Address issue 169 air density, M third body, catch unexpected JSON (#186

)

* Added logic to catch unexpected JSON config - eg, missing keys.

* Clearer code for setting initial reaction rates.

* Changed for musica 0.7.3; air density and M third body.

* Musica version is now 0.7.3.

* Removed commented-out logging code.

requirements.txt

@@ -1,3 +1,4 @@
+musica==0.7.3
 pandas
 pipx
 pytest

src/acom_music_box/music_box.py

@@ -488,7 +488,7 @@ def solve(self, output_path = None):
         next_output_time = curr_time
         #runs the simulation at each timestep
 
-       
+
         while(curr_time <= self.box_model_options.simulation_length):
 
             #outputs to output_array if enough time has elapsed
@@ -502,7 +502,7 @@ def solve(self, output_path = None):
                 output_array.append(row)
                 next_output_time += self.box_model_options.output_step_time
 
-            #iterates evolvings conditons if enough time has elapsed
+            #iterates evolving  conditions if enough time has elapsed
             while(next_conditions != None and next_conditions_time <= curr_time):
 
                 curr_conditions.update_conditions(next_conditions)
@@ -523,7 +523,8 @@ def solve(self, output_path = None):
             BOLTZMANN_CONSTANT = 1.380649e-23
             AVOGADRO_CONSTANT = 6.02214076e23;  
             GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
-            air_density = curr_conditions.pressure / (GAS_CONSTANT * curr_conditions.temperature) 
+            air_density = curr_conditions.pressure / (GAS_CONSTANT * curr_conditions.temperature)
+
 
             #solves and updates concentration values in concentration array
             if (not ordered_concentrations):
@@ -535,7 +536,7 @@ def solve(self, output_path = None):
 
             #increments time
             curr_time += self.box_model_options.chem_step_time  
-            
+
         #outputs to file if output is present
         if(output_path != None):
             logger.info("path_to_output = {}".format(output_path))
@@ -705,7 +706,7 @@ def order_species_concentrations(self, curr_conditions, species_constant_orderin
             concentrations[concentraton.species.name] = concentraton.concentration
 
         ordered_concentrations = len(concentrations.keys()) * [0.0]
-        
+
         for key, value in concentrations.items():
             ordered_concentrations[species_constant_ordering[key]] = value
         return ordered_concentrations

src/acom_music_box/music_box_conditions.py

@@ -1,5 +1,9 @@
 import csv
 import os
+
+import logging
+logger = logging.getLogger(__name__)
+
 from typing import List
 from .music_box_reaction_rate import ReactionRate
 from .music_box_species import Species
@@ -137,9 +141,10 @@ def from_config_JSON(cls, path_to_json, config_JSON, species_list, reaction_list
                 species_concentrations.append(SpeciesConcentration(species, 0)) 
 
         # Set initial reaction rates
-
         for reaction in reaction_list.reactions:
-            if reaction.name != None and not any(reac.reaction.name == reaction.name for reac in reaction_rates):
+            if (reaction.name is None):
+                continue
+            if not any(rate.reaction.name == reaction.name for rate in reaction_rates):
                 reaction_rates.append(ReactionRate(reaction, 0)) 
 
 

src/acom_music_box/music_box_evolving_conditions.py

@@ -108,9 +108,12 @@ def from_config_JSON(cls, path_to_json ,config_JSON, species_list, reaction_list
 
         # Check if 'evolving conditions' is a key in the JSON config
         if 'evolving conditions' in config_JSON:
-            # Construct the path to the evolving conditions file
-            evolving_conditions_path = os.path.dirname(path_to_json) + "/" + list(config_JSON['evolving conditions'].keys())[0]
-            evolving_conditions =  EvolvingConditions.read_conditions_from_file( evolving_conditions_path, species_list, reaction_list)
+            if len(config_JSON['evolving conditions'].keys()) > 0:
+                # Construct the path to the evolving conditions file
+                evolving_conditions_path = (os.path.dirname(path_to_json) + "/"
+                    + list(config_JSON['evolving conditions'].keys())[0])
+                evolving_conditions =  EvolvingConditions.read_conditions_from_file(
+                    evolving_conditions_path, species_list, reaction_list)
 
         return evolving_conditions
 

src/acom_music_box/music_box_reaction_list.py

@@ -5,6 +5,9 @@
 from .music_box_reactant import Reactant
 from .music_box_product import Product
 
+import logging
+logger = logging.getLogger(__name__)
+
 class ReactionList:
     """
     Represents a list of chemical reactions.
@@ -114,12 +117,13 @@ def get_reactants_from_JSON(self, reaction, species_list):
         """
         reactants = []
 
-        for reactant, reactant_info in reaction['reactants'].items():
-            match = filter(lambda x: x.name == reactant, species_list.species)
-            species = next(match, None)
-            quantity = reactant_info['qty'] if 'qty' in reactant_info else None
+        if ('reactants' in reaction.keys()):
+            for reactant, reactant_info in reaction['reactants'].items():
+                match = filter(lambda x: x.name == reactant, species_list.species)
+                species = next(match, None)
+                quantity = reactant_info['qty'] if 'qty' in reactant_info else None
 
-            reactants.append(Reactant(species, quantity))
+                reactants.append(Reactant(species, quantity))
         return reactants
 
     @classmethod