From 652fe37501e4d3bf4674ed7d38172a5a6021a814 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Wed, 5 Jun 2024 18:17:40 -0600
Subject: [PATCH 01/22] Hello World from the new MusicBox main().

---
 src/acom_music_box/goMusicBox.bat    |  1 +
 src/acom_music_box/music_box_main.py | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)
 create mode 100644 src/acom_music_box/goMusicBox.bat
 create mode 100644 src/acom_music_box/music_box_main.py

diff --git a/src/acom_music_box/goMusicBox.bat b/src/acom_music_box/goMusicBox.bat
new file mode 100644
index 00000000..1c159795
--- /dev/null
+++ b/src/acom_music_box/goMusicBox.bat
@@ -0,0 +1 @@
+python music_box_main.py
\ No newline at end of file
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
new file mode 100644
index 00000000..30ad43b5
--- /dev/null
+++ b/src/acom_music_box/music_box_main.py
@@ -0,0 +1,19 @@
+from acom_music_box import MusicBox
+
+import math
+import sys
+
+
+
+# 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__":
+    progress("Hello, MusicBox World!")
+    sys.exit(0)

From 5e5b6be9eb0888aa2f325cb12e18d04d5aabaf61 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 11 Jun 2024 16:20:04 -0600
Subject: [PATCH 02/22] Python main() is producing valid floating-point output.

---
 src/acom_music_box/goBuild.bat                |  3 ++
 src/acom_music_box/music_box.py               | 36 +++++++++++++------
 src/acom_music_box/music_box_conditions.py    |  2 +-
 src/acom_music_box/music_box_logger.py        | 32 +++++++++++++++++
 src/acom_music_box/music_box_main.py          | 28 ++++++++++-----
 src/acom_music_box/music_box_model_options.py |  2 +-
 tests/goTest.bat                              |  1 +
 7 files changed, 83 insertions(+), 21 deletions(-)
 create mode 100644 src/acom_music_box/goBuild.bat
 create mode 100644 src/acom_music_box/music_box_logger.py
 create mode 100644 tests/goTest.bat

diff --git a/src/acom_music_box/goBuild.bat b/src/acom_music_box/goBuild.bat
new file mode 100644
index 00000000..2d958737
--- /dev/null
+++ b/src/acom_music_box/goBuild.bat
@@ -0,0 +1,3 @@
+cd ..\..
+pip install .
+cd src\acom_music_box
\ No newline at end of file
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index f9b2b112..763c9a7b 100644
--- a/src/acom_music_box/music_box.py
+++ b/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 = []
@@ -507,8 +518,10 @@ 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
@@ -516,21 +529,22 @@ def solve(self, path_to_output = None):
                 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
         
diff --git a/src/acom_music_box/music_box_conditions.py b/src/acom_music_box/music_box_conditions.py
index f44c5076..7870d8a6 100644
--- a/src/acom_music_box/music_box_conditions.py
+++ b/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.
 
diff --git a/src/acom_music_box/music_box_logger.py b/src/acom_music_box/music_box_logger.py
new file mode 100644
index 00000000..4ca3f4bf
--- /dev/null
+++ b/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()
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 30ad43b5..9086923f 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/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)
diff --git a/src/acom_music_box/music_box_model_options.py b/src/acom_music_box/music_box_model_options.py
index 4f9989b8..e20843fe 100644
--- a/src/acom_music_box/music_box_model_options.py
+++ b/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.
 
diff --git a/tests/goTest.bat b/tests/goTest.bat
new file mode 100644
index 00000000..55b033e9
--- /dev/null
+++ b/tests/goTest.bat
@@ -0,0 +1 @@
+pytest
\ No newline at end of file

From 321d2b9452a43b471670ac77a38726444858ab4f Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 24 Jun 2024 17:33:24 -0600
Subject: [PATCH 03/22] Added command-line arguments.

---
 src/acom_music_box/goMusicBox.bat      |  2 +-
 src/acom_music_box/music_box.py        |  7 +-----
 src/acom_music_box/music_box_logger.py |  6 +-----
 src/acom_music_box/music_box_main.py   | 30 ++++++++++++++++++++++++--
 4 files changed, 31 insertions(+), 14 deletions(-)

diff --git a/src/acom_music_box/goMusicBox.bat b/src/acom_music_box/goMusicBox.bat
index 1c159795..3af2a04f 100644
--- a/src/acom_music_box/goMusicBox.bat
+++ b/src/acom_music_box/goMusicBox.bat
@@ -1 +1 @@
-python music_box_main.py
\ No newline at end of file
+python music_box_main.py homeDir="C:\\2024\MusicBox\music-box\\tests\\configs\\analytical_config\\"
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index 763c9a7b..ffbc3d74 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -487,9 +487,7 @@ 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
@@ -518,9 +516,7 @@ 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:
@@ -529,7 +525,6 @@ def solve(self, path_to_output = None):
                 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.")               
diff --git a/src/acom_music_box/music_box_logger.py b/src/acom_music_box/music_box_logger.py
index 4ca3f4bf..5cd213c0 100644
--- a/src/acom_music_box/music_box_logger.py
+++ b/src/acom_music_box/music_box_logger.py
@@ -1,7 +1,7 @@
 import sys
 
 # Class Logger is included here for completeness,
-# but not used because progress() is such a lighweight function.
+# but not used because progress() is such a lightweight function.
 class Logger:
     """
     Logs messages to the console, which can then be captured to a log file.
@@ -15,10 +15,6 @@ def __init__(self):
 
         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
 
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 9086923f..614517c4 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -8,14 +8,40 @@
 
 
 
+# Retrieve named arguments from the command line and
+# return in a dictionary of keywords.
+# argPairs = list of arguments, probably from sys.argv
+#       named arguments are formatted like this=3.14159
+# return dictionary of keywords and values
+def getArgsDictionary(argPairs):
+   argDict = {}
+
+   for argPair in argPairs:
+      # the arguments are: arg=value
+      pairValue = argPair.split('=')
+      if (len(pairValue) < 2):
+         argDict[pairValue[0]] = None
+         continue
+
+      argDict[pairValue[0]] = pairValue[1]
+
+   return(argDict)
+
+
+
 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\\"
+    # retrieve and parse the command-line arguments
+    myArgs = getArgsDictionary(sys.argv)
+    
+    # set up the home configuration directory
+    musicBoxHomeDir = "music-box\\tests\\configs\\analytical_config\\"      # default
+    if ("homeDir" in myArgs):
+        musicBoxHomeDir = myArgs.get("homeDir")
     
     # create and load a MusicBox object
     myBox = MusicBox()

From 509037bdf0626a69ac0e1d288d6c79b4a185163e Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 25 Jun 2024 10:36:59 -0600
Subject: [PATCH 04/22] Write out the solution.

---
 src/acom_music_box/music_box_main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 614517c4..cb0d583d 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -50,7 +50,7 @@ def getArgsDictionary(argPairs):
 
     # create solver and solve
     myBox.create_solver(musicBoxHomeDir + myBox.config_file)
-    mySolution = myBox.solve()
+    mySolution = myBox.solve(musicBoxHomeDir + "my_solution.csv")
     music_box_logger.progress("mySolution = {}".format(mySolution))
 
     music_box_logger.progress("End time: {}".format(datetime.datetime.now()))

From 5851f6ed015943fde3dbaf7b93f4931868580992 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Wed, 26 Jun 2024 16:42:54 -0600
Subject: [PATCH 05/22] Import music_box_logger the right way.

---
 src/acom_music_box/__init__.py       | 1 +
 src/acom_music_box/music_box.py      | 4 +++-
 src/acom_music_box/music_box_main.py | 4 ++--
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/acom_music_box/__init__.py b/src/acom_music_box/__init__.py
index 17fdbe40..ff481af8 100644
--- a/src/acom_music_box/__init__.py
+++ b/src/acom_music_box/__init__.py
@@ -18,5 +18,6 @@
 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
 
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index ffbc3d74..32f6a63a 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -7,9 +7,11 @@
 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
-import music_box_logger
+
 
 class MusicBox:
     """
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index cb0d583d..fbe9756f 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -1,11 +1,11 @@
 from acom_music_box import MusicBox
+from acom_music_box import music_box_logger
+
 
 import math
 import datetime
 import sys
 
-import music_box_logger
-
 
 
 # Retrieve named arguments from the command line and

From be55094fb63018232d73ed1662783fb086ae2820 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 28 Jun 2024 11:13:05 -0600
Subject: [PATCH 06/22] Move log statements into main().

---
 src/acom_music_box/music_box.py      | 2 +-
 src/acom_music_box/music_box_main.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index 32f6a63a..2c67d55c 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -463,7 +463,7 @@ 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))
+        #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."
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index fbe9756f..fdf2b48b 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -50,6 +50,7 @@ def getArgsDictionary(argPairs):
 
     # create solver and solve
     myBox.create_solver(musicBoxHomeDir + myBox.config_file)
+    music_box_logger.progress("myBox.solver = {}".format(myBox.solver))
     mySolution = myBox.solve(musicBoxHomeDir + "my_solution.csv")
     music_box_logger.progress("mySolution = {}".format(mySolution))
 

From a388a2bb98fff769cc7e95c1e335585b63b340dd Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 28 Jun 2024 16:14:35 -0600
Subject: [PATCH 07/22] Removed realistic physical defaults, replaced with
 None.

---
 src/acom_music_box/music_box.py               | 1 -
 src/acom_music_box/music_box_conditions.py    | 3 ++-
 src/acom_music_box/music_box_model_options.py | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index 2c67d55c..fd948ba4 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -463,7 +463,6 @@ 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."
diff --git a/src/acom_music_box/music_box_conditions.py b/src/acom_music_box/music_box_conditions.py
index 7870d8a6..73c8ba0f 100644
--- a/src/acom_music_box/music_box_conditions.py
+++ b/src/acom_music_box/music_box_conditions.py
@@ -19,7 +19,8 @@ class Conditions:
         reactionRates (List[ReactionRate]): A list of reaction rates.
     """
 
-    def __init__(self, pressure=0.83, temperature=303.0, species_concentrations=None, reaction_rates=None):
+    def __init__(self, pressure=None, temperature=None, species_concentrations=None, reaction_rates=None):
+
         """
         Initializes a new instance of the Conditions class.
 
diff --git a/src/acom_music_box/music_box_model_options.py b/src/acom_music_box/music_box_model_options.py
index e20843fe..b2a9c4ef 100644
--- a/src/acom_music_box/music_box_model_options.py
+++ b/src/acom_music_box/music_box_model_options.py
@@ -12,7 +12,8 @@ class BoxModelOptions:
         simulationLength (float): Length of the simulation in hours.
     """
 
-    def __init__(self, chem_step_time=1.0, output_step_time=5.0, simulation_length=100.0, grid="box"):
+    def __init__(self, chem_step_time=None, output_step_time=None, simulation_length=None, grid="box"):
+
         """
         Initializes a new instance of the BoxModelOptions class.
 

From b1cd963c8b484938d8325d0dde1b68e093f8575b Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 1 Jul 2024 16:16:56 -0600
Subject: [PATCH 08/22] Throw exception for None solver instead of Warning.

---
 src/acom_music_box/music_box.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index fd948ba4..6cc43374 100644
--- a/src/acom_music_box/music_box.py
+++ b/src/acom_music_box/music_box.py
@@ -465,7 +465,7 @@ def solve(self, path_to_output = None):
 
 
         if (self.solver is None):
-            music_box_logger.progress("Warning: MusicBox object {} has no solver."
+            raise Exception("Error: MusicBox object {} has no solver."
                 .format(self))
         rate_constant_ordering = musica.user_defined_reaction_rates(self.solver)
 

From bf52a88aeaf70d4fb9c655fed529e6aec3263c60 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 2 Jul 2024 14:08:23 -0600
Subject: [PATCH 09/22] Removed ACOM Logger. Set up music_box operation as
 executable script and python command line.

---
 pyproject.toml                         |  7 +++++--
 src/acom_music_box/__init__.py         |  1 -
 src/acom_music_box/music_box.py        | 25 +++++++++++++++--------
 src/acom_music_box/music_box_logger.py | 28 --------------------------
 src/acom_music_box/music_box_main.py   | 26 +++++++++++++++---------
 5 files changed, 39 insertions(+), 48 deletions(-)
 delete mode 100644 src/acom_music_box/music_box_logger.py

diff --git a/pyproject.toml b/pyproject.toml
index e9952782..ef84a7a5 100644
--- a/pyproject.toml
+++ b/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"
\ No newline at end of file
+Home = "https://github.com/NCAR/music-box"
+
+[project.scripts]
+music_box = "acom_music_box.music_box_main:main"
diff --git a/src/acom_music_box/__init__.py b/src/acom_music_box/__init__.py
index ff481af8..17fdbe40 100644
--- a/src/acom_music_box/__init__.py
+++ b/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
 
diff --git a/src/acom_music_box/music_box.py b/src/acom_music_box/music_box.py
index 6cc43374..e1378ed8 100644
--- a/src/acom_music_box/music_box.py
+++ b/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):
@@ -519,17 +522,22 @@ 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
@@ -537,6 +545,7 @@ def solve(self, path_to_output = None):
             
         #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)
diff --git a/src/acom_music_box/music_box_logger.py b/src/acom_music_box/music_box_logger.py
deleted file mode 100644
index 5cd213c0..00000000
--- a/src/acom_music_box/music_box_logger.py
+++ /dev/null
@@ -1,28 +0,0 @@
-import sys
-
-# Class Logger is included here for completeness,
-# but not used because progress() is such a lightweight 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.
-        """
-        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()
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index fdf2b48b..dd949b8e 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/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()

From 1893020f8b134f4f5772eaef3477da35f5fef00b Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 2 Jul 2024 15:25:49 -0600
Subject: [PATCH 10/22] Use argparse and configure it for key=value pairs.

---
 src/acom_music_box/music_box_main.py | 37 +++++++++++++++++-----------
 1 file changed, 23 insertions(+), 14 deletions(-)

diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index dd949b8e..f716e8ad 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -8,26 +8,34 @@
 import logging
 logger = logging.getLogger(__name__)
 
+import argparse
 
 
+
+# configure argparse for key-value pairs
+class KeyValueAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        for value in values:
+            key, val = value.split('=')
+            setattr(namespace, key, val)
+
 # Retrieve named arguments from the command line and
 # return in a dictionary of keywords.
-# argPairs = list of arguments, probably from sys.argv
+# argPairs = list of arguments, probably from sys.argv[1:]
 #       named arguments are formatted like this=3.14159
 # return dictionary of keywords and values
 def getArgsDictionary(argPairs):
-   argDict = {}
-
-   for argPair in argPairs:
-      # the arguments are: arg=value
-      pairValue = argPair.split('=')
-      if (len(pairValue) < 2):
-         argDict[pairValue[0]] = None
-         continue
+    parser = argparse.ArgumentParser(description='Process some key=value pairs.')
+    parser.add_argument(
+        'key_value_pairs',
+        nargs='+',  # This means one or more arguments are expected
+        action=KeyValueAction,
+        help='Arguments in key=value format'
+    )
 
-      argDict[pairValue[0]] = pairValue[1]
+    argDict = vars(parser.parse_args(argPairs))      # return dictionary
 
-   return(argDict)
+    return(argDict)
 
 
 
@@ -38,10 +46,11 @@ def main():
     
     logger.info("Hello, MusicBox World!")
     
-
     # retrieve and parse the command-line arguments
-    myArgs = getArgsDictionary(sys.argv)
-    
+    logger.info("sys.argv = {}".format(sys.argv))
+    myArgs = getArgsDictionary(sys.argv[1:])
+    logger.info("Command line = {}".format(myArgs))
+
     # set up the home configuration directory
     musicBoxHomeDir = "music-box\\tests\\configs\\analytical_config\\"      # default
     if ("homeDir" in myArgs):

From 37aeb2f4391f49217e736c6cc47a10b43c15e750 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Tue, 2 Jul 2024 16:13:57 -0600
Subject: [PATCH 11/22] Revise command-line arguments to configFile and
 outputDir.

---
 src/acom_music_box/goMusicBox.bat    |  2 +-
 src/acom_music_box/music_box_main.py | 27 +++++++++++++++++----------
 2 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/src/acom_music_box/goMusicBox.bat b/src/acom_music_box/goMusicBox.bat
index 3af2a04f..84ee4585 100644
--- a/src/acom_music_box/goMusicBox.bat
+++ b/src/acom_music_box/goMusicBox.bat
@@ -1 +1 @@
-python music_box_main.py homeDir="C:\\2024\MusicBox\music-box\\tests\\configs\\analytical_config\\"
+python music_box_main.py configFile="C:\2024\MusicBox\music-box\tests\configs\analytical_config\my_config.json" outputDir="C:\2024\MusicBox\music-box\tests\configs\analytical_config"
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index f716e8ad..e1d5bb10 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -9,6 +9,7 @@
 logger = logging.getLogger(__name__)
 
 import argparse
+import os
 
 
 
@@ -47,24 +48,30 @@ def main():
     logger.info("Hello, MusicBox World!")
     
     # retrieve and parse the command-line arguments
-    logger.info("sys.argv = {}".format(sys.argv))
     myArgs = getArgsDictionary(sys.argv[1:])
     logger.info("Command line = {}".format(myArgs))
 
-    # set up the home configuration directory
-    musicBoxHomeDir = "music-box\\tests\\configs\\analytical_config\\"      # default
-    if ("homeDir" in myArgs):
-        musicBoxHomeDir = myArgs.get("homeDir")
-    
+    # set up the home configuration file
+    musicBoxConfigFile = "music-box\\tests\\configs\\analytical_config\\my_config.json"      # default
+    if ("configFile" in myArgs):
+        musicBoxConfigFile = myArgs.get("configFile")
+
+    # set up the output directory
+    musicBoxOutputDir = ".\\"      # default
+    if ("outputDir" in myArgs):
+        musicBoxOutputDir = myArgs.get("outputDir")
+
     # create and load a MusicBox object
     myBox = MusicBox()
-    myBox.readConditionsFromJson(musicBoxHomeDir + "my_config.json")
+    myBox.readConditionsFromJson(musicBoxConfigFile)
     logger.info("myBox = {}".format(myBox))
 
-    # create solver and solve
-    myBox.create_solver(musicBoxHomeDir + myBox.config_file)
+    # create solver and solve, writing output to requested directory
+    campConfig = os.path.dirname(musicBoxConfigFile) + "\\" + myBox.config_file
+    logger.info("CAMP config = {}".format(campConfig))
+    myBox.create_solver(campConfig)
     logger.info("myBox.solver = {}".format(myBox.solver))
-    mySolution = myBox.solve(musicBoxHomeDir + "my_solution.csv")
+    mySolution = myBox.solve(musicBoxOutputDir + "\\my_solution.csv")
     logger.info("mySolution = {}".format(mySolution))
 
     logger.info("End time: {}".format(datetime.datetime.now()))

From 287f23ed511323cf1e50f8ac77a95290f26e7620 Mon Sep 17 00:00:00 2001
From: Matt Dawson <mattdawson@ucar.edu>
Date: Wed, 3 Jul 2024 09:28:29 -0700
Subject: [PATCH 12/22] pull smoke test action from other branch

---
 .github/workflows/smoke_test.yml | 34 ++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/smoke_test.yml

diff --git a/.github/workflows/smoke_test.yml b/.github/workflows/smoke_test.yml
new file mode 100644
index 00000000..40c8f363
--- /dev/null
+++ b/.github/workflows/smoke_test.yml
@@ -0,0 +1,34 @@
+# This is a basic workflow that is manually triggered
+
+name: Manual workflow
+
+# Controls when the action will run. Workflow runs when manually triggered using the UI
+# or API.
+on:
+  workflow_dispatch:
+    # Inputs the workflow accepts.
+    inputs:
+      name:
+        # Friendly description to be shown in the UI instead of 'name'
+        description: 'Person to greet'
+        # Default value if no value is explicitly provided
+        default: 'World'
+        # Input has to be provided for the workflow to run
+        required: true
+        # The data type of the input
+        type: string
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "greet"
+  greet:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+    # Runs a single command using the runners shell
+    - name: Install
+      run: pip install .
+    - name: Solve
+      run: music_box configFile="music-box\tests\configs\analytical_config\my_config.json" outputDir="music-box\tests\configs\analytical_config"

From bb13ecd33ac1857f627dbb3df017c9f50fb3e633 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Wed, 3 Jul 2024 15:26:34 -0600
Subject: [PATCH 13/22] Modified to look like the MusicBox template.

---
 .github/workflows/smoke_test.yml | 65 +++++++++++++++++---------------
 1 file changed, 34 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/smoke_test.yml b/.github/workflows/smoke_test.yml
index 40c8f363..27cca0dc 100644
--- a/.github/workflows/smoke_test.yml
+++ b/.github/workflows/smoke_test.yml
@@ -1,34 +1,37 @@
-# This is a basic workflow that is manually triggered
-
-name: Manual workflow
-
-# Controls when the action will run. Workflow runs when manually triggered using the UI
-# or API.
-on:
-  workflow_dispatch:
-    # Inputs the workflow accepts.
-    inputs:
-      name:
-        # Friendly description to be shown in the UI instead of 'name'
-        description: 'Person to greet'
-        # Default value if no value is explicitly provided
-        default: 'World'
-        # Input has to be provided for the workflow to run
-        required: true
-        # The data type of the input
-        type: string
-
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+name: smoke
+
+on: [push, workflow_dispatch]
+
 jobs:
-  # This workflow contains a single job called "greet"
-  greet:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
+  build:
+    strategy:
+        matrix:
+          os: [ubuntu-latest, macos-latest, windows-latest]
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
+    runs-on: ${{ matrix.os }}
     steps:
-    # Runs a single command using the runners shell
-    - name: Install
-      run: pip install .
-    - name: Solve
-      run: music_box configFile="music-box\tests\configs\analytical_config\my_config.json" outputDir="music-box\tests\configs\analytical_config"
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+        cache: 'pip' 
+
+    - run: pip install -r requirements.txt
+
+    - name: Install this package
+      run: pip install -e .
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    
+    - name: Run the smoke tests
+      run: |
+        pip install .
+        music_box configFile="tests\configs\analytical_config\my_config.json" outputDir="tests\configs\analytical_config"
+

From 25976774282d792a71002ed407b828ad8b7bf5fe Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Wed, 3 Jul 2024 15:46:33 -0600
Subject: [PATCH 14/22] Display the working directory.

---
 src/acom_music_box/music_box_main.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index e1d5bb10..1016dc4f 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -46,6 +46,7 @@ def main():
     logger.info("Start time: {}".format(datetime.datetime.now()))
     
     logger.info("Hello, MusicBox World!")
+    logger.info("Working directory = {}".format(os.getcwd()))
     
     # retrieve and parse the command-line arguments
     myArgs = getArgsDictionary(sys.argv[1:])

From 71f0b83b15ea19d915c48879f245346ca793bb1f Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Wed, 3 Jul 2024 17:55:56 -0600
Subject: [PATCH 15/22] Removed redundant pip install.

---
 .github/workflows/smoke_test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/smoke_test.yml b/.github/workflows/smoke_test.yml
index 27cca0dc..b90845ee 100644
--- a/.github/workflows/smoke_test.yml
+++ b/.github/workflows/smoke_test.yml
@@ -32,6 +32,5 @@ jobs:
     
     - name: Run the smoke tests
       run: |
-        pip install .
         music_box configFile="tests\configs\analytical_config\my_config.json" outputDir="tests\configs\analytical_config"
 

From 3e0072a0d9ffebf104bf1f13b83c6ee92b5173ef Mon Sep 17 00:00:00 2001
From: Kyle Shores <kyle.shores44@gmail.com>
Date: Tue, 9 Jul 2024 18:15:25 -0500
Subject: [PATCH 16/22] Action test (#174)

* listing debug information

* ok actually printing wd

* trying forward slashes

* trying to join files independent of os slashes

* removing csv file
---
 .github/workflows/smoke_test.yml     | 11 ++++-------
 requirements.txt                     |  5 -----
 src/acom_music_box/music_box_main.py |  4 ++--
 3 files changed, 6 insertions(+), 14 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/.github/workflows/smoke_test.yml b/.github/workflows/smoke_test.yml
index b90845ee..4fcece83 100644
--- a/.github/workflows/smoke_test.yml
+++ b/.github/workflows/smoke_test.yml
@@ -4,6 +4,7 @@ on: [push, workflow_dispatch]
 
 jobs:
   build:
+    continue-on-error: true
     strategy:
         matrix:
           os: [ubuntu-latest, macos-latest, windows-latest]
@@ -20,17 +21,13 @@ jobs:
         python-version: '3.9'
         cache: 'pip' 
 
-    - run: pip install -r requirements.txt
+    - name: Install dependencies
+      run: python -m pip install --upgrade pip
 
     - name: Install this package
       run: pip install -e .
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
     
     - name: Run the smoke tests
       run: |
-        music_box configFile="tests\configs\analytical_config\my_config.json" outputDir="tests\configs\analytical_config"
+        music_box configFile=tests/configs/analytical_config/my_config.json outputDir=tests/configs/analytical_config
 
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index d32852a8..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-musica==0.6.1.dev0
-pandas
-pipx
-pytest
-twine
\ No newline at end of file
diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 1016dc4f..8035e88f 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -68,11 +68,11 @@ def main():
     logger.info("myBox = {}".format(myBox))
 
     # create solver and solve, writing output to requested directory
-    campConfig = os.path.dirname(musicBoxConfigFile) + "\\" + myBox.config_file
+    campConfig = os.path.join(os.path.dirname(musicBoxConfigFile), myBox.config_file)
     logger.info("CAMP config = {}".format(campConfig))
     myBox.create_solver(campConfig)
     logger.info("myBox.solver = {}".format(myBox.solver))
-    mySolution = myBox.solve(musicBoxOutputDir + "\\my_solution.csv")
+    mySolution = myBox.solve(os.path.join(musicBoxOutputDir, "mySolution.csv"))
     logger.info("mySolution = {}".format(mySolution))
 
     logger.info("End time: {}".format(datetime.datetime.now()))

From b739bd751fc27d9d1955cb8d703f27f46139a26a Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 12 Jul 2024 14:51:36 -0600
Subject: [PATCH 17/22] Re-added file that was inadvertently deleted, and
 updated musica version tp 0.7.0

---
 requirements.txt | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 requirements.txt

diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..f3ddcdcc
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,5 @@
+musica==0.7.0
+pandas
+pipx
+pytest
+twine
\ No newline at end of file

From 1ca853f9f92ed88c67d174298f2c64c7707ff828 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 12 Jul 2024 16:03:01 -0600
Subject: [PATCH 18/22] Removed helper scripts from repository.

---
 src/acom_music_box/goBuild.bat    | 3 ---
 src/acom_music_box/goMusicBox.bat | 1 -
 2 files changed, 4 deletions(-)
 delete mode 100644 src/acom_music_box/goBuild.bat
 delete mode 100644 src/acom_music_box/goMusicBox.bat

diff --git a/src/acom_music_box/goBuild.bat b/src/acom_music_box/goBuild.bat
deleted file mode 100644
index 2d958737..00000000
--- a/src/acom_music_box/goBuild.bat
+++ /dev/null
@@ -1,3 +0,0 @@
-cd ..\..
-pip install .
-cd src\acom_music_box
\ No newline at end of file
diff --git a/src/acom_music_box/goMusicBox.bat b/src/acom_music_box/goMusicBox.bat
deleted file mode 100644
index 84ee4585..00000000
--- a/src/acom_music_box/goMusicBox.bat
+++ /dev/null
@@ -1 +0,0 @@
-python music_box_main.py configFile="C:\2024\MusicBox\music-box\tests\configs\analytical_config\my_config.json" outputDir="C:\2024\MusicBox\music-box\tests\configs\analytical_config"

From 3c4a16d34e9ad90e5ecaae68c2d5ec6215b2dd01 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 12 Jul 2024 17:24:32 -0600
Subject: [PATCH 19/22] Removed another batch helper script.

---
 tests/goTest.bat | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 tests/goTest.bat

diff --git a/tests/goTest.bat b/tests/goTest.bat
deleted file mode 100644
index 55b033e9..00000000
--- a/tests/goTest.bat
+++ /dev/null
@@ -1 +0,0 @@
-pytest
\ No newline at end of file

From ff332ca47961e61928699f2347b248edc7e1b369 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 12 Jul 2024 18:35:30 -0600
Subject: [PATCH 20/22] Check for configFile parameter. Give error and example
 if not found.

---
 src/acom_music_box/music_box_main.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 8035e88f..1c5bd6a7 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -53,7 +53,7 @@ def main():
     logger.info("Command line = {}".format(myArgs))
 
     # set up the home configuration file
-    musicBoxConfigFile = "music-box\\tests\\configs\\analytical_config\\my_config.json"      # default
+    musicBoxConfigFile = None
     if ("configFile" in myArgs):
         musicBoxConfigFile = myArgs.get("configFile")
 
@@ -62,6 +62,13 @@ def main():
     if ("outputDir" in myArgs):
         musicBoxOutputDir = myArgs.get("outputDir")
 
+    # check for required arguments and provide examples
+    if (musicBoxConfigFile is None):
+        errorString = "Error: The configFile parameter is required."
+        errorString += (" Example: configFile={}"
+            .format(os.path.join("tests", "configs", "analytical_config", "my_config.json")))
+        raise Exception(errorString)
+                
     # create and load a MusicBox object
     myBox = MusicBox()
     myBox.readConditionsFromJson(musicBoxConfigFile)

From 0b3989eaaa081d6d0264ad5bed9c9075b26b9186 Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Fri, 12 Jul 2024 18:44:16 -0600
Subject: [PATCH 21/22] Add key=value required parameter to argparse help.

---
 src/acom_music_box/music_box_main.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/acom_music_box/music_box_main.py b/src/acom_music_box/music_box_main.py
index 1c5bd6a7..3a3c6f08 100644
--- a/src/acom_music_box/music_box_main.py
+++ b/src/acom_music_box/music_box_main.py
@@ -31,7 +31,7 @@ def getArgsDictionary(argPairs):
         'key_value_pairs',
         nargs='+',  # This means one or more arguments are expected
         action=KeyValueAction,
-        help='Arguments in key=value format'
+        help="Arguments in key=value format. Example: configFile=my_config.json"
     )
 
     argDict = vars(parser.parse_args(argPairs))      # return dictionary

From 23740dd00c49b1746fda6fa50cf031929c8dcf0c Mon Sep 17 00:00:00 2001
From: Carl Drews <drews@ucar.edu>
Date: Mon, 15 Jul 2024 14:53:27 -0600
Subject: [PATCH 22/22] Rename smoke test to CI Tests. Deleted test.yml.

---
 .../{smoke_test.yml => CI_Tests.yml}          |  2 +-
 .github/workflows/test.yml                    | 36 -------------------
 2 files changed, 1 insertion(+), 37 deletions(-)
 rename .github/workflows/{smoke_test.yml => CI_Tests.yml} (97%)
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/smoke_test.yml b/.github/workflows/CI_Tests.yml
similarity index 97%
rename from .github/workflows/smoke_test.yml
rename to .github/workflows/CI_Tests.yml
index 4fcece83..ac1c6fa0 100644
--- a/.github/workflows/smoke_test.yml
+++ b/.github/workflows/CI_Tests.yml
@@ -1,4 +1,4 @@
-name: smoke
+name: CI Tests
 
 on: [push, workflow_dispatch]
 
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index c2dfb4f2..00000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-name: build
-
-on: [push, workflow_dispatch]
-
-jobs:
-  build:
-    strategy:
-        matrix:
-          os: [ubuntu-latest, macos-latest, windows-latest]
-
-    runs-on: ${{ matrix.os }}
-    steps:
-
-    - uses: actions/checkout@v4
-      with:
-        submodules: recursive
-
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-        cache: 'pip' 
-
-    - run: pip install -r requirements.txt
-
-    - name: Install this package
-      run: pip install -e .
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-    
-    - name: Run tests
-      run: |
-        cd tests
-        pytest
\ No newline at end of file