Backport PR scverse#1416: Transfer when copy detected

scvi/model/base/_base_model.py

@@ -255,10 +255,12 @@ def get_anndata_manager(
 
         adata_manager = cls._per_instance_manager_store[self.id][adata_id]
         if adata_manager.adata is not adata:
-            raise ValueError(
-                "The provided AnnData object does not match the AnnData object "
-                "previously provided for setup. Did you make a copy?"
+            logger.info(
+                "AnnData object appears to be a copy. Attempting to transfer setup."
             )
+            _assign_adata_uuid(adata, overwrite=True)
+            adata_manager = self.adata_manager.transfer_fields(adata)
+            self._register_manager_for_instance(adata_manager)
 
         return adata_manager
 
@@ -355,7 +357,7 @@ def _validate_anndata(
         if adata.is_view:
             if copy_if_view:
                 logger.info("Received view of anndata, making copy.")
-                adata = adata.copy()
+                adata._init_as_actual(adata.copy())
                 # Reassign AnnData UUID to produce a separate AnnDataManager.
                 _assign_adata_uuid(adata, overwrite=True)
             else:

tests/models/test_models.py

@@ -225,7 +225,7 @@ def test_scvi(save_path):
     model._validate_anndata(adata2)
     model.get_elbo(adata2)
 
-    # test automatic transfer_anndata_setup + on a view
+    # test automatic transfer_anndata_setup on a view
     adata = synthetic_iid()
     SCVI.setup_anndata(
         adata,
@@ -236,6 +236,18 @@ def test_scvi(save_path):
     adata2 = synthetic_iid()
     model.get_elbo(adata2[:10])
 
+    # test automatic transfer_anndata_setup on a copy
+    adata = synthetic_iid()
+    SCVI.setup_anndata(
+        adata,
+        batch_key="batch",
+        labels_key="labels",
+    )
+    model = SCVI(adata)
+    adata2 = adata.copy()
+    model.get_elbo(adata2)
+    assert adata.uns[_constants._SCVI_UUID_KEY] != adata2.uns[_constants._SCVI_UUID_KEY]
+
     # test mismatched categories raises ValueError
     adata2 = synthetic_iid()
     adata2.obs.labels.cat.rename_categories(["a", "b", "c"], inplace=True)