LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
data/README.md
data/calibration/README.md
data/calibration/synthetic/first_order_ab/calibration_config.yml
data/environments/alvarez_gonzalez_2022_50c_ph5.yml
data/environments/lab_30C_pH7.yml
data/enzymes/petase_like.yml
data/enzymes/toy_generic_surface_catalyst.yml
data/experiments/README.md
data/experiments/synthetic_pet_surface.yml
data/experiments/candidate_reviews/README.md
data/experiments/candidate_reviews/ariaeenejad_2020_persibgl1_cellobiose_hydrolysis_review.yml
data/experiments/candidate_reviews/fake_candidate_review.yml
data/experiments/candidate_reviews/resa_buckin_2011_cellobiose_hydrolysis_review.yml
data/experiments/literature/README.md
data/experiments/literature/alvarez_gonzalez_2022_free_beta_glucosidase/alvarez_gonzalez_2022_figure_s1a_filled_squares.csv
data/experiments/literature/alvarez_gonzalez_2022_free_beta_glucosidase/alvarez_gonzalez_2022_free_beta_glucosidase.yml
data/experiments/literature_schema_examples/fake_literature_dataset.yml
data/experiments/synthetic/README.md
data/experiments/synthetic/first_order_ab/generation_record.json
data/experiments/synthetic/first_order_ab/synthetic_first_order_ab.yml
data/experiments/synthetic/first_order_ab/synthetic_first_order_ab_observations.csv
data/experiments/validation/README.md
data/fungi/pleurotus_ostreatus.yml
data/fungi/toy_pet_fungus.yml
data/geometries/alvarez_gonzalez_2022_well_mixed_20ml.yml
data/geometries/pet_film_1d.yml
data/geometries/well_mixed_100ml.yml
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/README.md
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/source_notes.md
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/curated/kinetic_record.yml
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/curated/parameter_range_summary.json
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/curated/parameter_range_summary.md
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/curated/reaction_618_eligible_entries.csv
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/curated/reaction_618_excluded_entries.csv
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/raw/fetch_metadata.json
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/raw/kinlaw_entries_reaction_618.json
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/raw/selected_kinlaw_entry_35622.json
data/kinetic_records/sabiork/case_001_reaction_618_beta_glucosidase/raw/selection_report.json
data/model_configs/README.md
data/model_configs/alvarez_gonzalez_2022_free_beta_glucosidase_comparison.yml
data/model_configs/phanerochaete_bgl1b_cellobiose_transglycosylation.yml
data/model_configs/showcase_dynamic_thermodynamics.yml
data/model_configs/synthetic_first_order_calibration.yml
data/model_configs/toy_homogeneous_ab.yml
data/model_configs/toy_homogeneous_competitive_inhibition.yml
data/model_configs/toy_homogeneous_substrate_inhibition.yml
data/model_configs/toy_surface_dummy_non_pet.yml
data/model_configs/toy_surface_dummy_non_pet_product_inhibition.yml
data/model_configs/toy_surface_pet_plugin.yml
data/parameters/pet_surface_benchmark.yml
data/product_maps/README.md
data/product_maps/alvarez_gonzalez_2022_cellobiose_to_glucose.yml
data/product_maps/phanerochaete_bgl1b_cellobiose_hydrolysis.yml
data/product_maps/phanerochaete_bgl1b_cellobiose_transfer_pool.yml
data/product_maps/toy_surface_dummy_mass_equivalent.yml
data/product_maps/toy_surface_plugin_mass_equivalent.yml
data/showcases/five_fungal_beta_glucosidases.yml
data/substrates/cellulose_powder.yml
data/substrates/pet_film.yml
data_registry/README.md
data_registry/registry_index.yml
data_registry/case_templates/case_templates.yml
data_registry/environments/environments.yml
data_registry/enzymes/enzyme_classes.yml
data_registry/fungi/fungi.yml
data_registry/parameters/parameter_records.yml
data_registry/processes/process_compatibility.yml
data_registry/product_maps/product_maps.yml
data_registry/substrates/substrates.yml
scripts/stage_packaged_resources.py
src/fungal_model/__init__.py
src/fungal_model/provenance.py
src/fungal_model/resources.py
src/fungal_model/api/__init__.py
src/fungal_model/api/_integrity.py
src/fungal_model/api/curation.py
src/fungal_model/api/curator_signatures.py
src/fungal_model/api/environment_grid.py
src/fungal_model/api/metrics.py
src/fungal_model/api/output_schema.py
src/fungal_model/api/parameter_conversion.py
src/fungal_model/api/parameter_record_authoring.py
src/fungal_model/api/quicklook.py
src/fungal_model/api/registry_promotion.py
src/fungal_model/api/registry_record_authoring.py
src/fungal_model/api/report.py
src/fungal_model/api/result_tables.py
src/fungal_model/api/source_provider.py
src/fungal_model/api/virtual_experiment.py
src/fungal_model/calibration/__init__.py
src/fungal_model/calibration/bayesian.py
src/fungal_model/calibration/configured.py
src/fungal_model/calibration/evidence.py
src/fungal_model/calibration/fitting.py
src/fungal_model/calibration/residuals.py
src/fungal_model/chemistry/__init__.py
src/fungal_model/chemistry/nonideal_thermodynamics.py
src/fungal_model/chemistry/reactions.py
src/fungal_model/chemistry/stoichiometry.py
src/fungal_model/chemistry/thermodynamics.py
src/fungal_model/core/__init__.py
src/fungal_model/core/assumptions.py
src/fungal_model/core/errors.py
src/fungal_model/core/logging.py
src/fungal_model/core/parameters.py
src/fungal_model/core/provenance.py
src/fungal_model/core/simulation.py
src/fungal_model/core/state.py
src/fungal_model/core/units.py
src/fungal_model/core/validators.py
src/fungal_model/core/value_spec.py
src/fungal_model/data/__init__.py
src/fungal_model/data/candidate_review.py
src/fungal_model/data/comparison.py
src/fungal_model/data/datasets.py
src/fungal_model/data/kinetic_record_loaders.py
src/fungal_model/data/kinetic_records.py
src/fungal_model/data/literature_schema.py
src/fungal_model/data/loaders.py
src/fungal_model/data/sabiork.py
src/fungal_model/data/synthetic.py
src/fungal_model/entities/__init__.py
src/fungal_model/entities/environment.py
src/fungal_model/entities/enzyme.py
src/fungal_model/examples/__init__.py
src/fungal_model/examples/product_inhibition.py
src/fungal_model/fungi/__init__.py
src/fungal_model/fungi/base.py
src/fungal_model/fungi/coupling.py
src/fungal_model/fungi/enzyme_profile.py
src/fungal_model/fungi/growth.py
src/fungal_model/fungi/metabolism.py
src/fungal_model/geometry/__init__.py
src/fungal_model/geometry/base.py
src/fungal_model/geometry/film_1d.py
src/fungal_model/geometry/particle.py
src/fungal_model/geometry/porous_medium.py
src/fungal_model/geometry/slab.py
src/fungal_model/geometry/well_mixed.py
src/fungal_model/io/__init__.py
src/fungal_model/io/json_export.py
src/fungal_model/io/model_config.py
src/fungal_model/io/parameters.py
src/fungal_model/io/product_maps.py
src/fungal_model/io/registries.py
src/fungal_model/io/schema.py
src/fungal_model/io/yaml_loader.py
src/fungal_model/kinetics/__init__.py
src/fungal_model/kinetics/arrhenius.py
src/fungal_model/kinetics/langmuir.py
src/fungal_model/kinetics/michaelis_menten.py
src/fungal_model/kinetics/ph.py
src/fungal_model/kinetics/surface_kinetics.py
src/fungal_model/modifiers/__init__.py
src/fungal_model/modifiers/base.py
src/fungal_model/modifiers/enzyme_inhibition.py
src/fungal_model/modifiers/oxygen.py
src/fungal_model/modifiers/ph.py
src/fungal_model/modifiers/product_inhibition.py
src/fungal_model/modifiers/temperature.py
src/fungal_model/modifiers/water_activity.py
src/fungal_model/plugins/__init__.py
src/fungal_model/plugins/pet/__init__.py
src/fungal_model/plugins/pet/loaders.py
src/fungal_model/plugins/pet/workflows.py
src/fungal_model/processes/__init__.py
src/fungal_model/processes/assembly.py
src/fungal_model/processes/base.py
src/fungal_model/processes/factories.py
src/fungal_model/processes/homogeneous.py
src/fungal_model/processes/rate_modifiers.py
src/fungal_model/processes/registry.py
src/fungal_model/processes/surface.py
src/fungal_model/processes/transglycosylation.py
src/fungal_model/registry/__init__.py
src/fungal_model/registry/loaders.py
src/fungal_model/registry/records.py
src/fungal_model/registry/resolver.py
src/fungal_model/registry/store.py
src/fungal_model/results/__init__.py
src/fungal_model/results/result.py
src/fungal_model/screening/__init__.py
src/fungal_model/screening/case_builder.py
src/fungal_model/screening/ensemble.py
src/fungal_model/screening/enzyme_chain.py
src/fungal_model/screening/modelability.py
src/fungal_model/screening/parameter_resolution.py
src/fungal_model/screening/template_environment_modifiers.py
src/fungal_model/solvers/__init__.py
src/fungal_model/solvers/process_ode.py
src/fungal_model/sources/__init__.py
src/fungal_model/sources/sabiork/__init__.py
src/fungal_model/sources/sabiork/fetch.py
src/fungal_model/substrates/__init__.py
src/fungal_model/substrates/base.py
src/fungal_model/substrates/cellulose.py
src/fungal_model/substrates/chitin.py
src/fungal_model/substrates/lignin.py
src/fungal_model/substrates/pet.py
src/fungal_model/substrates/starch.py
src/fungal_model/transport/__init__.py
src/fungal_model/transport/cartesian.py
src/fungal_model/transport/diffusion.py
src/fungal_model/transport/geometry.py
src/fungal_model/transport/reaction_diffusion.py
src/fungal_model/transport/reaction_diffusion_nd.py
src/fungal_model/uncertainty/__init__.py
src/fungal_model/uncertainty/global_sensitivity.py
src/fungal_model/uncertainty/monte_carlo.py
src/fungal_model/uncertainty/sensitivity.py
src/fungal_model/validation/__init__.py
src/fungal_model/validation/benchmark_cases.py
src/fungal_model/validation/bio_readiness.py
src/fungal_model/validation/limiting_cases.py
src/fungal_model/validation/mass_balance.py
src/fungal_model/validation/maturity.py
src/fungal_model/validation/non_negative.py
src/fungal_model/validation/spatial.py
src/fungal_model/validation/stoichiometry.py
src/fungal_model/workflows/__init__.py
src/fungal_model/workflows/configured_errors.py
src/fungal_model/workflows/configured_inputs.py
src/fungal_model/workflows/configured_model.py
src/fungal_model/workflows/configured_outputs.py
src/fungal_model/workflows/configured_processes.py
src/fungal_model/workflows/dynamic_thermodynamics.py
src/fungal_model/workflows/static_balance.py
src/fungmod/__init__.py
src/fungmod.egg-info/PKG-INFO
src/fungmod.egg-info/SOURCES.txt
src/fungmod.egg-info/dependency_links.txt
src/fungmod.egg-info/requires.txt
src/fungmod.egg-info/top_level.txt
tests/test_active_instruction_hierarchy.py
tests/test_api003_researcher_virtual_experiment.py
tests/test_bio001_notebook.py
tests/test_bio001_surface_cellulose_virtual_experiment.py
tests/test_bio002_extracellular_enzyme_chain.py
tests/test_bio002_generic_chain_assembly.py
tests/test_bio_readiness_lite.py
tests/test_calibration.py
tests/test_calibration_config_contract.py
tests/test_calibration_evidence.py
tests/test_case001_researcher_enzyme_chain_virtual_experiment.py
tests/test_config_driven_case_assembly.py
tests/test_config_io.py
tests/test_configured_model_workflow.py
tests/test_configured_output_bundle_reproducibility.py
tests/test_configured_synthetic_calibration.py
tests/test_configured_workflow_components.py
tests/test_configured_workflow_failures.py
tests/test_curation_review.py
tests/test_curator_signatures.py
tests/test_dataset_candidate_review.py
tests/test_dynamic_thermodynamic_enforcement.py
tests/test_environment_grid.py
tests/test_environment_modifiers.py
tests/test_environmental_modifiers.py
tests/test_enzyme_compatibility.py
tests/test_experiment_dataset_loading.py
tests/test_experiment_dataset_validation_rules.py
tests/test_findings_catalogue.py
tests/test_foundation_complete_gate.py
tests/test_full_integration_workflow.py
tests/test_fungal_beta_glucosidase_showcase.py
tests/test_fungal_coupling.py
tests/test_fungal_dynamics.py
tests/test_generic_surface_processes.py
tests/test_geometry_abstractions.py
tests/test_global_sensitivity.py
tests/test_guardrails_config_generality.py
tests/test_guardrails_native_execution.py
tests/test_guardrails_no_hardcoding.py
tests/test_guardrails_no_shortcuts.py
tests/test_guardrails_public_api.py
tests/test_homogeneous_processes.py
tests/test_kinetic_record_loading.py
tests/test_limiting_cases.py
tests/test_literature_schema_contract.py
tests/test_literature_time_course_comparison.py
tests/test_literature_time_course_dataset.py
tests/test_mass_balance.py
tests/test_maturity_policy.py
tests/test_michaelis_menten.py
tests/test_model_config_loading.py
tests/test_model_dataset_comparison.py
tests/test_modelability_report.py
tests/test_native_assembled_model_run.py
tests/test_non_negative.py
tests/test_nonideal_reversible_thermodynamics.py
tests/test_notebooks.py
tests/test_packaged_distribution.py
tests/test_parameter_conversion.py
tests/test_parameter_record_authoring.py
tests/test_parameter_resolution_contract.py
tests/test_parameters.py
tests/test_pet_substrate.py
tests/test_phase1_documentation_sync.py
tests/test_pre_bio001_stoichiometry_and_assembly.py
tests/test_process_assembly.py
tests/test_process_factory_library.py
tests/test_product_inhibition_examples.py
tests/test_product_map_configs.py
tests/test_provenance_backed_inhibition_laws.py
tests/test_provenance_backed_transglycosylation.py
tests/test_quality_config.py
tests/test_reaction_diffusion.py
tests/test_reaction_diffusion_nd.py
tests/test_reaction_engine.py
tests/test_registry_based_loading.py
tests/test_registry_case_builder.py
tests/test_registry_case_templates.py
tests/test_registry_ensemble_homogeneous_mm.py
tests/test_registry_ensemble_simulation.py
tests/test_registry_loading.py
tests/test_registry_promotion_apply.py
tests/test_registry_promotion_plan.py
tests/test_registry_record_authoring.py
tests/test_registry_resolver.py
tests/test_release_configuration.py
tests/test_release_notebooks.py
tests/test_repository_hygiene.py
tests/test_results.py
tests/test_roadmap_orchestration_status.py
tests/test_sabiork_discovery_workflow.py
tests/test_sabiork_fetch_script.py
tests/test_sabiork_parser.py
tests/test_sabiork_reaction_618_notebook.py
tests/test_sabiork_reaction_618_parameter_ranges.py
tests/test_sabiork_reaction_618_registry_case.py
tests/test_sabiork_source_adapter.py
tests/test_simulation_record.py
tests/test_source_provider_api.py
tests/test_static_balance_thermodynamic_validators.py
tests/test_stoichiometry_thermodynamics.py
tests/test_surface_pet.py
tests/test_synthetic_dataset_generation.py
tests/test_transglycosylation_process.py
tests/test_uncertainty_sensitivity.py
tests/test_units.py
tests/test_universal_substrates.py
tests/test_value_spec.py
tests/test_virtual_experiment_api.py
tests/test_virtual_experiment_environment_grid.py
tests/test_virtual_experiment_name_resolution.py