avoid deleting a file by copying it to itself

Author: FynnBe

bioimageio/spec/_internal/io_utils.py

@@ -287,6 +287,16 @@ def write_content_to_zip(
             else:
                 reader = get_reader(file)
 
+            if (
+                isinstance(reader.original_root, ZipFile)
+                and reader.original_root.filename == zip.filename
+                and reader.original_file_name == arc_name
+            ):
+                logger.debug(
+                    f"Not copying {reader.original_root}/{reader.original_file_name} to itself."
+                )
+                continue
+
             with zip.open(arc_name, "w") as dest:
                 shutil.copyfileobj(reader, dest, 1024 * 8)
 

bioimageio/spec/_package.py

@@ -188,6 +188,13 @@ def save_bioimageio_package_as_folder(
     for name, src in package_content.items():
         if isinstance(src, collections.abc.Mapping):
             write_yaml(src, output_path / name)
+        elif (
+            isinstance(src.original_root, Path)
+            and src.original_root / src.original_file_name == output_path / name
+        ):
+            logger.debug(
+                f"Not copying {src.original_root / src.original_file_name} to itself."
+            )
         else:
             with (output_path / name).open("wb") as dest:
                 _ = shutil.copyfileobj(src, dest)