Integrate ODEs, SBML test suite, and other code from fall 2018 wc_sim branch

KarrLab / wc_sim

A multi-algorithmic simulator for whole-cell models

MIT License

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Integrate ODEs, SBML test suite, and other code from fall 2018 wc_sim branch #60

Closed artgoldberg closed 4 years ago

artgoldberg commented 4 years ago

done integrating:

submodels/odes.py
dynamic_components.py
message_types.py
model_utilities.py
multialgorithm_checkpointing.py
multialgorithm_errors.py
multialgorithm_simulation.py
run_results.py
simulation.py
species_populations.py

artgoldberg commented 4 years ago

Retain MassActionKinetics, verify_reactants_and_modifiers_compartment

artgoldberg commented 4 years ago

Also add dashed lines to verification plots so that both expected and actual are visible, as use in plot_expected_vs_simulated()

artgoldberg commented 4 years ago

done. record of old wc_sim saved in https://github.com/artgoldberg/wc_sim_fall_18