Updated matches variable in list_files.

src/alpineer/io_utils.py

@@ -82,18 +82,18 @@ def list_files(dir_name, substrs=None, exact_match=False, ignore_hidden=True):
             if any([substr == os.path.splitext(file)[0] for substr in substrs])
         ]
     else:
-        matches = []
+        matches_list = []
         for substr in substrs:
             # Create a regular expression pattern from substrs with word boundaries
             pattern = "|".join(re.escape(part) + r"\b" for part in substr.split("_"))
             # Use re.search to check if any of the substrings exactly match in the file names
             substr_matches = [file for file in files if re.search(pattern, file)]
             # append matches for this substr to larger matches list.
-            matches.append(substr_matches)
+            matches_list.append(substr_matches)
         # Flatten the list of match lists
-        flattened_matches = [file for match in matches for file in match]
+        matches = [file for match in matches_list for file in match]
 
-    return flattened_matches
+    return matches
 
 
 def remove_file_extensions(files):