Update to various arguments names to ensure consistency is maintainted:

- Updated `waterEntropy` to `water_entropy`
- Updated `mout` to `matrix_out`
- Updated `outfile` to `output_file`
- Ensured that any instance of any of these arguments have been changed throughout the codebase to match
- Updated some of the test cases so that they match the new arguments names and made sure they have the correct file format to maintain consistency

Author: harryswift01

CodeEntropy/config/arg_config_manager.py

@@ -48,18 +48,22 @@
         "help": "Enable verbose output",
     },
     "thread": {"type": int, "help": "How many multiprocess to use", "default": 1},
-    "outfile": {
+    "output_file": {
         "type": str,
         "help": "Name of the file where the output will be written",
-        "default": "outfile.json",
+        "default": "output_file.json",
     },
-    "mout": {
+    "matrix_out": {
         "type": str,
         "help": "Name of the file where certain matrices will be written",
         "default": None,
     },
     "force_partitioning": {"type": float, "help": "Force partitioning", "default": 0.5},
-    "waterEntropy": {"type": bool, "help": "Calculate water entropy", "default": False},
+    "water_entropy": {
+        "type": bool,
+        "help": "Calculate water entropy",
+        "default": False,
+    },
 }
 
 

CodeEntropy/config/data_logger.py

@@ -12,15 +12,15 @@ def __init__(self):
         self.molecule_data = []
         self.residue_data = []
 
-    def save_dataframes_as_json(self, molecule_df, residue_df, outfile):
+    def save_dataframes_as_json(self, molecule_df, residue_df, output_file):
         """Save multiple DataFrames into a single JSON file with separate keys"""
         data = {
             "molecule_data": molecule_df.to_dict(orient="records"),
             "residue_data": residue_df.to_dict(orient="records"),
         }
 
         # Write JSON data to file
-        with open(outfile, "w") as out:
+        with open(output_file, "w") as out:
             json.dump(data, out, indent=4)
 
     def add_results_data(self, molecule, level, type, S_molecule):

CodeEntropy/main_mcc.py

@@ -65,7 +65,7 @@ def main():
 
     parser = arg_config.setup_argparse()
     args, unknown = parser.parse_known_args()
-    args.outfile = os.path.join(folder, args.outfile)
+    args.output_file = os.path.join(folder, args.output_file)
 
     try:
         # Initialize the logging system once
@@ -432,7 +432,7 @@ def main():
             #            'Type':['Orientational (J/mol/K)'],
             #            'Result': [S_orient],})
             #        results_df = pd.concat([results_df, new_row], ignore_index=True)
-            #        with open(args.outfile, "a") as out:
+            #        with open(args.output_file, "a") as out:
             #    print(molecule,
             #          "\t",
             #          level,
@@ -457,7 +457,7 @@ def main():
             molecule, level, "Molecule Total Entropy", S_molecule
         )
         data_logger.save_dataframes_as_json(
-            results_df, residue_results_df, args.outfile
+            results_df, residue_results_df, args.output_file
         )
 
     logger.info("Molecules:")

config.yaml

@@ -10,7 +10,7 @@ run1:
   temperature:
   verbose:
   thread: 
-  outfile:
-  mout: 
+  output_file:
+  matrix_output: 
   force_partitioning:
-  waterEntropy:
+  water_entropy:

tests/test_EntropyFunctions/test_arg_config_manager.py

@@ -62,11 +62,10 @@ def setup_file(self, mock_file):
             "tempra: 298.0\n  "
             "verbose: False\n  "
             "thread: 1\n  "
-            "outfile: 'outfile.out'\n  "
-            "resfile: 'res_outfile.out'\n  "
-            "mout: null\n  "
+            "output_file: 'output_file.json'\n  "
+            "matrix_out: null\n  "
             "force_partitioning: 0.5\n  "
-            "waterEntropy: False"
+            "water_entropy: False"
         ).return_value
 
     @patch("builtins.open", new_callable=mock_open)
@@ -126,11 +125,10 @@ def test_invalid_run_config_type(self):
             tempra=298.0,
             verbose=False,
             thread=1,
-            outfile="outfile.out",
-            resfile="res_outfile.out",
-            mout=None,
+            output_file="output_file.json",
+            matrix_out=None,
             force_partitioning=0.5,
-            waterEntropy=False,
+            water_entropy=False,
         ),
     )
     def test_setup_argparse(self, mock_args):
@@ -271,11 +269,10 @@ def test_merge_configs(self):
             tempra=None,
             verbose=None,
             thread=None,
-            outfile=None,
-            resfile=None,
-            mout=None,
+            output_file=None,
+            matrix_out=None,
             force_partitioning=None,
-            waterEntropy=None,
+            water_entropy=None,
         )
         run_config = {
             "top_traj_file": ["/path/to/tpr", "/path/to/trr"],
@@ -287,11 +284,10 @@ def test_merge_configs(self):
             "tempra": 298.0,
             "verbose": False,
             "thread": 1,
-            "outfile": "outfile.out",
-            "resfile": "res_outfile.out",
-            "mout": None,
+            "output_file": "output_file.json",
+            "matrix_out": None,
             "force_partitioning": 0.5,
-            "waterEntropy": False,
+            "water_entropy": False,
         }
         merged_args = arg_config.merge_configs(args, run_config)
         self.assertEqual(merged_args.top_traj_file, ["/path/to/tpr", "/path/to/trr"])

tests/test_EntropyFunctions/test_main_mcc.py

@@ -54,11 +54,10 @@ def setup_file(self, mock_file):
             "tempra: 298.0\n  "
             "verbose: False\n  "
             "thread: 1\n  "
-            "outfile: 'outfile.out'\n  "
-            "resfile: 'res_outfile.out'\n  "
-            "mout: null\n  "
+            "output_file: 'output_file.json'\n  "
+            "matrix_out: null\n  "
             "force_partitioning: 0.5\n  "
-            "waterEntropy: False"
+            "water_entropy: False"
         ).return_value
 
     def test_CodeEntropy_imported(self):