Fix: Ensure verbose flag in YAML sets logging to DEBUG mode

- Updated `merge_configs` method to explicitly handle the `verbose` flag from YAML configuration
- Added `update_logging_level` method to `LoggingConfig` class to update logging levels for all loggers and handlers
- Modified `main` function to use the new method for updating logging levels
- Ensured `DEBUG` level messages are directed to file handlers while console handler remains at `INFO` level
- Updated the input YAML file template to make sure they correctly match up to the arguments in argsparse

Author: harryswift01

CodeEntropy/config/logging_config.py

@@ -4,7 +4,7 @@
 
 
 class LoggingConfig:
-    def __init__(self, folder, default_level=logging.INFO):
+    def __init__(self, folder, log_level=logging.INFO):
         log_directory = os.path.join(folder, "logs")
         os.makedirs(log_directory, exist_ok=True)
 
@@ -26,52 +26,52 @@ def __init__(self, folder, default_level=logging.INFO):
                 "console": {
                     "class": "logging.StreamHandler",
                     "formatter": "simple",
-                    "level": "INFO",
+                    "level": logging.INFO,
                 },
                 "stdout": {
                     "class": "logging.FileHandler",
                     "filename": os.path.join(log_directory, "program.out"),
                     "formatter": "simple",
-                    "level": "INFO",
+                    "level": logging.INFO,
                 },
                 "logfile": {
                     "class": "logging.FileHandler",
                     "filename": os.path.join(log_directory, "program.log"),
                     "formatter": "detailed",
-                    "level": "DEBUG",
+                    "level": logging.DEBUG,
                 },
                 "errorfile": {
                     "class": "logging.FileHandler",
                     "filename": os.path.join(log_directory, "program.err"),
                     "formatter": "detailed",
-                    "level": "ERROR",
+                    "level": logging.ERROR,
                 },
                 "commandfile": {
                     "class": "logging.FileHandler",
                     "filename": os.path.join(log_directory, "program.com"),
                     "formatter": "simple",
-                    "level": "INFO",
+                    "level": logging.INFO,
                 },
                 "mdanalysis_log": {
                     "class": "logging.FileHandler",
                     "filename": os.path.join(log_directory, "mdanalysis.log"),
                     "formatter": "detailed",
-                    "level": "DEBUG",
+                    "level": logging.DEBUG,
                 },
             },
             "loggers": {
                 "": {
                     "handlers": ["console", "stdout", "logfile", "errorfile"],
-                    "level": default_level,
+                    "level": log_level,
                 },
                 "MDAnalysis": {
                     "handlers": ["mdanalysis_log"],
-                    "level": "DEBUG",
+                    "level": logging.DEBUG,
                     "propagate": False,
                 },
                 "commands": {
                     "handlers": ["commandfile"],
-                    "level": "INFO",
+                    "level": logging.INFO,
                     "propagate": False,
                 },
             },
@@ -82,3 +82,23 @@ def setup_logging(self):
         logging.getLogger("MDAnalysis")
         logging.getLogger("commands")
         return logging.getLogger(__name__)
+
+    def update_logging_level(self, log_level):
+        # Update the root logger level
+        root_logger = logging.getLogger()
+        root_logger.setLevel(log_level)
+        for handler in root_logger.handlers:
+            if isinstance(handler, logging.FileHandler):
+                handler.setLevel(logging.DEBUG)
+            else:
+                handler.setLevel(logging.INFO)
+
+        # Update all other loggers and their handlers
+        for logger_name in self.LOGGING["loggers"]:
+            logger = logging.getLogger(logger_name)
+            logger.setLevel(log_level)
+            for handler in logger.handlers:
+                if isinstance(handler, logging.FileHandler):
+                    handler.setLevel(logging.DEBUG)
+                else:
+                    handler.setLevel(logging.INFO)

CodeEntropy/main_mcc.py

@@ -67,24 +67,27 @@ def main():
     args, unknown = parser.parse_known_args()
     args.outfile = os.path.join(folder, args.outfile)
 
-    # Determine logging level
-    log_level = logging.DEBUG if args.verbose else logging.INFO
-
-    # Initialize the logging system with the determined log level
-    logging_config = LoggingConfig(folder, default_level=log_level)
-    logger = logging_config.setup_logging()
-
-    # Capture and log the command-line invocation
-    command = " ".join(sys.argv)
-    logging.getLogger("commands").info(command)
-
     try:
+        # Initialize the logging system once
+        logging_config = LoggingConfig(folder)
+        logger = logging_config.setup_logging()
+
         # Process each run in the YAML configuration
         for run_name, run_config in config.items():
             if isinstance(run_config, dict):
                 # Merging CLI arguments with YAML configuration
                 args = arg_config.merge_configs(args, run_config)
 
+                # Determine logging level
+                log_level = logging.DEBUG if args.verbose else logging.INFO
+
+                # Update the logging level
+                logging_config.update_logging_level(log_level)
+
+                # Capture and log the command-line invocation
+                command = " ".join(sys.argv)
+                logging.getLogger("commands").info(command)
+
                 # Ensure necessary arguments are provided
                 if not getattr(args, "top_traj_file"):
                     raise ValueError(

config.yaml

@@ -7,11 +7,10 @@ run1:
   end: 
   step:
   bin_width:
-  tempra:
+  temperature:
   verbose:
   thread: 
   outfile:
-  resfile:
   mout: 
   force_partitioning:
-  waterEntropy: 
+  waterEntropy: