CHANGELOG.md
CONTRIBUTORS.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
pybnf/__init__.py
pybnf/__main__.py
pybnf/_bngsim_caps.py
pybnf/_bngsim_failure.py
pybnf/_seed.py
pybnf/analytical_model.py
pybnf/bngsim_antimony_model.py
pybnf/bngsim_sbml_model.py
pybnf/budget.py
pybnf/cluster.py
pybnf/config.py
pybnf/config_schema.py
pybnf/constraint.py
pybnf/data.py
pybnf/diagnostics.py
pybnf/edition.py
pybnf/inference_data.py
pybnf/objective.py
pybnf/parse.py
pybnf/printing.py
pybnf/pset.py
pybnf/pybnf.py
pybnf/registry.py
pybnf/sbml_runner.py
pybnf.egg-info/PKG-INFO
pybnf.egg-info/SOURCES.txt
pybnf.egg-info/dependency_links.txt
pybnf.egg-info/entry_points.txt
pybnf.egg-info/requires.txt
pybnf.egg-info/top_level.txt
pybnf/algorithms/__init__.py
pybnf/algorithms/base.py
pybnf/algorithms/core.py
pybnf/algorithms/model_check.py
pybnf/algorithms/optimizers/__init__.py
pybnf/algorithms/optimizers/cmaes.py
pybnf/algorithms/optimizers/concurrent_multistart.py
pybnf/algorithms/optimizers/differential_evolution.py
pybnf/algorithms/optimizers/gntr.py
pybnf/algorithms/optimizers/gradient_base.py
pybnf/algorithms/optimizers/lbfgs.py
pybnf/algorithms/optimizers/local_base.py
pybnf/algorithms/optimizers/local_multistart.py
pybnf/algorithms/optimizers/multistart.py
pybnf/algorithms/optimizers/particle_swarm.py
pybnf/algorithms/optimizers/powell.py
pybnf/algorithms/optimizers/profile_likelihood.py
pybnf/algorithms/optimizers/scatter_search.py
pybnf/algorithms/optimizers/simplex.py
pybnf/algorithms/optimizers/simulated_annealing.py
pybnf/algorithms/optimizers/trf.py
pybnf/algorithms/samplers/__init__.py
pybnf/algorithms/samplers/adaptive_mcmc.py
pybnf/algorithms/samplers/base.py
pybnf/algorithms/samplers/basic_mcmc.py
pybnf/algorithms/samplers/dream.py
pybnf/algorithms/samplers/hmc.py
pybnf/algorithms/samplers/pdream.py
pybnf/bngsim_model/__init__.py
pybnf/bngsim_model/_runtime.py
pybnf/bngsim_model/classification.py
pybnf/bngsim_model/expressions.py
pybnf/bngsim_model/net_model.py
pybnf/bngsim_model/nf_model.py
pybnf/bngsim_model/output.py
pybnf/bngsim_model/parsing.py
pybnf/bngsim_model/scan.py
pybnf/gradient/__init__.py
pybnf/gradient/assembly.py
pybnf/gradient/derivative.py
pybnf/gradient/errors.py
pybnf/gradient/routing.py
pybnf/measurement/__init__.py
pybnf/measurement/base.py
pybnf/noise/__init__.py
pybnf/noise/base.py
pybnf/noise/gaussian.py
pybnf/noise/laplace.py
pybnf/noise/location.py
pybnf/noise/negative_binomial.py
pybnf/noise/scale.py
pybnf/noise/source.py
pybnf/noise/student_t.py
pybnf/petab/__init__.py
pybnf/petab/_bngl.py
pybnf/petab/_measurement_params.py
pybnf/petab/_sbml.py
pybnf/petab/_tsv.py
pybnf/petab/bngl_model.py
pybnf/petab/conditions.py
pybnf/petab/convert.py
pybnf/petab/export.py
pybnf/petab/formula.py
pybnf/petab/import_.py
pybnf/petab/measurements.py
pybnf/petab/observables.py
pybnf/petab/parameters.py
pybnf/priors/__init__.py
pybnf/priors/base.py
pybnf/priors/beta.py
pybnf/priors/bijector.py
pybnf/priors/cauchy.py
pybnf/priors/chisquare.py
pybnf/priors/exponential.py
pybnf/priors/gamma.py
pybnf/priors/gumbel.py
pybnf/priors/half_cauchy.py
pybnf/priors/half_normal.py
pybnf/priors/inv_gamma.py
pybnf/priors/laplace.py
pybnf/priors/logistic.py
pybnf/priors/normal.py
pybnf/priors/rayleigh.py
pybnf/priors/scale.py
pybnf/priors/student_t.py
pybnf/priors/truncated.py
pybnf/priors/uniform.py
pybnf/priors/weibull.py
tests/test_adaptive_mcmc.py
tests/test_analytical_bind_by_name.py
tests/test_analytical_model.py
tests/test_basic_mcmc_class.py
tests/test_bayes_mcmc.py
tests/test_bayesian_diagnostics.py
tests/test_benchmark_harness.py
tests/test_best_fit_bngl.py
tests/test_bngsim_action_expressions.py
tests/test_bngsim_antimony_bridge.py
tests/test_bngsim_bngl_e2e.py
tests/test_bngsim_bridge.py
tests/test_bngsim_capabilities.py
tests/test_bngsim_expressions.py
tests/test_bngsim_model.py
tests/test_bngsim_nf_e2e.py
tests/test_bngsim_output_sensitivities.py
tests/test_bngsim_parsing.py
tests/test_bngsim_protocol.py
tests/test_bngsim_runtime_seam.py
tests/test_bngsim_sbml_bridge.py
tests/test_bngsim_scan.py
tests/test_bngsim_ssa_replaces_rr.py
tests/test_callable_objective.py
tests/test_cluster.py
tests/test_config_class.py
tests/test_config_golden.py
tests/test_config_schema.py
tests/test_config_unused_keys.py
tests/test_constraint.py
tests/test_constraint_satisfaction.py
tests/test_dask_future_regression.py
tests/test_data_class.py
tests/test_diff_evolution.py
tests/test_distributions.py
tests/test_dream_class.py
tests/test_dream_config_surface.py
tests/test_edition.py
tests/test_emit_pruning.py
tests/test_experiment_constraints.py
tests/test_explicit_output_points.py
tests/test_expression_data_binding.py
tests/test_expression_objective.py
tests/test_failed_sim_handling.py
tests/test_freeparameter_class.py
tests/test_gradient_assembly.py
tests/test_gradient_derivative.py
tests/test_gradient_events.py
tests/test_gradient_optimizer.py
tests/test_gradient_routing.py
tests/test_gradient_runner.py
tests/test_gradient_sbml.py
tests/test_hmc.py
tests/test_inference_data.py
tests/test_job_class.py
tests/test_job_execution.py
tests/test_job_groups.py
tests/test_kalman_dream.py
tests/test_load_obj_func.py
tests/test_measurement_layer.py
tests/test_model_check.py
tests/test_model_class.py
tests/test_multitry_dream.py
tests/test_named_objective_target.py
tests/test_network_free_bngsim_supported.py
tests/test_new_era_validation.py
tests/test_noise_model_config.py
tests/test_notebooks.py
tests/test_objective_funcs.py
tests/test_objective_surface.py
tests/test_optimizer_integration.py
tests/test_packaging_metadata.py
tests/test_parse_class.py
tests/test_particle_swarm.py
tests/test_pdream_class.py
tests/test_petab_bngl_corpus.py
tests/test_petab_convert.py
tests/test_petab_export.py
tests/test_petab_formula.py
tests/test_petab_import.py
tests/test_petab_observables.py
tests/test_petab_parameters.py
tests/test_petab_sbml_layer.py
tests/test_petab_sbml_scanner.py
tests/test_powell_line_search.py
tests/test_preequilibration.py
tests/test_preequilibration_sbml.py
tests/test_printing.py
tests/test_priors.py
tests/test_profile_likelihood.py
tests/test_pset_class.py
tests/test_pybnf_cleanup.py
tests/test_pybnf_main_helpers.py
tests/test_random_seed.py
tests/test_real_world_examples.py
tests/test_recovery.py
tests/test_run_job.py
tests/test_run_loop.py
tests/test_sampler_integration.py
tests/test_sbml_model.py
tests/test_sbml_runner_reuse.py
tests/test_sbml_solver_tolerances.py
tests/test_scatter.py
tests/test_seed_determinism.py
tests/test_sim_registry.py
tests/test_simplex.py
tests/test_simplex_collinearity.py
tests/test_simulated_annealing.py
tests/test_steady_state_experiment.py
tests/test_stochastic_seed_policy.py
tests/test_subprocess_handling.py
tests/test_trajectory_class.py
tests/test_tutorial_am_diagnostics.py
tests/test_tutorial_bayesian.py
tests/test_tutorial_bayesian_priors.py
tests/test_tutorial_bootstrap.py
tests/test_tutorial_callable.py
tests/test_tutorial_estimate_noise.py
tests/test_tutorial_examples.py
tests/test_tutorial_hmc.py
tests/test_tutorial_lint_clinic.py
tests/test_tutorial_mcmc.py
tests/test_tutorial_model_selection.py
tests/test_tutorial_neg_bin_dynamic.py
tests/test_tutorial_pdream.py
tests/test_tutorial_petab.py
tests/test_tutorial_petab_import.py
tests/test_tutorial_petab_observable_formula.py
tests/test_tutorial_petab_protocols.py
tests/test_tutorial_prior_gallery.py
tests/test_tutorial_priors.py
tests/test_tutorial_resume.py
tests/test_tutorial_sbml_petab.py
tests/test_tutorial_state_dependent_noise.py
tests/test_wall_time_fit.py