Closed jonrkarr closed 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.
Issue realized through discussion with @eagmon
This should be added to
biosimulators_utils.sedml.model_utils.get_parameters_variables_outputs_for_simulation
.