GillesPy2 1.6.5 cannot read some SBML files

[jonrkarr]

This appears to be a new regression in 1.6.5. This issue was not present in 1.6.4 and earlier. Other tools such as COPASI, tellurium, and VCell are able to read such files.

Detected in biosimulators/Biosimulators#458.

Example: model_ODE_stochastic.xml

Steps to reproduce

import gillespy2
gillespy2.import_SBML('model_ODE_stochastic.xml')

Error

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/usr/local/lib/python3.9/dist-packages/gillespy2/core/parameter.py in _evaluate(self, namespace)
     82         try:
---> 83             self.value = (float(eval(self.expression, namespace)))
     84         except Exception as error:

<string> in <module>

NameError: name 'nan' is not defined

The above exception was the direct cause of the following exception:

ParameterError                            Traceback (most recent call last)
<ipython-input-2-11e49c19eadd> in <module>
----> 1 gillespy2.import_SBML('../Biosimulators_test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/model_ODE_stochastic.xml')

/usr/local/lib/python3.9/dist-packages/gillespy2/core/model.py in import_SBML(filename, name, gillespy_model)
     61         raise ImportError('SBML conversion not imported successfully')
     62 
---> 63     return convert(filename, model_name=name, gillespy_model=gillespy_model)
     64 
     65 

/usr/local/lib/python3.9/dist-packages/gillespy2/sbml/SBMLimport.py in convert(filename, model_name, gillespy_model)
    393 
    394     __get_function_definitions(sbml_model, gillespy_model)
--> 395     __get_parameters(sbml_model, gillespy_model)
    396     __get_species(sbml_model, gillespy_model, errors)
    397     __get_compartments(sbml_model, gillespy_model)

/usr/local/lib/python3.9/dist-packages/gillespy2/sbml/SBMLimport.py in __get_parameters(sbml_model, gillespy_model)
    132         if parameter.isSetConstant():
    133             gillespy_parameter = gillespy2.Parameter(name=name, expression=value)
--> 134             gillespy_model.add_parameter([gillespy_parameter])
    135         else:
    136             gillespy_species = gillespy2.Species(name=name,initial_value=value)

/usr/local/lib/python3.9/dist-packages/gillespy2/core/model.py in add_parameter(self, params)
    415         if isinstance(params, list):
    416             for p in sorted(params):
--> 417                 self.add_parameter(p)
    418         else:
    419             if isinstance(params, Parameter) or type(params).__name__ == 'Parameter':

/usr/local/lib/python3.9/dist-packages/gillespy2/core/model.py in add_parameter(self, params)
    422                     raise problem
    423                 self.update_namespace()
--> 424                 params._evaluate(self.namespace)
    425                 self.listOfParameters[params.name] = params
    426                 self._listOfParameters[params.name] = 'P{}'.format(len(self._listOfParameters))

/usr/local/lib/python3.9/dist-packages/gillespy2/core/parameter.py in _evaluate(self, namespace)
     83             self.value = (float(eval(self.expression, namespace)))
     84         except Exception as error:
---> 85             raise ParameterError("Could not evaluate expression: {}.".format(str(error))) from error
     86 
     87     def sanitized_expression(self, species_mappings, parameter_mappings):

ParameterError: Could not evaluate expression: name 'nan' is not defined.

Environment

• GillesPy2 1.6.5
• libSBML 5.19.2 (the same problem also occurs with 5.19.0)
• Python: 3.9.5
• OS: Ubuntu 20