add notes

examples/atlas/setup_run.py

@@ -11,11 +11,14 @@
 
 
 def load_commands(config_path):
+    """Load YAML configuration file containing command templates for different
+    algorithms."""
     with open(config_path, encoding='utf-8') as f:
         return yaml.safe_load(f)
 
 
 def load_run_configs(run_config_path):
+    """Load CSV file containing run configurations for different experiments."""
     return pd.read_csv(run_config_path)
 
 
@@ -25,11 +28,13 @@ def main():
 
     args = parser.parse_args()
 
+    # Load configuration files
     run_configs_df = load_run_configs(args.config)
-
     commands_config = load_commands("config/commands.yaml")
 
+    # Process each run configuration
     for _, run in run_configs_df.iterrows():
+        # Extract parameters for current run
         algorithm_name = run['algorithm_name']
         dataset_id = run['dataset_id']
         species = run['species']
@@ -38,31 +43,36 @@ def main():
         count = run['count']
         device = run['device']
 
-        # Define paths
+        # Setup directory structure for the algorithm configuration
         template_path = os.path.join("config/atlas_template_yamls",
                                      f"{algorithm_name}/pipeline_params_tuning_config.yaml")
         config_dir = f"{DANCEDIR}/examples/tuning/{algorithm_name}/{dataset_id}"
+
+        # Create configuration directory if it doesn't exist
         try:
             os.makedirs(config_dir, exist_ok=False)
         except FileExistsError:
             logger.warning(f"Error: Directory {config_dir} already exists. Please remove it before running again.")
             continue
+
         config_filename = f"pipeline_params_tuning_config.yaml"
         config_path = os.path.join(config_dir, config_filename)
 
         # Copy configuration file
         shutil.copy(template_path, config_path)
         print(f"Template copied to {config_path}")
 
+        # Validate algorithm exists in commands configuration
         if algorithm_name not in commands_config.get("algorithms", {}):
             print(f"Error: Command not found for algorithm '{algorithm_name}'. Please check commands.yaml file.")
             continue
 
+        # Format command template with run parameters
         command_template = commands_config["algorithms"][algorithm_name]["command"]
         run_command = command_template.format(dataset_id=dataset_id, species=species, tissue=tissue, filetype=filetype,
                                               count=count, device=device)
 
-        # Append the run command to run.sh
+        # Append generated command to run script
         run_sh_path = f"{DANCEDIR}/examples/tuning/{algorithm_name}/run.sh"
         with open(run_sh_path, "a", encoding='utf-8') as run_script:
             run_script.write(f"{run_command}\n")