Update src/hdf5_ops.py to allow for replicates after flattening directory structures.

src/hdf5_ops.py

@@ -737,9 +737,29 @@ def save_file_dict_to_hdf5(h5file, group_name, file_dict):
     try:
         # Create group and add their attributes
         filename = file_dict['name']
-        group = h5file[group_name].create_group(name=filename)
+
+        # Base filename to use as group name
+        base_filename = file_dict['name']
+        candidate_name = base_filename
+        replicate_index = 0
+
+        # Check for existing group and find a free name
+        parent_group = h5file.require_group(group_name)
+        while candidate_name in parent_group:
+            replicate_index += 1
+            candidate_name = f"{base_filename}_{replicate_index}"
+
+        group = h5file[group_name].create_group(name=candidate_name )
         # Add group attributes                                
         group.attrs.update(file_dict['attributes_dict'])
+
+        # Annotate replicate if renamed
+        if replicate_index > 0:
+            group.attrs['replicate_of'] = base_filename
+            group.attrs['replicate_info'] = (
+                f"Renamed due to existing group with same name. "
+                f"This is replicate #{replicate_index}."
+            )
         
         # Add datasets to the just created group
         for dataset in file_dict['datasets']: