Fixed attr_dict

src/scvi/model/base/_archesmixin.py

@@ -8,6 +8,7 @@
 import pandas as pd
 import torch
 from anndata import AnnData
+from lightning import LightningDataModule
 from mudata import MuData
 from scipy.sparse import csr_matrix
 
@@ -39,8 +40,9 @@ class ArchesMixin:
     @devices_dsp.dedent
     def load_query_data(
         cls,
-        adata: AnnOrMuData,
-        reference_model: Union[str, BaseModelClass],
+        adata: None | AnnOrMuData = None,
+        reference_model: Union[str, BaseModelClass] = None,
+        datamodule: None | LightningDataModule = None,
         inplace_subset_query_vars: bool = False,
         accelerator: str = "auto",
         device: Union[int, str] = "auto",
@@ -83,6 +85,11 @@ def load_query_data(
         freeze_classifier
             Whether to freeze classifier completely. Only applies to `SCANVI`.
         """
+        if reference_model is None:
+            raise ValueError("Please provide a reference model as string or loaded model.")
+        if adata is None and datamodule is None:
+            raise ValueError("Please provide either an AnnData or a datamodule.")
+
         _, _, device = parse_device_args(
             accelerator=accelerator,
             devices=device,
@@ -92,44 +99,45 @@ def load_query_data(
 
         attr_dict, var_names, load_state_dict = _get_loaded_data(reference_model, device=device)
 
-        if isinstance(adata, MuData):
-            for modality in adata.mod:
+        if adata is not None:
+            if isinstance(adata, MuData):
+                for modality in adata.mod:
+                    if inplace_subset_query_vars:
+                        logger.debug(f"Subsetting {modality} query vars to reference vars.")
+                        adata[modality]._inplace_subset_var(var_names[modality])
+                    _validate_var_names(adata[modality], var_names[modality])
+
+            else:
                 if inplace_subset_query_vars:
-                    logger.debug(f"Subsetting {modality} query vars to reference vars.")
-                    adata[modality]._inplace_subset_var(var_names[modality])
-                _validate_var_names(adata[modality], var_names[modality])
+                    logger.debug("Subsetting query vars to reference vars.")
+                    adata._inplace_subset_var(var_names)
+                _validate_var_names(adata, var_names)
 
-        else:
             if inplace_subset_query_vars:
                 logger.debug("Subsetting query vars to reference vars.")
                 adata._inplace_subset_var(var_names)
             _validate_var_names(adata, var_names)
 
-        if inplace_subset_query_vars:
-            logger.debug("Subsetting query vars to reference vars.")
-            adata._inplace_subset_var(var_names)
-        _validate_var_names(adata, var_names)
+            registry = attr_dict.pop("registry_")
+            if _MODEL_NAME_KEY in registry and registry[_MODEL_NAME_KEY] != cls.__name__:
+                raise ValueError("It appears you are loading a model from a different class.")
 
-        registry = attr_dict.pop("registry_")
-        if _MODEL_NAME_KEY in registry and registry[_MODEL_NAME_KEY] != cls.__name__:
-            raise ValueError("It appears you are loading a model from a different class.")
+            if _SETUP_ARGS_KEY not in registry:
+                raise ValueError(
+                    "Saved model does not contain original setup inputs. "
+                    "Cannot load the original setup."
+                )
 
-        if _SETUP_ARGS_KEY not in registry:
-            raise ValueError(
-                "Saved model does not contain original setup inputs. "
-                "Cannot load the original setup."
+            setup_method = getattr(cls, registry[_SETUP_METHOD_NAME])
+            setup_method(
+                adata,
+                source_registry=registry,
+                extend_categories=True,
+                allow_missing_labels=True,
+                **registry[_SETUP_ARGS_KEY],
             )
 
-        setup_method = getattr(cls, registry[_SETUP_METHOD_NAME])
-        setup_method(
-            adata,
-            source_registry=registry,
-            extend_categories=True,
-            allow_missing_labels=True,
-            **registry[_SETUP_ARGS_KEY],
-        )
-
-        model = _initialize_model(cls, adata, attr_dict)
+        model = _initialize_model(cls, adata, datamodule, attr_dict)
         adata_manager = model.get_anndata_manager(adata, required=True)
 
         if REGISTRY_KEYS.CAT_COVS_KEY in adata_manager.data_registry: