Removed ACOM Logger. Set up music_box operation as executable script …

…and python command line.

pyproject.toml

@@ -11,8 +11,11 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
 dynamic = ["version", "description"]
 
 dependencies = [
-  "musica==0.6.1.dev0"
+  "musica==0.7.0"
 ]
 
 [project.urls]
-Home = "https://github.com/NCAR/music-box"
+Home = "https://github.com/NCAR/music-box"
+
+[project.scripts]
+music_box = "acom_music_box.music_box_main:main"

src/acom_music_box/__init__.py

@@ -18,6 +18,5 @@
 from .music_box_conditions import Conditions
 
 from .music_box_evolving_conditions import EvolvingConditions
-from acom_music_box import music_box_logger
 from .music_box import MusicBox
 

src/acom_music_box/music_box.py

@@ -1,18 +1,21 @@
 import json
 import os
 
+import logging
+logger = logging.getLogger(__name__)
+
 from .music_box_evolving_conditions import EvolvingConditions
 from .music_box_reaction_list import ReactionList
 from .music_box_reaction import Reaction, Branched, Arrhenius, Tunneling, Troe_Ternary
 from .music_box_species_list import SpeciesList
 from .music_box_model_options import BoxModelOptions
 from .music_box_conditions import Conditions
-from acom_music_box import music_box_logger
 
 import csv
 import musica
 
 
+
 class MusicBox:
     """
     Represents a box model with attributes such as box model options, species list, reaction list,
@@ -414,7 +417,7 @@ def create_solver(self, path_to_config):
             None
         """
         # Create a solver object using the configuration file
-        self.solver = musica.create_micm(path_to_config)
+        self.solver = musica.create_solver(path_to_config)
 
 
     def solve(self, path_to_output = None):
@@ -519,24 +522,30 @@ def solve(self, path_to_output = None):
                     next_conditions = None
 
 
+            #  calculate air density from the ideal gas law
+            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) 
+
             #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)
+                ordered_concentrations[species_constant_ordering['M']] = air_density
 
             #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)
+                logger.info("Warning: ordered_concentrations list is empty.")
+            musica.micm_solve(self.solver, self.box_model_options.chem_step_time,
+                curr_conditions.temperature, curr_conditions.pressure, air_density,
+                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):
+            logger.info("path_to_output = {}".format(path_to_output))
             with open(path_to_output, 'w', newline='') as output:
                 writer = csv.writer(output)
                 writer.writerows(output_array)

src/acom_music_box/music_box_main.py

@@ -1,11 +1,13 @@
 from acom_music_box import MusicBox
-from acom_music_box import music_box_logger
 
 
 import math
 import datetime
 import sys
 
+import logging
+logger = logging.getLogger(__name__)
+
 
 
 # Retrieve named arguments from the command line and
@@ -29,12 +31,14 @@ def getArgsDictionary(argPairs):
 
 
 
-if __name__ == "__main__":
-    music_box_logger.progress("{}".format(__file__))
-    music_box_logger.progress("Start time: {}".format(datetime.datetime.now()))
+def main():
+    logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+    logger.info("{}".format(__file__))
+    logger.info("Start time: {}".format(datetime.datetime.now()))
 
-    music_box_logger.progress("Hello, MusicBox World!")
+    logger.info("Hello, MusicBox World!")
 
+
     # retrieve and parse the command-line arguments
     myArgs = getArgsDictionary(sys.argv)
 
@@ -46,13 +50,17 @@ def getArgsDictionary(argPairs):
     # create and load a MusicBox object
     myBox = MusicBox()
     myBox.readConditionsFromJson(musicBoxHomeDir + "my_config.json")
-    music_box_logger.progress("myBox = {}".format(myBox))
+    logger.info("myBox = {}".format(myBox))
 
     # create solver and solve
     myBox.create_solver(musicBoxHomeDir + myBox.config_file)
-    music_box_logger.progress("myBox.solver = {}".format(myBox.solver))
+    logger.info("myBox.solver = {}".format(myBox.solver))
     mySolution = myBox.solve(musicBoxHomeDir + "my_solution.csv")
-    music_box_logger.progress("mySolution = {}".format(mySolution))
+    logger.info("mySolution = {}".format(mySolution))
 
-    music_box_logger.progress("End time: {}".format(datetime.datetime.now()))
+    logger.info("End time: {}".format(datetime.datetime.now()))
     sys.exit(0)
+
+
+if __name__ == "__main__":
+    main()