fix refcopuy

src/ome_types/_mixins/_ome.py

@@ -10,6 +10,7 @@
 
 if TYPE_CHECKING:
     from pathlib import Path
+    from typing import Self
 
     from ome_types._autogenerated.ome_2016_06 import OME, Reference
 
@@ -31,6 +32,11 @@ def _link_refs(self) -> None:
             else:
                 warnings.warn(f"Reference to unknown ID: {ref.id}", stacklevel=2)
 
+    def __deepcopy__(self, memo: dict[int, Any] | None = None) -> Self:
+        copy = super().__deepcopy__(memo)  # type: ignore
+        copy._link_refs()
+        return copy
+
     def __setstate__(self, state: dict[str, Any]) -> None:
         """Support unpickle of our weakref references."""
         super().__setstate__(state)  # type: ignore

tests/test_model.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import copy
 import datetime
 import io
 import warnings
@@ -10,6 +11,7 @@
 from pydantic import ValidationError
 
 from ome_types import from_tiff, from_xml, model, to_xml
+from ome_types.model import OME, AnnotationRef, CommentAnnotation, Instrument
 
 DATA = Path(__file__).parent / "data"
 
@@ -42,6 +44,27 @@ def test_refs() -> None:
     assert ome.screens[0].plate_refs[0].ref is ome.plates[0]
 
 
+def test_ref_copy() -> None:
+    aref = AnnotationRef(id=1)
+    ome = OME(
+        instruments=[Instrument(annotation_refs=[aref])],
+        structured_annotations=[CommentAnnotation(id=1, value="test")],
+    )
+
+    ome2 = ome.model_copy(deep=True)
+    assert ome2.instruments[0].annotation_refs[0].ref is not aref.ref
+
+    ome3 = copy.deepcopy(ome)
+    assert ome3.instruments[0].annotation_refs[0].ref is not aref.ref
+    ome4 = OME(**ome.dict())
+    assert ome4.instruments[0].annotation_refs[0].ref is not aref.ref
+
+    del ome, aref
+    assert ome2.instruments[0].annotation_refs[0].ref is not None
+    assert ome3.instruments[0].annotation_refs[0].ref is not None
+    assert ome4.instruments[0].annotation_refs[0].ref is not None
+
+
 def test_datetimes() -> None:
     now = datetime.datetime.now()
     anno = model.TimestampAnnotation(value=now)