LICENSE
README.md
pyproject.toml
src/checks/__init__.py
src/emulators/__init__.py
src/generators/__init__.py
src/libcuflynx/__init__.py
src/libcuflynx/_deprecated_aliases.py
src/libcuflynx.egg-info/PKG-INFO
src/libcuflynx.egg-info/SOURCES.txt
src/libcuflynx.egg-info/dependency_links.txt
src/libcuflynx.egg-info/entry_points.txt
src/libcuflynx.egg-info/requires.txt
src/libcuflynx.egg-info/top_level.txt
src/libcuflynx/checks/LumpedModelChecks.py
src/libcuflynx/checks/__init__.py
src/libcuflynx/coupler/__init__.py
src/libcuflynx/emulators/__init__.py
src/libcuflynx/emulators/emulator_bundle.py
src/libcuflynx/emulators/emulator_trainer.py
src/libcuflynx/funcs/__init__.py
src/libcuflynx/funcs/cost_funcs_user.py
src/libcuflynx/funcs/modifier_funcs_user.py
src/libcuflynx/funcs/operation_funcs_user.py
src/libcuflynx/generators/CVSCellMLGenerator.py
src/libcuflynx/generators/CVSCppGenerator.py
src/libcuflynx/generators/Python1DModelFilesGenerator.py
src/libcuflynx/generators/PythonGenerator.py
src/libcuflynx/generators/__init__.py
src/libcuflynx/generators/cppGeneratorTemplateFunctions.cpp
src/libcuflynx/generators/main0dTemplate.cpp
src/libcuflynx/generators/resources/BG_modules.cellml
src/libcuflynx/generators/resources/BG_modules_config.json
src/libcuflynx/generators/resources/FitzHugh_Nagumo_module_config.json
src/libcuflynx/generators/resources/FitzHugh_Nagumo_modules.cellml
src/libcuflynx/generators/resources/Lotka_Volterra_module_config.json
src/libcuflynx/generators/resources/Lotka_Volterra_modules.cellml
src/libcuflynx/generators/resources/TwoMinima_module_config.json
src/libcuflynx/generators/resources/TwoMinima_modules.cellml
src/libcuflynx/generators/resources/VanDerPol_module_config.json
src/libcuflynx/generators/resources/VanDerPol_modules.cellml
src/libcuflynx/generators/resources/base_script.cellml
src/libcuflynx/generators/resources/boundary_condition_modules.cellml
src/libcuflynx/generators/resources/boundary_condition_modules_config.json
src/libcuflynx/generators/resources/cell_modules.cellml
src/libcuflynx/generators/resources/cell_modules_config.json
src/libcuflynx/generators/resources/control_modules.cellml
src/libcuflynx/generators/resources/control_modules_config.json
src/libcuflynx/generators/resources/control_system_modules.cellml
src/libcuflynx/generators/resources/control_system_modules_config.json
src/libcuflynx/generators/resources/coupling_modules.cellml
src/libcuflynx/generators/resources/coupling_modules_config.json
src/libcuflynx/generators/resources/delay_modules.cellml
src/libcuflynx/generators/resources/delay_modules_config.json
src/libcuflynx/generators/resources/diffusion_volume_modules.cellml
src/libcuflynx/generators/resources/diffusion_volume_modules_config.json
src/libcuflynx/generators/resources/elic_modules.cellml
src/libcuflynx/generators/resources/elic_modules_config.json
src/libcuflynx/generators/resources/gas_exchange_modules.cellml
src/libcuflynx/generators/resources/gas_exchange_modules_config.json
src/libcuflynx/generators/resources/heart_modules.cellml
src/libcuflynx/generators/resources/heart_modules_config.json
src/libcuflynx/generators/resources/input_stimulation_modules.cellml
src/libcuflynx/generators/resources/input_stimulation_modules_config.json
src/libcuflynx/generators/resources/ion_channel_modules.cellml
src/libcuflynx/generators/resources/ion_channel_modules_config.json
src/libcuflynx/generators/resources/lung_modules.cellml
src/libcuflynx/generators/resources/lung_modules_config.json
src/libcuflynx/generators/resources/open_loop_modules.cellml
src/libcuflynx/generators/resources/open_loop_modules_config.json
src/libcuflynx/generators/resources/parasympathetic_modules.cellml
src/libcuflynx/generators/resources/parasympathetic_modules_config.json
src/libcuflynx/generators/resources/test_modules.cellml
src/libcuflynx/generators/resources/test_modules_config.json
src/libcuflynx/generators/resources/units.cellml
src/libcuflynx/generators/resources/vessel_properties_modules.cellml
src/libcuflynx/generators/resources/vessel_properties_modules_config.json
src/libcuflynx/identifiabilty_analysis/__init__.py
src/libcuflynx/identifiabilty_analysis/identifiabilityAnalysis.py
src/libcuflynx/models/LumpedModels.py
src/libcuflynx/models/__init__.py
src/libcuflynx/param_id/__init__.py
src/libcuflynx/param_id/aadc_backend.py
src/libcuflynx/param_id/casadi_backend.py
src/libcuflynx/param_id/cost_kwargs.py
src/libcuflynx/param_id/differentiable.py
src/libcuflynx/param_id/external_funcs.py
src/libcuflynx/param_id/fd_backend.py
src/libcuflynx/param_id/fsa_backend.py
src/libcuflynx/param_id/math_backend.py
src/libcuflynx/param_id/modifier_funcs.py
src/libcuflynx/param_id/operation_funcs.py
src/libcuflynx/param_id/optimisers.py
src/libcuflynx/param_id/paramID.py
src/libcuflynx/param_id/plot_outputs.py
src/libcuflynx/param_id/pymc_backend.py
src/libcuflynx/param_id/run_history.py
src/libcuflynx/parsers/ModelParsers.py
src/libcuflynx/parsers/OMEXParsers.py
src/libcuflynx/parsers/PrimitiveParsers.py
src/libcuflynx/parsers/__init__.py
src/libcuflynx/protocol_runners/__init__.py
src/libcuflynx/protocol_runners/protocol_executor.py
src/libcuflynx/protocol_runners/protocol_runner.py
src/libcuflynx/scripts/__init__.py
src/libcuflynx/scripts/_cli.py
src/libcuflynx/scripts/convert_0d_to_1d.py
src/libcuflynx/scripts/example_format_obs_data_json_file.py
src/libcuflynx/scripts/generate_modules_files.py
src/libcuflynx/scripts/generate_obs_json.py
src/libcuflynx/scripts/generate_omex_analysis_script.py
src/libcuflynx/scripts/heart_paper_plots.py
src/libcuflynx/scripts/identifiability_run_script.py
src/libcuflynx/scripts/param_id_run_script.py
src/libcuflynx/scripts/plot_param_id_script.py
src/libcuflynx/scripts/read_and_insert_parameters.py
src/libcuflynx/scripts/run_multiple_param_id.py
src/libcuflynx/scripts/script_generate_with_new_architecture.py
src/libcuflynx/scripts/sensitivity_analysis_run_script.py
src/libcuflynx/scripts/sequential_param_id_run_script.py
src/libcuflynx/scripts/train_emulator_run_script.py
src/libcuflynx/scripts/example_data/example_data_for_conversion.csv
src/libcuflynx/sensitivity_analysis/__init__.py
src/libcuflynx/sensitivity_analysis/sensitivityAnalysis.py
src/libcuflynx/sensitivity_analysis/sobolSA.py
src/libcuflynx/solver1d/__init__.py
src/libcuflynx/solver1d/auxCouplingFunctions.py
src/libcuflynx/solver1d/auxPipeFunctions.py
src/libcuflynx/solver1d/bcs.py
src/libcuflynx/solver1d/main1D.py
src/libcuflynx/solver1d/model.py
src/libcuflynx/solver1d/numerics.py
src/libcuflynx/solver1d/vessel.py
src/libcuflynx/solver1d/windkessel.py
src/libcuflynx/solver1d/Make_files/Makefile
src/libcuflynx/solver1d/Make_files/MakefilePETSC
src/libcuflynx/solver1d/Make_files/runCVODE.bash
src/libcuflynx/solver1d/Make_files/runPETSc.bash
src/libcuflynx/solver_wrappers/__init__.py
src/libcuflynx/solver_wrappers/aadc_python_solver_helper.py
src/libcuflynx/solver_wrappers/casadi_python_solver_helper.py
src/libcuflynx/solver_wrappers/emulator_solver_helper.py
src/libcuflynx/solver_wrappers/external_simulation_helper.py
src/libcuflynx/solver_wrappers/myokit_helper.py
src/libcuflynx/solver_wrappers/name_resolver.py
src/libcuflynx/solver_wrappers/opencor_helper.py
src/libcuflynx/solver_wrappers/param_grouping.py
src/libcuflynx/solver_wrappers/python_solver_helper.py
src/libcuflynx/utilities/__init__.py
src/libcuflynx/utilities/casadi_solver_diagnostics.py
src/libcuflynx/utilities/diagnostics.py
src/libcuflynx/utilities/elic_run.py
src/libcuflynx/utilities/libcellml_helper_funcs.py
src/libcuflynx/utilities/libcellml_utilities.py
src/libcuflynx/utilities/mpi_utils.py
src/libcuflynx/utilities/obs_data_helpers.py
src/libcuflynx/utilities/package_resources.py
src/libcuflynx/utilities/paperPlotSetup.py
src/libcuflynx/utilities/params_for_id_helpers.py
src/libcuflynx/utilities/paths.py
src/libcuflynx/utilities/plot_generated_model_outputs.py
src/libcuflynx/utilities/protocol_funcs.py
src/libcuflynx/utilities/protocol_shapes.py
src/libcuflynx/utilities/stat_distributions.py
src/libcuflynx/utilities/utility_funcs.py
src/models/__init__.py
src/param_id/__init__.py
src/parsers/__init__.py
src/protocol_runners/__init__.py
src/scripts/__init__.py
src/sensitivity_analysis/__init__.py
src/solver_wrappers/__init__.py
src/utilities/__init__.py
tests/test_UQ.py
tests/test_aadc_conditionals.py
tests/test_aadc_coupled_pipeline.py
tests/test_aadc_solvers.py
tests/test_aadc_vs_casadi_3compartment.py
tests/test_autogeneration.py
tests/test_backend_import_errors.py
tests/test_benchmarks.py
tests/test_casadi_conditionals.py
tests/test_cellml_connection_uniqueness.py
tests/test_collect_only_no_summary_wait.py
tests/test_console_entry_points.py
tests/test_cost_kwargs.py
tests/test_cost_weight_indexing.py
tests/test_csv_header_parsing.py
tests/test_dependency_extras.py
tests/test_deprecated_flat_imports.py
tests/test_distribution_ground_truth.py
tests/test_docs_consistency.py
tests/test_emulator_settings.py
tests/test_emulator_solver_helper.py
tests/test_emulator_training.py
tests/test_error_vector_names.py
tests/test_external_simulation_helper.py
tests/test_external_user_funcs.py
tests/test_fd_observable_sensitivities.py
tests/test_flattened_cellml_naming.py
tests/test_fsa_analytic_accuracy.py
tests/test_fsa_grouped_sensitivities.py
tests/test_ga_objective_and_selection.py
tests/test_ga_population.py
tests/test_generate_modules_files.py
tests/test_grouped_params.py
tests/test_heat_fenics_example.py
tests/test_issue_fixes.py
tests/test_laplace_identifiability.py
tests/test_libcellml_shims.py
tests/test_manual_marker.py
tests/test_mcmc_chain_checkpoints.py
tests/test_mcmc_statistics.py
tests/test_modifier_backend_equivalence.py
tests/test_modifier_funcs.py
tests/test_mpi_utils.py
tests/test_myokit_import_race.py
tests/test_myokit_import_race_live.py
tests/test_next_sub_release_asks.py
tests/test_no_writes_into_package.py
tests/test_obs_data_conventions.py
tests/test_omex_analysis_pipeline.py
tests/test_operation_kwargs.py
tests/test_package_resources.py
tests/test_package_syntax.py
tests/test_param_id.py
tests/test_param_id_model_type.py
tests/test_param_modifiers.py
tests/test_param_priors.py
tests/test_params_for_id_json.py
tests/test_protocol_funcs.py
tests/test_protocol_shapes.py
tests/test_protocol_state_continuity.py
tests/test_release_workflow.py
tests/test_scipy_ode_example.py
tests/test_sensitivity_analysis.py
tests/test_solver_info_validation.py
tests/test_solvers.py
tests/test_tmpdir_independence.py
tests/test_unit_conversion.py
tests/test_uq_cost_funcs.py
tests/test_uq_diagnostics.py
tests/test_uq_equal_weights.py
tests/test_uq_on_emulator.py
tests/test_uq_posterior_plots.py
tests/test_uq_pymc_backend.py
tests/test_uq_pymc_live_chain.py
tests/test_uq_pymc_mpi.py
tests/test_user_inputs_archive.py