Python main() is producing valid floating-point output.

src/acom_music_box/goBuild.bat

@@ -0,0 +1,3 @@
+cd ..\..
+pip install .
+cd src\acom_music_box

src/acom_music_box/music_box.py

@@ -9,6 +9,7 @@
 from .music_box_conditions import Conditions
 import csv
 import musica
+import music_box_logger
 
 class MusicBox:
     """
@@ -36,13 +37,15 @@ def __init__(self, box_model_options=None, species_list=None, reaction_list=None
             evolving_conditions (List[EvolvingConditions]): List of evolving conditions over time.
             config_file (String): File path for the configuration file to be located. Default is "camp_data/config.json".
         """
-        self.box_model_options = box_model_options
+        self.box_model_options = box_model_options if box_model_options is not None else BoxModelOptions()
         self.species_list = species_list if species_list is not None else SpeciesList()
         self.reaction_list = reaction_list if reaction_list is not None else ReactionList()
-        self.initial_conditions = initial_conditions
+        self.initial_conditions = initial_conditions if initial_conditions is not None else Conditions()
         self.evolving_conditions = evolving_conditions if evolving_conditions is not None else EvolvingConditions([], [])
         self.config_file = config_file if config_file is not None else "camp_data/config.json"
 
+        self.solver = None
+
 
 
     def add_evolving_condition(self, time_point, conditions):
@@ -428,7 +431,7 @@ def solve(self, path_to_output = None):
             list: A 2D list where each inner list represents the results of the simulation 
             at a specific time step.
         """
-
+       
         #sets up initial conditions to be current conditions
         curr_conditions = self.initial_conditions
 
@@ -448,7 +451,7 @@ def solve(self, path_to_output = None):
                 next_conditions_index = 1
                 next_conditions = self.evolving_conditions.conditions[1]
                 next_conditions_time = self.evolving_conditions.times[1]    
-                
+
 
         #initalizes output headers
         output_array = []
@@ -458,10 +461,16 @@ def solve(self, path_to_output = None):
         headers.append("ENV.temperature")
         headers.append("ENV.pressure")
 
+        music_box_logger.progress("solve0152 self.solver = {}".format(self.solver))
+
+        if (self.solver is None):
+            music_box_logger.progress("Warning: MusicBox object {} has no solver."
+                .format(self))
         rate_constant_ordering = musica.user_defined_reaction_rates(self.solver)
+
         species_constant_ordering = musica.species_ordering(self.solver)
 
-        
+
         #adds species headers to output
         ordered_species_headers =  [k for k, v in sorted(species_constant_ordering.items(), key=lambda item: item[1])]
         for spec in ordered_species_headers:
@@ -478,9 +487,11 @@ def solve(self, path_to_output = None):
         next_output_time = curr_time
         #runs the simulation at each timestep
 
-
+        music_box_logger.progress("solve03 path_to_output = {}".format(path_to_output))
+
 
         while(curr_time <= self.box_model_options.simulation_length):
+
             #outputs to output_array if enough time has elapsed
             if(next_output_time <= curr_time):   
                 row = []
@@ -507,30 +518,33 @@ def solve(self, path_to_output = None):
 
                 else:
                     next_conditions = None
+
+            music_box_logger.progress("solve033 species_constant_ordering = {}".format(species_constant_ordering))
 
-            
+
             #updates M accordingly
             if 'M' in species_constant_ordering:
                 BOLTZMANN_CONSTANT = 1.380649e-23
                 AVOGADRO_CONSTANT = 6.02214076e23;  
                 GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
                 ordered_concentrations[species_constant_ordering['M']] = curr_conditions.pressure / (GAS_CONSTANT * curr_conditions.temperature)
 
+            music_box_logger.progress("solve035 args = {} {} {} {} {}".format(self.box_model_options.chem_step_time, curr_conditions.temperature, curr_conditions.pressure, ordered_concentrations, ordered_rate_constants))
             #solves and updates concentration values in concentration array
+            if (not ordered_concentrations):
+                music_box_logger.progress("Warning: ordered_concentrations list is empty.")               
             musica.micm_solve(self.solver, self.box_model_options.chem_step_time, curr_conditions.temperature, curr_conditions.pressure, ordered_concentrations, ordered_rate_constants)
 
-
-
 
             #increments time
             curr_time += self.box_model_options.chem_step_time  
-
+            
         #outputs to file if output is present
         if(path_to_output != None):
             with open(path_to_output, 'w', newline='') as output:
                 writer = csv.writer(output)
                 writer.writerows(output_array)
-        
+
         #returns output_array 
         return output_array
 

src/acom_music_box/music_box_conditions.py

@@ -19,7 +19,7 @@ class Conditions:
         reactionRates (List[ReactionRate]): A list of reaction rates.
     """
 
-    def __init__(self, pressure, temperature, species_concentrations=None, reaction_rates=None):
+    def __init__(self, pressure=0.83, temperature=303.0, species_concentrations=None, reaction_rates=None):
         """
         Initializes a new instance of the Conditions class.
 

src/acom_music_box/music_box_logger.py

@@ -0,0 +1,32 @@
+import sys
+
+# Class Logger is included here for completeness,
+# but not used because progress() is such a lighweight function.
+class Logger:
+    """
+    Logs messages to the console, which can then be captured to a log file.
+
+    Attributes:
+    """
+
+    def __init__(self):
+        """
+        Initializes a new instance of the Reaction class.
+
+        Args:
+            name (str): The name of the reaction.
+            reaction_type (str): The type of the reaction.
+            reactants (List[Reactant]): A list of Reactant instances representing the reactants. Default is an empty list.
+            products (List[Product]): A list of Product instances representing the products. Default is an empty list.
+            scaling_factor (float, optional): A scaling factor for the reaction rate. Defaults to None.
+        """
+        pass
+
+
+
+# Display progress message on the console.
+# endString = set this to '' for no return
+def progress(message, endString='\n'):
+    if (True):   # disable here in production
+        print(message, end=endString)
+        sys.stdout.flush()

src/acom_music_box/music_box_main.py

@@ -1,19 +1,31 @@
 from acom_music_box import MusicBox
 
 import math
+import datetime
 import sys
 
+import music_box_logger
 
 
-# Display progress message on the console.
-# endString = set this to '' for no return
-def progress(message, endString='\n'):
-    if (True):   # disable here in production
-        print(message, end=endString)
-        sys.stdout.flush()
 
+if __name__ == "__main__":
+    music_box_logger.progress("{}".format(__file__))
+    music_box_logger.progress("Start time: {}".format(datetime.datetime.now()))
+
+    music_box_logger.progress("Hello, MusicBox World!")
+
+    # set up the home configuration directory TODO: Make this a command-line argument.
+    musicBoxHomeDir = "C:\\2024\\MusicBox\\music-box\\tests\\configs\\analytical_config\\"
+
+    # create and load a MusicBox object
+    myBox = MusicBox()
+    myBox.readConditionsFromJson(musicBoxHomeDir + "my_config.json")
+    music_box_logger.progress("myBox = {}".format(myBox))
 
+    # create solver and solve
+    myBox.create_solver(musicBoxHomeDir + myBox.config_file)
+    mySolution = myBox.solve()
+    music_box_logger.progress("mySolution = {}".format(mySolution))
 
-if __name__ == "__main__":
-    progress("Hello, MusicBox World!")
+    music_box_logger.progress("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)

src/acom_music_box/music_box_model_options.py

@@ -12,7 +12,7 @@ class BoxModelOptions:
         simulationLength (float): Length of the simulation in hours.
     """
 
-    def __init__(self, chem_step_time, output_step_time, simulation_length, grid="box"):
+    def __init__(self, chem_step_time=1.0, output_step_time=5.0, simulation_length=100.0, grid="box"):
         """
         Initializes a new instance of the BoxModelOptions class.
 

tests/goTest.bat

@@ -0,0 +1 @@
+pytest