Fixed parameter bug in initial values and with reaction expressions. Version 2.6.0

Author: fabriciocravo

debugging_script.py

@@ -34,7 +34,7 @@
              test_update_parameter_for_multi_model, test_update_parameter_through_str,
              test_update_multiple_parameters_in_expression, test_update_parameter_with_unit,
              test_species_value_modification, test_all_value_modification, test_new_reversible_reaction_notation,
-             test_2D_reaction_with_units]
+             test_2D_reaction_with_units, test_parameters_as_initial_values, test_parameters_in_lambda_expression]
 
 # test_no_species_in_asg
 # test_illegal_unit_op_in_assignment

docs/example_models/journal_models/PySB_Comparison.py

@@ -3,8 +3,9 @@
 L, R = BaseSpecies()
 
 L_0, R_0, kf, kr = ModelParameters(100, 200, 1e-3, 1e-3)
-Rev[ L.sl_0(L_0) + R.sr_0(R_0) >> L.sl_1 + R.sr_1 ]  [kf, lambda r: kr*r]
+L.sl_0 + R.sr_0 >> L.sl_1 + R.sr_1 [kf, lambda r: kr*r]
 
+L(L_0), R(R_0)
 S = Simulation(L | R)
 print(S.compile())
 

for_local_use.py

@@ -3,4 +3,13 @@
 
 if __name__ == '__main__':
 
-    pass
+    L, R = BaseSpecies()
+
+    kf, kr = ModelParameters(1e-3, 1e-3)
+    L.sl_0 + R.sr_0 >> L.sl_1 + R.sr_1[kf, lambda r: kr * r]
+
+    S = Simulation(L | R)
+    print(S.compile())
+
+
+

mobspy/_version.py

@@ -1 +1 @@
-__version__ = "2.5.1"
+__version__ = "2.6.0"

mobspy/modules/compiler.py

@@ -38,6 +38,7 @@ def add_to_parameters_to_sbml(cls, parameters_used, parameters_for_sbml, paramet
             except:
                 parameters_for_sbml[parameter.name] = (parameter.value, f'dimensionless')
 
+
     @classmethod
     def override_get_item(cls, object_to_return, item):
         """
@@ -169,6 +170,7 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
 
         # Check volume:
         volume = uh_convert_volume(volume, dimension)
+        parameters_for_sbml = {'volume': (volume, f'dimensionless')}
 
         # Add the flag species used for verifying if the simulation is over
         if continuous_sim:
@@ -183,6 +185,7 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
 
         # Assignments with all do not take priority
         # This allows specific assignments to override All assignments
+        # I should encapsulate this, to make my life easier lol
         assigned_species = []
         parameters_in_counts = set()
         for count in species_counts:
@@ -245,6 +248,8 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
                 species_for_sbml[species_string] = temp_count
                 assigned_species.append(species_string)
 
+        cls.add_to_parameters_to_sbml(parameters_used, parameters_for_sbml, parameters_in_counts)
+
         # BaseSpecies reactions for SBML with theirs respective parameters and rates
         # What do I have so far
         # Species_String_Dict and a set of reaction objects in Reactions_Set
@@ -256,7 +261,6 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
                                                                              parameter_exist, parameters_in_reaction,
                                                                              skip_expression_check)
 
-        parameters_for_sbml = {'volume': (volume, f'dimensionless')}
         cls.add_to_parameters_to_sbml(parameters_used, parameters_for_sbml, parameters_in_reaction)
 
         # O(n^2) reaction check for doubles

mobspy/modules/function_rate_code.py

@@ -82,11 +82,13 @@ def extract_reaction_rate(combination_of_reactant_species, reactant_string_list
             if parameter_exist:
                 parameters_in_reaction = search_for_parameters_in_str(reaction_rate_string,
                                                                       parameter_exist, parameters_in_reaction)
+
         elif isinstance(rate, mbe_MobsPyExpression):
 
             # Having an expression variable implies it is a constructed expression - not mass action
             if len(rate._expression_variables) > 0:
                 reaction_rate_string, _ = rate.generate_string_operation(skip_check=skip_check, dimension=dimension)
+                parameters_in_reaction = parameters_in_reaction.union(rate._parameter_set)
 
             # Having no expression variables implies it is a constant for mass - action kinetics.
             elif len(rate._expression_variables) == 0:

test_script.py

@@ -2092,3 +2092,27 @@ def test_2D_reaction_with_units():
     S.level = -1
     S.volume = 1 * u.m ** 2
     assert compare_model(S.compile(), 'test_tools/model_64.txt')
+
+
+def test_parameters_as_initial_values():
+
+    L, R = BaseSpecies()
+
+    L_0, R_0 = ModelParameters(100, 200)
+
+    L(L_0), R(R_0)
+    S = Simulation(L | R)
+    S.level = -1
+    assert compare_model(S.compile(), 'test_tools/model_65.txt')
+
+
+def test_parameters_in_lambda_expression():
+    L, R = BaseSpecies()
+
+    kf, kr = ModelParameters(1e-3, 1e-3)
+    L.sl_0 + R.sr_0 >> L.sl_1 + R.sr_1[kf, lambda r: kr * r]
+
+    S = Simulation(L | R)
+    S.level = -1
+    assert compare_model(S.compile(), 'test_tools/model_66.txt')
+

test_tools/model_65.txt

@@ -0,0 +1,17 @@
+
+Species
+L,L_0
+R,R_0
+
+Mappings
+L :
+L
+R :
+R
+
+Parameters
+L_0,100
+R_0,200
+volume,1
+
+Reactions

test_tools/model_66.txt

@@ -0,0 +1,24 @@
+
+Species
+L.sl_0,0
+L.sl_1,0
+R.sr_0,0
+R.sr_1,0
+
+Mappings
+L :
+L.sl_0
+L.sl_1
+R :
+R.sr_0
+R.sr_1
+
+Parameters
+kf,0.001
+kr,0.001
+volume,1
+
+Reactions
+reaction_0,{'re': [(1, 'L.sl_0'), (1, 'R.sr_0')], 'pr': [(1, 'L.sl_1'), (1, 'R.sr_1')], 'kin': 'L.sl_0 * R.sr_0 * kf * volume^-1'}
+reaction_1,{'re': [(1, 'L.sl_1'), (1, 'R.sr_1')], 'pr': [(1, 'L.sl_0'), (1, 'R.sr_0')], 'kin': '(kr*L.sl_1)'}
+