_kefir_smoothie.json
src/biology_as_code/data/fixtures/meals/49_bc_39_premier_shake_almonds.json
src/biology_as_code/data/fixtures/meals/50_bc_40_cottage_cheese_pita.json
src/biology_as_code/data/fixtures/meals/51_sup_01_whey_postworkout_shake.json
src/biology_as_code/data/fixtures/meals/52_sup_02_collagen_coffee_yogurt.json
src/biology_as_code/data/fixtures/meals/53_sup_03_protein_greens_smoothie.json
src/biology_as_code/data/fixtures/meals/54_sup_04_electrolyte_recovery_snack.json
src/biology_as_code/data/fixtures/meals/55_sup_05_creatine_lemon_water.json
src/biology_as_code/data/fixtures/meals/56_sup_06_spirulina_berry_smoothie.json
src/biology_as_code/data/fixtures/meals/57_sup_07_muscle_milk_apple.json
src/biology_as_code/data/fixtures/meals/58_upf_01_instant_ramen.json
src/biology_as_code/data/fixtures/meals/59_upf_02_frozen_pizza_cola.json
src/biology_as_code/data/fixtures/meals/60_upf_03_mac_and_hot_dogs.json
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src/biology_as_code/data/fixtures/meals/62_upf_05_poptarts_choc_milk.json
src/biology_as_code/data/fixtures/meals/63_upf_06_froot_loops_breakfast.json
src/biology_as_code/data/fixtures/meals/64_upf_07_bologna_sandwich_chips.json
src/biology_as_code/data/fixtures/meals/65_upf_08_gas_station_refuel.json
src/biology_as_code/data/fixtures/meals/66_upf_09_zebra_cakes_snack.json
src/biology_as_code/data/fixtures/meals/67_upf_10_twinkies_cola.json
src/biology_as_code/data/fixtures/meals/__init__.py
src/biology_as_code/data/fixtures/meals/index.json
src/biology_as_code/data/kibo_core/__init__.py
src/biology_as_code/data/kibo_core/demo.py
src/biology_as_code/data/kibo_core/paths.py
src/biology_as_code/data/kibo_core/systems.py
src/biology_as_code/data/kibo_core/data/LAW026_PMID_FILTER.md
src/biology_as_code/data/kibo_core/data/LAW026_PROMOTION_DECISION.md
src/biology_as_code/data/kibo_core/data/all_laws_system_bound.json
src/biology_as_code/data/kibo_core/data/ascorbate_dual_chain.json
src/biology_as_code/data/kibo_core/data/atomic_stage.schema.json
src/biology_as_code/data/kibo_core/data/base_unit_colon_fermentation.skeleton.json
src/biology_as_code/data/kibo_core/data/base_unit_lumen_iron.filled.json
src/biology_as_code/data/kibo_core/data/evidence_candidates_LAW026.json
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src/biology_as_code/data/kibo_core/data/rule_L2_REDOX_COMPETITION.json
src/biology_as_code/data/kibo_core/data/system_cascade_risk.json
src/biology_as_code/data/kibo_core/data/textbook_to_code_laws.json
src/biology_as_code/data/kibo_core/data/topics_ontology.json
src/biology_as_code/data/kibo_core/geography/__init__.py
src/biology_as_code/data/kibo_core/geography/kingdoms.py
src/biology_as_code/data/kibo_core/geography/organ_bounds.py
src/biology_as_code/data/kibo_core/laws/__init__.py
src/biology_as_code/data/kibo_core/laws/atomic.py
src/biology_as_code/data/kibo_core/laws/base_unit.py
src/biology_as_code/data/kibo_core/laws/models.py
src/biology_as_code/data/kibo_core/laws/qa.py
src/biology_as_code/data/kibo_core/laws/registry.py
src/biology_as_code/data/kibo_core/laws/walk.py
src/biology_as_code/data/kibo_core/pathways/__init__.py
src/biology_as_code/data/kibo_core/pathways/cascade_risk.py
src/biology_as_code/data/kibo_core/pathways/colon_scfa.py
src/biology_as_code/data/kibo_core/pathways/food_quality.py
src/biology_as_code/data/kibo_core/pathways/nonhaem_iron.py
src/biology_as_code/data/kibo_core/sim/__init__.py
src/biology_as_code/data/kibo_core/sim/engine.py
src/biology_as_code/data/kibo_core/sim/phases.py
src/biology_as_code/data/kibo_core/sim/rules_redox.py
src/biology_as_code/data/kibo_core/sim/state.py
src/biology_as_code/data/kibo_core/topics/__init__.py
src/biology_as_code/data/kibo_core/topics/registry.py
src/biology_as_code/data/kibo_core/topics/sim_map.py
src/biology_as_code/dig/__init__.py
src/biology_as_code/dig/digestion_capacity_routing.py
src/biology_as_code/dig/digestion_flow_simulator.py
src/biology_as_code/dig/digestive_definition_layer.py
src/biology_as_code/dig/digestive_enzymes.py
src/biology_as_code/dig/digestive_mechanism_layer.py
src/biology_as_code/dig/fiber_rs_model.py
src/biology_as_code/dig/food_additives_registry.py
src/biology_as_code/dig/mineral_interactions.py
src/biology_as_code/dig/protein_quality.py
src/biology_as_code/dig/vitamin_absorption.py
src/biology_as_code/machines/README.md
src/biology_as_code/machines/__init__.py
src/biology_as_code/machines/digestion.py
src/biology_as_code/machines/executor.py
src/biology_as_code/machines/loader.py
src/biology_as_code/machines/validate.py
src/biology_as_code/machines/data/registry.json
src/biology_as_code/machines/data/_schema/machine.schema.json
src/biology_as_code/machines/data/process/full-digest.json
src/biology_as_code/machines/data/stage/cell.json
src/biology_as_code/machines/data/stage/colon.json
src/biology_as_code/machines/data/stage/duodenum.json
src/biology_as_code/machines/data/stage/jejunum.json
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src/biology_as_code/machines/data/stage/portal.json
src/biology_as_code/machines/data/stage/stomach.json
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src/biology_as_code/models/__init__.py
src/biology_as_code/models/biochemical_mechanisms.py
src/biology_as_code/models/causal_inference.py
src/biology_as_code/models/causal_join_graph.py
src/biology_as_code/models/do_calculus.py
src/biology_as_code/models/kibo_nutrition_ontology.py
src/biology_as_code/models/nutrient_compound.py
src/biology_as_code/models/system_interaction_principles.py
src/biology_as_code/pathways/__init__.py
src/biology_as_code/pathways/beta_oxidation.py
src/biology_as_code/pathways/cholesterol_pathway.py
src/biology_as_code/pathways/digestion_absorption_pathways.py
src/biology_as_code/pathways/etc_oxphos.py
src/biology_as_code/pathways/fatty_acid_synthesis.py
src/biology_as_code/pathways/gluconeogenesis.py
src/biology_as_code/pathways/glycogen_metabolism.py
src/biology_as_code/pathways/ketogenesis.py
src/biology_as_code/pathways/ketolysis.py
src/biology_as_code/pathways/metabolic_mechanisms.py
src/biology_as_code/pathways/metabolic_pathways.py
src/biology_as_code/pathways/nutrient_sensing.py
src/biology_as_code/pathways/pathway_regulation.py
src/biology_as_code/pathways/pentose_phosphate.py
src/biology_as_code/pathways/registry.py
src/biology_as_code/pathways/supporting_pathways.py
src/biology_as_code/pathways/tca_cycle.py
src/biology_as_code/pathways/urea_cycle.py
src/biology_as_code/product_score/README.md
src/biology_as_code/product_score/__init__.py
src/biology_as_code/product_score/interface.py
src/biology_as_code/product_score/loader.py
src/biology_as_code/product_score/proprietary/README.md
src/biology_as_code/product_score/proprietary/__init__.py
src/biology_as_code/simulation/__init__.py
src/biology_as_code/simulation/body_composition_energy.py
src/biology_as_code/simulation/energy_intake_need.py
src/biology_as_code/simulation/energy_routing.py
src/biology_as_code/simulation/health_outcomes.py
src/biology_as_code/simulation/hormonal_energy.py
src/biology_as_code/simulation/kibo_engine.py
src/biology_as_code/simulation/life_stage_dri.py
src/biology_as_code/simulation/metabolic_state.py
src/biology_as_code/simulation/nitrogen_balance.py
src/biology_as_code/simulation/organ_pathway_network.py
src/biology_as_code/simulation/physiological_effects.py
src/biology_as_code/simulation/physiological_state.py
src/biology_as_code/simulation/respiratory_quotient.py
src/biology_as_code/simulation/runner.py
src/biology_as_code/simulation/scenarios.py
src/biology_as_code/simulation/signaling_pathways.py
src/biology_as_code/simulation/unified_facade.py
src/biology_as_code/utils/__init__.py
src/biology_as_code/utils/logging.py
src/biology_as_code/visualization/__init__.py
src/biology_as_code/visualization/graphs.py
tests/test_deferred_quality.py
tests/test_evidence.py
tests/test_fixtures_packaged.py
tests/test_ketolysis.py
tests/test_laws.py
tests/test_machine_trace.py
tests/test_machines.py
tests/test_nutrient_sensing.py
tests/test_nutrient_sensing_exec.py
tests/test_pathway_packs.py
tests/test_public_api.py
tests/test_quiet.py