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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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Add option to get model changes for `exec_sed_task` for SBML-FBC which support different changes than `exec_sed_doc` #67

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

Issue realized through discussion with @eagmon

This should be added to biosimulators_utils.sedml.model_utils.get_parameters_variables_outputs_for_simulation.

jonrkarr commented 3 years ago

Added change_level=biosimulators_utils.sedml.data_model.Task argument to get inputs for lower and upper bounds for reactions. This returns the default value of each bound, which is looked up from the value of the SBML parameter that each bound is associated to.

These task-level changes are analogous to the COBRApy API. In contrast, change_level=biosimulators_utils.sedml.data_model.SedDocument (default) supports changes that follow the SBML/SED-ML XML XPath conventions (where bounds have to changed through SBML parameters).

Will released with 0.1.133.

Note, biosimulators_utils.sedml.model_utils.get_parameters_variables_outputs_for_simulation passes along options for each model language. The documentation for these options is in the methods for each language (e.g., biosimulators_utils.model_lang.sbml.utils.get_parameters_variables_outputs_for_simulation).

Note, the online tool for generating SED-ML uses change_level=biosimulators_utils.sedml.data_model.SedDocument which follows the SBML/SED-ML conventions.