Update files with ruff

Author: Alirezak2n

ideeplc/__main__.py

@@ -103,12 +103,12 @@ def main():
     args = parser.parse_args()
 
     # Set up logging to file: ideeplc_run.log
-    log_file = Path(f"ideeplc.log")
+    log_file = Path("ideeplc.log")
     _setup_logging(args.log_level, log_file=log_file)
 
     try:
         run_ideeplc(args)  # This should be the entry function from your main logic
-    except Exception as e:
+    except Exception:
         LOGGER.exception("Execution failed.")
         sys.exit(1)
 

ideeplc/data_initialize.py

@@ -1,6 +1,5 @@
-import platform
 import logging
-from typing import Tuple, Optional, Union
+from typing import Tuple, Union
 import pandas as pd
 import numpy as np
 from torch.utils.data import Dataset, DataLoader
@@ -47,7 +46,7 @@ def data_initialize(
         raise
 
     if "seq" not in df.columns:
-        LOGGER.error(f"CSV file must contain a 'seq' column with peptide sequences.")
+        LOGGER.error("CSV file must contain a 'seq' column with peptide sequences.")
         raise ValueError("Missing 'seq' column in the CSV file.")
     if "modifications" not in df.columns:
         LOGGER.error(

ideeplc/ideeplc_core.py

@@ -1,4 +1,3 @@
-import argparse
 import datetime
 import logging
 import torch
@@ -92,7 +91,7 @@ def main(args):
             input_file=args.input,
             save_results=args.save,
         )
-        LOGGER.info(f"Prediction completed.")
+        LOGGER.info("Prediction completed.")
         # Generate Figures
         make_figures(
             predictions=pred_results,