Fix SbmlModel.get_free_parameter_ids_with_values to handle InitialA… (

#248)

So far, `SbmlModel.get_free_parameter_ids_with_values` ignored InitialAssignments,
resulting in incorrect parameter values in the parameter mapping.

Now the correct values are used in case of initial assignments that are parameter-independent, and parameters with other initial assignments are ignored.

petab/models/sbml_model.py

@@ -5,6 +5,7 @@
 from typing import Iterable, Optional, Tuple
 
 import libsbml
+import sympy as sp
 
 from ..sbml import (
  get_sbml_model,
@@ -103,10 +104,41 @@ def get_free_parameter_ids_with_values(
  ar.getVariable() for ar in self.sbml_model.getListOfRules()
  }
 
+ parser_settings = libsbml.L3ParserSettings(
+ self.sbml_model,
+ libsbml.L3P_PARSE_LOG_AS_LOG10,
+ libsbml.L3P_EXPAND_UNARY_MINUS,
+ libsbml.L3P_NO_UNITS,
+ libsbml.L3P_AVOGADRO_IS_CSYMBOL,
+ libsbml.L3P_COMPARE_BUILTINS_CASE_INSENSITIVE,
+ None,
+ libsbml.L3P_MODULO_IS_PIECEWISE,
+ )
+
+ def get_initial(p):
+ # return the initial assignment value if there is one, and it is a
+ # number; `None`, if there is a non-numeric initial assignment;
+ # otherwise, the parameter value
+ if ia := self.sbml_model.getInitialAssignmentBySymbol(p.getId()):
+ formula_str = libsbml.formulaToL3StringWithSettings(
+ ia.getMath(), parser_settings
+ )
+ try:
+ return float(formula_str)
+ except ValueError:
+ sym_expr = sp.sympify(formula_str)
+ return (
+ float(sym_expr.evalf())
+ if sym_expr.evalf().is_Number
+ else None
+ )
+ return p.getValue()
+
  return (
- (p.getId(), p.getValue())
+ (p.getId(), initial)
  for p in self.sbml_model.getListOfParameters()
  if p.getId() not in rule_targets
+ and (initial := get_initial(p)) is not None
  )
 
  def get_parameter_ids(self) -> Iterable[str]: