Unspecified initial states in PEtab conditions table default to SBML initial value

python/amici/petab_import.py

@@ -532,6 +532,13 @@ def import_model_sbml(
         if assignment is None:
             assignment = sbml_model.createInitialAssignment()
             assignment.setSymbol(assignee_id)
+        else:
+            logger.debug('The SBML model has an initial assignment defined '
+                         f'for model entity {assignee_id}, but this entity '
+                         'also has an initial value defined in the PEtab '
+                         'condition table. The SBML initial assignment will '
+                         'be overwritten to handle preequilibration and '
+                         'initial values specified by the PEtab problem.')
         formula = f'{PREEQ_INDICATOR_ID} * {init_par_id_preeq} ' \
                   f'+ (1 - {PREEQ_INDICATOR_ID}) * {init_par_id_sim}'
         math_ast = libsbml.parseL3Formula(formula)

python/amici/petab_objective.py

@@ -12,6 +12,7 @@
                     Collection, Iterator)
 
 import amici
+from amici.sbml_import import get_species_initial
 import libsbml
 import numpy as np
 import pandas as pd
@@ -343,6 +344,17 @@ def _set_initial_concentration(condition_id, species_id, init_par_id,
                                        par_map, scale_map):
             value = petab.to_float_if_float(
                 petab_problem.condition_df.loc[condition_id, species_id])
+            if pd.isna(value):
+                value = float(
+                    get_species_initial(
+                        petab_problem.sbml_model.getSpecies(species_id)
+                    )
+                )
+                logger.debug(f'The species {species_id} has no initial value '
+                             f'defined for the condition {condition_id} in '
+                             'the PEtab conditions table. The initial value is '
+                             f'now set to {value}, which is the initial value '
+                             'defined in the SBML model.')
             par_map[init_par_id] = value
             if isinstance(value, float):
                 # numeric initial state

python/amici/sbml_import.py

@@ -582,7 +582,7 @@ def _process_species_initial(self):
         Extract initial values and initial assignments from species
         """
         for species_variable in self.sbml.getListOfSpecies():
-            initial = _get_species_initial(species_variable)
+            initial = get_species_initial(species_variable)
 
             species_id = _get_identifier_symbol(species_variable)
             # If species_id is a target of an AssignmentRule, species will be
@@ -1798,7 +1798,7 @@ def _get_identifier_symbol(var: sbml.SBase) -> sp.Symbol:
     return symbol_with_assumptions(var.getId())
 
 
-def _get_species_initial(species: sbml.Species) -> sp.Expr:
+def get_species_initial(species: sbml.Species) -> sp.Expr:
     """
     Extract the initial concentration from a given species