Merge pull request #8 from ROBACON/update_model_implementation

Update model implementation

Author: fabriciocravo

debugging_script.py

@@ -0,0 +1,55 @@
+from test_script import *
+
+# This is here because pytest is too slow - so it's a faster test that avoid the collection step.
+# Pytest is used in the GitHub while pushing
+# This script is oriented towards fast debugging and development
+# Also in the future, it might be nice to add an automated way to get the test names
+test_list = [test_model_1, test_model_2, test_model_3, test_model_4, test_model_5, test_model_6, test_model_7,
+             test_orthogonal_spaces, test_average_value, test_hybrid_sim, test_concatenated_simulation,
+             test_event_type, test_reacting_species_event, test_unit_event_test, test_reaction_deactivation,
+             test_double_rate, test_single_rate, test_triple_rate, test_stochastic_event_duration,
+             test_logic_operator_syntax, test_stack_position, test_empty_arguments,
+             test_conditional_between_meta_species, test_conditional_between_meta_species_2,
+             test_event_reaction_not_allowed, all_test, all_test_2, test_error_mult, test_set_counts,
+             test_bool_error, test_event_all, test_one_value_concatenation_sim, test_crash_after_modification,
+             test_unit_bi_dimension, test_bi_dimensional_rates, test_dimension_in_function_only,
+             test_multiple_simulation_counts, test_string_events_assignment, test_plotting,
+             test_volume_after_sim, test_parameters_with_sbml, test_shared_parameter_name,
+             test_set_counts_parameters, test_repeated_parameters, initial_expression_test,
+             test_wrong_dimension_error, test_more_than_used, zero_rate_test, test_wrong_rate,
+             test_conversion_outside, test_first_characteristic_in_reacting_species, test_model_reference,
+             test_sbml_generation, test_multi_sim_sbml, test_inline_comment,
+             test_with_statement_any_and_species_characteristics, test_with_statement_on_any_and_event,
+             test_matching_characteristic_rate, test_changes_after_compilation, test_proper_unit_context_exit,
+             test_run_args, test_unit_args, test_multi_parameters_in_run, test_output_concentration_in_multi_sim,
+             test_parameter_operation_in_rate, test_multi_parameter_with_expression, test_double_parameters_with_units,
+             test_parameters_with_units, test_convert_back_parameter,
+             test_numpy_in_expression_function, test_numpy_in_rates,
+             test_numpy_in_counts, test_numpy_in_set_counts, test_multi_methods_plot, test_unit_x_conversion,
+             test_Silicon_valley, test_replacing_species_name_in_expression, test_basic_assignment,
+             test_all_asgn_ops, 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_blocked_names, test_blocked_names_2,
+             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_no_species_in_asg
+# test_illegal_unit_op_in_assignment
+# temporary_test_removal = [test_parameter_fit_with_units, test_multiple_runs_fit, test_simple_fit]
+test_remov = [test_antimony_compose_model_gen, test_antimony_model]
+sub_test = test_list
+#sub_test = [test_antimony_compose_model_gen]
+def perform_tests():
+    any_failed = False
+    for test in sub_test:
+        try:
+            test()
+            print(f'Test {test} passed')
+        except:
+            print('\033[91m' + f'Test {test} failed' + '\033[0m', file=sys.stderr)
+            any_failed = True
+    if any_failed:
+        assert False
+perform_tests()

for_local_use.py

@@ -3,18 +3,26 @@
 
 if __name__ == '__main__':
 
+    # TODO: Ask Matthias about removed tests
+
+    # Replace parameters using units
+    A = BaseSpecies()
+    A.a1, A.a2
+    B = New(A)
+    B.b1, B.b2
     k1 = ModelParameters(1)
-    A, B, C, D = BaseSpecies()
 
-    A >> 2 * B[modules.mobspy_parameters._Internal_Parameter_Constructor('k1', 3)]
-    B >> C + D[modules.mobspy_parameters._Internal_Parameter_Constructor('k2', 1.4)]
+    B >> Zero [k1]
+
+    B(100), B.b2(100)
+    S = Simulation(B)
+    S.level = -1
+    S.compile()
+
+    S.update_model([All[B], 200/u.l])
 
-    A(100)
-    S = Simulation(A | B | C | D)
-    S.duration = 10
-    print(S.compile())
-    # print(S.generate_sbml()[0])
+    print(S.generate_sbml()[0])
 
-    S.update_model()
+    # print(A.get_characteristics())
 
 

mobspy/data_handler/time_series_object.py

@@ -4,6 +4,7 @@
 import pandas as pd
 from mobspy.modules.meta_class import *
 from mobspy.modules.class_of_meta_specie_named_any import *
+import mobspy.simulation_logging as simlog
 import inspect
 
 

mobspy/modules/compiler.py

@@ -1,5 +1,5 @@
 from mobspy.simulation_logging.log_scripts import error as simlog_error, warning as simlog_warning
-from mobspy.modules.mobspy_parameters import _Internal_Parameter_Constructor as mp_Mobspy_Parameter
+from mobspy.modules.mobspy_parameters import Internal_Parameter_Constructor as mp_Mobspy_Parameter
 from mobspy.modules.species_string_generator import construct_all_combinations as ssg_construct_all_combinations, \
     construct_species_char_list as ssg_construct_species_char_list
 from pint import Quantity
@@ -29,7 +29,8 @@ def add_to_parameters_to_sbml(cls, parameters_used, parameters_for_sbml, paramet
             if parameter.name in parameters_used:
                 parameters_used[parameter.name]['used_in'].add('$sbml')
             else:
-                temp = {'name': parameter.name, 'values': parameter.value, 'used_in': {'$sbml'}}
+                temp = {'name': parameter.name, 'values': parameter.value, 'used_in': {'$sbml'},
+                        'object': parameter}
                 parameters_used[parameter.name] = temp
 
             try:
@@ -138,7 +139,7 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
             species.order_references()
 
         # Start by creating the Mappings for the SBML
-        # Convert to user friendly format as well
+        # Convert to user-friendly format as well
         mappings_for_sbml = {}
         for spe_object in meta_species_to_simulate:
             mappings_for_sbml[spe_object.get_name()] = []
@@ -202,7 +203,7 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
                         = parameters_used[count['quantity'].name]['used_in'].union(set(species_strings))
                 else:
                     temp = {'name': count['quantity'].name, 'values': count['quantity'].value,
-                            'used_in': set(species_strings)}
+                            'used_in': set(species_strings), 'object': count['quantity']}
                     parameters_used[count['quantity'].name] = temp
 
             temp_count = uh_convert_counts(count['quantity'], volume, dimension)
@@ -232,7 +233,7 @@ def compile(cls, meta_species_to_simulate, reactions_set, species_counts, orthog
                     parameters_used[count['quantity'].name]['used_in'].add(species_string)
                 else:
                     temp = {'name': count['quantity'].name, 'values': count['quantity'].value,
-                            'used_in': {species_string}}
+                            'used_in': {species_string}, 'object': count['quantity']}
                     parameters_used[count['quantity'].name] = temp
 
             temp_count = uh_convert_counts(count['quantity'], volume, dimension)

mobspy/modules/event_functions.py

@@ -3,7 +3,7 @@
 from mobspy.modules.species_string_generator import construct_all_combinations as ssg_construct_all_combinations, \
      construct_species_char_list as ssg_construct_species_char_list
 from pint import Quantity
-from mobspy.modules.mobspy_parameters import _Internal_Parameter_Constructor as mp_Mobspy_Parameter
+from mobspy.modules.mobspy_parameters import Internal_Parameter_Constructor as mp_Mobspy_Parameter
 from mobspy.modules.function_rate_code import search_for_parameters_in_str as frc_search_for_parameters_in_str
 
 

mobspy/modules/function_rate_code.py

@@ -15,7 +15,7 @@
 from mobspy.modules.mobspy_expressions import MobsPyExpression as mbe_MobsPyExpression, \
     ExpressionDefiner as mbe_ExpressionDefiner, Specific_Species_Operator as mbe_Specific_Species_Operator
 from pint import Quantity
-from mobspy.modules.mobspy_parameters import _Internal_Parameter_Constructor as mp_Mobspy_Parameter
+from mobspy.modules.mobspy_parameters import Internal_Parameter_Constructor as mp_Mobspy_Parameter
 from re import split as re_split
 import timeit
 

mobspy/modules/meta_class.py

@@ -13,7 +13,7 @@
 from mobspy.modules.mobspy_expressions import OverrideQuantity as me_OverrideQuantity, \
     MobsPyExpression as me_MobsPyExpression, Specific_Species_Operator as me_Specific_Species_Operator, \
     ExpressionDefiner as me_ExpressionDefiner
-from mobspy.modules.mobspy_parameters import _Internal_Parameter_Constructor as mp_Mobspy_Parameter
+from mobspy.modules.mobspy_parameters import Internal_Parameter_Constructor as mp_Mobspy_Parameter
 from numpy import integer as np_int_, floating as np_float_
 from inspect import stack as inspect_stack
 from mobspy.modules.meta_class_utils import unite_characteristics as mcu_unite_characteristics, \
@@ -356,6 +356,22 @@ def __init__(self, object_reference, characteristics, stoichiometry=1, label=Non
             self.list_of_reactants = [{'object': object_reference, 'characteristics': characteristics,
                                        'stoichiometry': stoichiometry, 'label': label}]
 
+    def get_spe_object(self):
+        if len(self.list_of_reactants) != 1:
+            simlog_error("The internal method get_queried_characteristics can only be used for "
+                         "Reacting_Species with a single ",
+                         full_exception_log=True)
+        else:
+            return self.list_of_reactants[0]['object']
+
+    def get_query_characteristics(self):
+        if len(self.list_of_reactants) != 1:
+            simlog_error("The internal method get_queried_characteristics can only be used for "
+                         "Reacting_Species with a single ",
+                         full_exception_log=True)
+        else:
+            return self.list_of_reactants[0]['characteristics']
+
     def __rmul__(self, stoichiometry):
         """
             Multiplication by the stoichiometry for reactions
@@ -442,7 +458,7 @@ def __call__(self, quantity):
             if len(self.list_of_reactants) != 1:
                 simlog_error('Assignment used incorrectly. Only one species at a time', stack_index=2)
             quantity_dict = species_object.add_quantities(characteristics, quantity)
-        # elif isinstance(quantity, ExpressionDefiner) and not isinstance(quantity, _Internal_Parameter_Constructor):
+        # elif isinstance(quantity, ExpressionDefiner) and not isinstance(quantity, Internal_Parameter_Constructor):
         #    simlog.error('Operations are not allowed for count assignment. Only individual parameters', stack_index=2)
         elif asgi_Assign.check_context():
             dummy_rsp = species_object
@@ -1096,6 +1112,12 @@ def __init__(self, name):
         # This will store the quantities relating to the species counts
         self._species_counts = []
 
+    def get_spe_object(self):
+        return self
+
+    def get_query_characteristics(self):
+        return 'std$'
+
     def link_a_species(self, other_species):
         """
             Links a species with another. So if one is added to the model, the other is also added to the model

mobspy/modules/mobspy_parameters.py

@@ -5,7 +5,7 @@
 from pint import Quantity, UnitRegistry
 
 
-class _Internal_Parameter_Constructor(me_ExpressionDefiner, me_QuantityConverter):
+class Internal_Parameter_Constructor(me_ExpressionDefiner, me_QuantityConverter):
     """
         This is the constructor that is called by ModelParameters to create a model parameter
         (not a simulation parameter). The user is not supposed to create parameters using this object.
@@ -28,34 +28,38 @@ def __init__(self, name, value):
         self._operation = str(name)
         self._parameter_set.add(self)
 
-        def unit_process(value):
-            # We convert into MobsPy units already during the definition of a parameter
-            self.value = self.convert_received_unit(value).magnitude
+        self.process_value(value)
 
-            self.original_magnitude = value.magnitude
-            self.conversion_factor = self.value / self.original_magnitude
-            self.original_unit = value.units
+    def unit_process(self, value):
+        # We convert into MobsPy units already during the definition of a parameter
+        self.value = self.convert_received_unit(value).magnitude
 
-            # For future developers, the T is there to avoid potential bugs with the . query
-            self._unit_count_op = value
-            self._unit_conc_op = value
-            self._unit_operation = value
-            self._has_units = 'T'
+        self.original_magnitude = value.magnitude
+        self.conversion_factor = self.value / self.original_magnitude
+        self.original_unit = value.units
 
-            return self.value, self.original_unit
+        # For future developers, the T is there to avoid potential bugs with the . query
+        self._unit_count_op = value
+        self._unit_conc_op = value
+        self._unit_operation = value
+        self._has_units = 'T'
+
+        return self.value, self.original_unit
+
+    def process_value(self, value):
 
         if isinstance(value, Quantity):
-            unit_process(value)
+            self.unit_process(value)
         elif type(value) == list or type(value) == tuple:
             new_list = []
             first_unit = None
             for i, val in enumerate(value):
                 if isinstance(val, Quantity) and i == 0:
-                    new_value, first_unit = unit_process(val)
+                    new_value, first_unit = self.unit_process(val)
                 elif isinstance(val, Quantity) and i > 0 and first_unit is None:
                     simlog.error("MobsPy parameters must all be the same unit", stack_index=1)
                 elif isinstance(val, Quantity) and i > 0 and first_unit is not None:
-                    new_value, unit = unit_process(val)
+                    new_value, unit = self.unit_process(val)
                     if unit != first_unit:
                         simlog.error("MobsPy parameters must all be the same unit", stack_index=1)
                 else:
@@ -72,6 +76,7 @@ def unit_process(value):
             self.conversion_factor = 1
             self._has_units = False
 
+
     def convert_to_original_unit(self):
         """
             Converts the parameter from the MobsPy standard unit to the original unit of the parameter
@@ -108,6 +113,21 @@ def has_units(self):
         else:
             return False
 
+    def update_value(self, new_value):
+
+        temp_set = set()
+        temp_set.add(self)
+        self.original_value = new_value
+
+        self._ms_active = True
+
+        self._parameter_set.add(self)
+
+        self.process_value(new_value)
+
+    def get_name(self):
+        return self.name
+
     def __str__(self):
         return str(self._operation)
 
@@ -124,9 +144,9 @@ def ModelParameters(*args):
         simlog.error('You must provide an initial value for every parameter variable declared', stack_index=2)
 
     if len(parameter_variable_names) > 1:
-        parameters_to_return = [_Internal_Parameter_Constructor(p, v) for p, v in zip(parameter_variable_names, args)]
+        parameters_to_return = [Internal_Parameter_Constructor(p, v) for p, v in zip(parameter_variable_names, args)]
     else:
-        parameters_to_return = _Internal_Parameter_Constructor(parameter_variable_names[0], args[0])
+        parameters_to_return = Internal_Parameter_Constructor(parameter_variable_names[0], args[0])
 
     return parameters_to_return
 
@@ -137,5 +157,5 @@ def ModelParameters(*args):
     r1 = (a + b + c)/5
     print(r1._operation)
     # print(type(r1._parameter_set))
-    # print(_Internal_Parameter_Constructor.parameter_stack)
+    # print(Internal_Parameter_Constructor.parameter_stack)
 

mobspy/modules/set_counts_module.py

@@ -1,7 +1,7 @@
 from mobspy.simulation_logging.log_scripts import error as simlog_error
 from inspect import stack as inspect_stack
 from mobspy.modules.meta_class import List_Species, Species, Reacting_Species
-from mobspy.modules.mobspy_parameters import _Internal_Parameter_Constructor as mp_Mobspy_Parameter
+from mobspy.modules.mobspy_parameters import Internal_Parameter_Constructor as mp_Mobspy_Parameter
 from pint import Quantity
 from numpy import integer as np_int_, floating as np_float_
 

mobspy/modules/species_string_generator.py

@@ -16,7 +16,8 @@ def characteristics_dictionary(characteristics, characteristics_to_object):
     return object_to_characteristic
 
 
-def construct_species_char_list(spe_object, characteristics, characteristics_to_object, symbol=None):
+def construct_species_char_list(spe_or_reactiong_object, characteristics,
+                                characteristics_to_object, symbol=None):
     """
         This function constructs a list in the format ['species_name', 'char1', 'char2', ...]. It generetes this list
         for a given meta-species and the specified characteristics. Values of characteristics not specified in a
@@ -31,26 +32,31 @@ def construct_species_char_list(spe_object, characteristics, characteristics_to_
     """
     if characteristics == 'std$':
         characteristics = set()
+    spe_object = spe_or_reactiong_object.get_spe_object()
 
     ordered_references_list = spe_object.get_ordered_references()
 
     objects_to_characteristic = characteristics_dictionary(characteristics, characteristics_to_object)
 
     species_char_list = [spe_object]
+
     for obj in ordered_references_list:
         if obj in objects_to_characteristic:
             species_char_list.append(objects_to_characteristic[obj])
         else:
             species_char_list.append(obj.first_characteristic)
 
+
     if symbol is not None:
         species_char_list = symbol.join([spe_object.get_name()] + species_char_list [1:]) \
             if len(species_char_list) > 1 else spe_object.get_name()
 
+
     return species_char_list
 
 
-def construct_all_combinations(spe_object, characteristics, characteristics_to_object, symbol=None):
+def construct_all_combinations(spe_or_reactiong_object,
+                               characteristics, characteristics_to_object, symbol=None):
     """
         This function constructs all possible list in the format ['species_name', 'char1', 'char2', ...] using
         all combinations of characteristics from the vector coordinates not used in the characteristics specified
@@ -65,6 +71,7 @@ def construct_all_combinations(spe_object, characteristics, characteristics_to_o
 
     if characteristics == 'std$':
         characteristics = set()
+    spe_object = spe_or_reactiong_object.get_spe_object()
 
     spe_object.order_references()
     ordered_references_list = spe_object.get_ordered_references()