Introduce Splash Screen with Metadata and Refactor Water Entropy Handling

CITATION.cff

@@ -37,6 +37,11 @@ authors:
     email: rhen7213@uni.sydney.edu.au
     affiliation: University of Sydney
     orcid: 'https://orcid.org/0000-0002-0461-6625'
+  - given-names: Jonathan
+    family-names: Higham
+    email: j.higham4@lancaster.ac.uk
+    affiliation: Lancaster University
+    orcid: 'https://orcid.org/0000-0002-9779-9968'
   - given-names: Jas
     family-names: Kalayan
     email: jas.kalayan@stfc.ac.uk

CodeEntropy/config/arg_config_manager.py

@@ -82,11 +82,6 @@ def load_config(self, file_path):
         yaml_files = glob.glob(os.path.join(file_path, "*.yaml"))
 
         if not yaml_files:
-            logger.warning(
-                f"No YAML configuration files found in directory: {file_path}. "
-                "Expected a file with extension '.yaml'. "
-                "Proceeding with default configuration: {'run1': {}}."
-            )
             return {"run1": {}}
 
         try:

CodeEntropy/config/data_logger.py

@@ -2,16 +2,23 @@
 import logging
 import re
 
-from tabulate import tabulate
+import numpy as np
+from rich.console import Console
+from rich.table import Table
+
+from CodeEntropy.config.logging_config import LoggingConfig
 
 # Set up logger
 logger = logging.getLogger(__name__)
+console = LoggingConfig.get_console()
 
 
 class DataLogger:
-    def __init__(self):
+    def __init__(self, console=None):
+        self.console = console or Console()
         self.molecule_data = []
         self.residue_data = []
+        self.group_labels = {}
 
     def save_dataframes_as_json(self, molecule_df, residue_df, output_file):
         """Save multiple DataFrames into a single JSON file with separate keys"""
@@ -28,44 +35,75 @@ def clean_residue_name(self, resname):
         """Ensures residue names are stripped and cleaned before being stored"""
         return re.sub(r"[-–—]", "", str(resname))
 
-    def add_results_data(self, resname, level, entropy_type, value):
+    def add_results_data(self, group_id, level, entropy_type, value):
         """Add data for molecule-level entries"""
-        resname = self.clean_residue_name(resname)
-        self.molecule_data.append((resname, level, entropy_type, value))
+        self.molecule_data.append((group_id, level, entropy_type, value))
 
-    def add_residue_data(self, resid, resname, level, entropy_type, value):
+    def add_residue_data(
+        self, group_id, resname, level, entropy_type, frame_count, value
+    ):
         """Add data for residue-level entries"""
         resname = self.clean_residue_name(resname)
-        self.residue_data.append([resid, resname, level, entropy_type, value])
+        if isinstance(frame_count, np.ndarray):
+            frame_count = frame_count.tolist()
+        self.residue_data.append(
+            [group_id, resname, level, entropy_type, frame_count, value]
+        )
+
+    def add_group_label(self, group_id, label, residue_count=None, atom_count=None):
+        """Store a mapping from group ID to a descriptive label and metadata"""
+        self.group_labels[group_id] = {
+            "label": label,
+            "residue_count": residue_count,
+            "atom_count": atom_count,
+        }
 
     def log_tables(self):
-        """Log both tables at once"""
-        # Log molecule data
+        """Display rich tables in terminal"""
+
         if self.molecule_data:
-            logger.info("Molecule Data Table:")
-            table_str = tabulate(
-                self.molecule_data,
-                headers=["Residue Name", "Level", "Type", "Result (J/mol/K)"],
-                tablefmt="grid",
-                numalign="center",
-                stralign="center",
+            table = Table(
+                title="Molecule Entropy Results", show_lines=True, expand=True
             )
-            logger.info(f"\n{table_str}")
+            table.add_column("Group ID", justify="center", style="bold cyan")
+            table.add_column("Level", justify="center", style="magenta")
+            table.add_column("Type", justify="center", style="green")
+            table.add_column("Result (J/mol/K)", justify="center", style="yellow")
+
+            for row in self.molecule_data:
+                table.add_row(*[str(cell) for cell in row])
+
+            console.print(table)
 
-        # Log residue data
         if self.residue_data:
-            logger.info("Residue Data Table:")
-            table_str = tabulate(
-                self.residue_data,
-                headers=[
-                    "Residue ID",
-                    "Residue Name",
-                    "Level",
-                    "Type",
-                    "Result (J/mol/K)",
-                ],
-                tablefmt="grid",
-                numalign="center",
-                stralign="center",
+            table = Table(title="Residue Entropy Results", show_lines=True, expand=True)
+            table.add_column("Group ID", justify="center", style="bold cyan")
+            table.add_column("Residue Name", justify="center", style="cyan")
+            table.add_column("Level", justify="center", style="magenta")
+            table.add_column("Type", justify="center", style="green")
+            table.add_column("Count", justify="center", style="green")
+            table.add_column("Result (J/mol/K)", justify="center", style="yellow")
+
+            for row in self.residue_data:
+                table.add_row(*[str(cell) for cell in row])
+
+            console.print(table)
+
+        if self.group_labels:
+            label_table = Table(
+                title="Group ID to Residue Label Mapping", show_lines=True, expand=True
             )
-            logger.info(f"\n{table_str}")
+            label_table.add_column("Group ID", justify="center", style="bold cyan")
+            label_table.add_column("Residue Label", justify="center", style="green")
+            label_table.add_column("Residue Count", justify="center", style="magenta")
+            label_table.add_column("Atom Count", justify="center", style="yellow")
+
+            for group_id, info in self.group_labels.items():
+                label_table.add_row(
+                    str(group_id),
+                    info["label"],
+                    str(info.get("residue_count", "")),
+                    str(info.get("atom_count", "")),
+                )
+
+            console.print(label_table)