Improve logging

Hopefully this will make debugging easier on HF

run_utils.py

@@ -117,7 +117,11 @@ def run_cli_command(
                 )
                 logging.debug(f"Command output:\n{result.stdout}")
                 if result.stderr:
-                    logging.error(f"Command error:\n{result.stderr}")
+                    # Skip progress bar lines
+                    stderr_lines = result.stderr.split("\n")
+                    stderr_lines = filter(lambda x: "%|" not in x, stderr_lines)
+                    stderr_text = "\n".join(stderr_lines)
+                    logging.error(f"Command error:\n{stderr_text}")
         except subprocess.CalledProcessError as e:
             logging.error(f"An error occurred while executing the command: {e}")
 
@@ -136,21 +140,25 @@ def run_cli_command(
             pdb_path = os.path.join(example_dir, "rank1_reverseprocess_protein.pdb")
             sdf_path = os.path.join(example_dir, "rank1.sdf")
 
+        logging.debug(f"PDB path: {pdb_path}")
+        logging.debug(f"SDF path: {sdf_path}")
         if pdb_path and os.path.exists(pdb_path):
             pdb_text = read_file_lines(pdb_path)
+        if sdf_path and os.path.exists(sdf_path):
             sdf_text = read_file_lines(sdf_path)
 
-        logging.debug(f"Display path: {pdb_path}")
-
         # Zip the output directory
         # Generate a unique filename using a timestamp and a UUID
         timestamp = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
         uuid_tag = str(uuid.uuid4())[0:8]
         unique_filename = f"diffdock_pocket_output_{timestamp}_{uuid_tag}"
         zip_base_name = os.path.join("tmp", unique_filename)
+
+        logging.debug(f"About to zip directory '{temp_dir}' to {unique_filename}")
+
         full_zip_path = shutil.make_archive(zip_base_name, "zip", temp_dir)
 
-        logging.debug(f"Directory '{temp_dir}' zipped to '{full_zip_path}'")
+        logging.debug(f"Directory '{temp_dir}' zipped to {unique_filename}'")
 
     return full_zip_path, pdb_text, sdf_text