added some fixes based on custom data loader test

src/scvi/model/base/_archesmixin.py

@@ -97,7 +97,9 @@ def load_query_data(
             validate_single_device=True,
         )
 
-        attr_dict, var_names, load_state_dict = _get_loaded_data(reference_model, device=device)
+        attr_dict, var_names, load_state_dict = _get_loaded_data(
+            reference_model, device=device, adata=adata
+        )
 
         if adata is not None:
             if isinstance(adata, MuData):
@@ -216,7 +218,7 @@ def prepare_query_anndata(
         Query adata ready to use in `load_query_data` unless `return_reference_var_names`
         in which case a pd.Index of reference var names is returned.
         """
-        _, var_names, _ = _get_loaded_data(reference_model, device="cpu")
+        _, var_names, _ = _get_loaded_data(reference_model, device="cpu", adata=adata)
         var_names = pd.Index(var_names)
 
         if return_reference_var_names:
@@ -364,15 +366,19 @@ def requires_grad(key):
             par.requires_grad = False
 
 
-def _get_loaded_data(reference_model, device=None):
+def _get_loaded_data(reference_model, device=None, adata=None):
     if isinstance(reference_model, str):
         attr_dict, var_names, load_state_dict, _ = _load_saved_files(
             reference_model, load_adata=False, map_location=device
         )
     else:
         attr_dict = reference_model._get_user_attributes()
         attr_dict = {a[0]: a[1] for a in attr_dict if a[0][-1] == "_"}
-        var_names = _get_var_names(reference_model.adata)
+        var_names = (
+            _get_var_names(reference_model.adata)
+            if attr_dict["registry_"]["setup_method_name"] != "setup_datamodule"
+            else _get_var_names(adata)
+        )
         load_state_dict = deepcopy(reference_model.module.state_dict())
 
     return attr_dict, var_names, load_state_dict

tests/dataloaders/test_custom_dataloader.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+from pprint import pprint
 
 import numpy as np
 import scanpy as sc
@@ -41,6 +42,11 @@
 # Loading the model (just as a compariosn)
 model_orig_loaded = scvi.model.SCVI.load(model_dir, adata=adata)
 
+# when loading from disk
+scvi.model.SCVI.prepare_query_anndata(adata, model_dir)
+# O
+scvi.model.SCVI.prepare_query_anndata(adata, model_orig_loaded)
+
 # Obtaining model outputs
 SCVI_LATENT_KEY = "X_scVI"
 latent = model_orig.get_latent_representation()
@@ -53,6 +59,8 @@
 # adata_manager.get_state_registry(SCVI.REGISTRY_KEYS.X_KEY).to_dict()
 adata_manager.registry[_constants._FIELD_REGISTRIES_KEY]
 
+pprint(adata_manager.registry)
+
 # Plot UMAP and save the figure for later check
 sc.pp.neighbors(adata, use_rep="scvi", key_added="scvi")
 sc.tl.umap(adata, neighbors_key="scvi")