Fixed species bug if named S0 or S1

for_local_use.py

@@ -2,11 +2,16 @@
 import matplotlib.pyplot as plt
 import os
 import basico
+import pint
 
 
 if __name__ == '__main__':
 
-    pass
+    _S0 = BaseSpecies()
 
+    _S0 >> Zero [1]
+
+    S = Simulation(_S0)
+    print(S.compile())
 
 

mobspy/modules/compiler.py

@@ -305,10 +305,10 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
         if continuous_sim:
             end_event = {'trigger': ending_condition.generate_string(orthogonal_vector_structure),
                          'delay': '0',
-                         'assignments': [('End_Flag_MetaSpecies', '1')]}
+                         'assignments': [('_End_Flag_MetaSpecies', '1')]}
 
-            reactions_for_sbml['phantom_reaction_end'] = {'re': [(10, 'End_Flag_MetaSpecies')], 'pr': [],
-                                                          'kin': 'End_Flag_MetaSpecies * 1e-100'}
+            reactions_for_sbml['phantom_reaction_end'] = {'re': [(10, '_End_Flag_MetaSpecies')], 'pr': [],
+                                                          'kin': '_End_Flag_MetaSpecies * 1e-100'}
             events_for_sbml['end_event'] = end_event
 
         set_to_double_parameter = \

mobspy/modules/meta_class.py

@@ -339,7 +339,7 @@ def __init__(self, object_reference, characteristics, stoichiometry=1, label=Non
             :param label: (int, float, str) value for the label for matching used in this reaction
         """
         super(Reacting_Species, self).__init__()
-        if object_reference.get_name() == 'S0' and characteristics == set():
+        if object_reference.get_name() == '_S0' and characteristics == set():
             self.list_of_reactants = []
         else:
             self.list_of_reactants = [{'object': object_reference, 'characteristics': characteristics,
@@ -1062,7 +1062,7 @@ def __init__(self, name):
             :param name: (str) Name of the species (can be placeholder if named with N$)
         """
         super(Species, self).__init__()
-        self._name = name
+        self.name(name)
         self._characteristics = set()
         self._references = {self}
         self._ordered_references = []
@@ -1088,6 +1088,13 @@ def name(self, name):
 
             :param name: (str) name of the species
         """
+        if '_' == name[0]:
+            simlog_error(f"In species  name {name}: Species cannot have a name starting with underscore")
+
+        name = clean_species_name(name)
+        self._name = name
+
+    def _bypass_name(self, name):
         name = clean_species_name(name)
         self._name = name
 
@@ -1255,7 +1262,7 @@ def _Create_Species(species, code_line, number_or_names=None):
         if species is None:
             to_return.append(Species(name))
         else:
-            temp = __S1 * species
+            temp = One * species
             temp.name(name)
             to_return.append(temp)
 
@@ -1292,12 +1299,10 @@ def New(species, number_or_names=None):
     return _Create_Species(species, code_line, number_or_names)
 
 
-__S0, __S1, __SF = BaseSpecies(3)
-__S0.name('S0')
-__S1.name('S1')
-__SF.name('End_Flag_MetaSpecies')
-EndFlagSpecies = __SF
-Zero = __S0
+Zero, One, EndFlagSpecies = BaseSpecies(3)
+Zero._bypass_name('_S0')
+One._bypass_name('_S1')
+EndFlagSpecies._bypass_name('_End_Flag_MetaSpecies')
 _methods_Species = set(dir(Species))
 
 if __name__ == '__main__':

mobspy/sbml_simulator/run.py

@@ -67,7 +67,7 @@ def __single_run(packed):
                 reformatted_data = reformat_time_series(data)
 
                 if sim_par['_continuous_simulation']:
-                    if reformatted_data['End_Flag_MetaSpecies'][-1] > 0:
+                    if reformatted_data['_End_Flag_MetaSpecies'][-1] > 0:
                         reformatted_data = __filter_condition_event_time_data(reformatted_data)
                         end_condition_not_satisfied = False
                     else:
@@ -144,7 +144,7 @@ def __filter_condition_event_time_data(data):
     """
     new_data = {}
 
-    for i, e in enumerate(data['End_Flag_MetaSpecies']):
+    for i, e in enumerate(data['_End_Flag_MetaSpecies']):
         if e == 1:
             stop_index = i
             break
@@ -186,7 +186,7 @@ def __sbml_new_initial_values(data, model, sim_para, new_model=False):
 
     if new_model:
         try:
-            species_for_sbml['End_Flag_MetaSpecies'] = 0
+            species_for_sbml['_End_Flag_MetaSpecies'] = 0
         except KeyError:
             pass
 

test_script.py

@@ -1823,6 +1823,17 @@ def test_assignment_similar_species():
     assert compare_model(S.compile(), 'test_tools/model_55.txt')
 
 
+def test_blocked_names():
+
+    try:
+        _S0 = BaseSpecies()
+
+        _S0 >> Zero[1]
+        assert False
+    except SystemExit:
+        assert True
+
+
 # This is here because pytest is slow - but this script works fine with pytest. Just make sure that the
 # python version in terminal is above 3.10
 test_list = [test_model_1, test_model_2, test_model_3, test_model_4, test_model_5, test_model_6, test_model_7,
@@ -1851,7 +1862,7 @@ def test_assignment_similar_species():
              test_illegal_unit_op_in_assignment, test_all_asgn_ops, test_no_species_in_asg, text_complex_assignments,
              text_assign_context_exit, text_even_more_complex_assignments, test_assign_context_complex,
              test_assign_context_constant, test_duration_with_run, test_rev, test_dimensionless_count,
-             test_assignment_similar_species]
+             test_assignment_similar_species, test_blocked_names]
 
 sub_test = test_list