Parse time course from actions in BNGL files

biosimulators / Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages

https://docs.biosimulators.org/Biosimulators_utils

MIT License

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Parse time course from actions in BNGL files #51

Open jonrkarr opened 3 years ago

jonrkarr commented 3 years ago

Place into biosimulators_utils.model_lang.bngl.utils

Can be done once RuleWorld/PyBioNetGen#10 is addressed.

[x] Time course settings
[x] Algorithm parameters e.g., seed

jonrkarr commented 3 years ago

Mostly done, except several minor issues need to be corrected in PyBioNetGen. In particular, the new version fails when no action is defined. See RuleWorld/PyBioNetGen#17. When this issue is closed, the required version of PyBioNetGen should be updated and the tests for this package should be updated (expected failure should be removed from test_get_parameters_variables_for_simulation_no_actions)