Merge pull request #1100 from YosefLab/scanvi_pred

fix scanvi predict typo

docs/release_notes/v0.12.0.rst

@@ -25,6 +25,7 @@ Bug fixes
 - Fix issue where anndata setup with a layer led to errors in :class:`~scvi.external.SOLO` (`#1098`_).
 - Fix `adata` parameter of :func:`scvi.external.SOLO.from_scvi_model`, which previously did nothing (`#1078`_).
 - Fix default `max_epochs` of :class:`~scvi.model.SCANVI` when initializing using pre-trained model of :class:`~scvi.model.SCVI` (`#1079`_).
+- Fix bug in `predict()` function of :class:`~scvi.model.SCANVI`, which only occurred for soft predictions (`#1100`_).
 
 
 
@@ -62,5 +63,5 @@ Contributors
 .. _`#1090`: https://github.com/YosefLab/scvi-tools/pull/1090
 .. _`#1098`: https://github.com/YosefLab/scvi-tools/pull/1098
 .. _`#1099`: https://github.com/YosefLab/scvi-tools/pull/1099
-
+.. _`#1100`: https://github.com/YosefLab/scvi-tools/pull/1100
 

scvi/model/_scanvi.py

@@ -296,7 +296,7 @@ def predict(
                 columns=self._label_mapping[:n_labels],
                 index=adata.obs_names[indices],
             )
-            return y_pred
+            return pred
 
     def train(
         self,

tests/models/test_models.py

@@ -3,6 +3,7 @@
 
 import anndata
 import numpy as np
+import pandas as pd
 import pytest
 from pytorch_lightning.callbacks import LearningRateMonitor
 from scipy.sparse import csr_matrix
@@ -479,7 +480,8 @@ def test_scanvi(save_path):
     predictions = model.predict(adata2, indices=[1, 2, 3])
     assert len(predictions) == 3
     model.predict()
-    model.predict(adata2, soft=True)
+    df = model.predict(adata2, soft=True)
+    assert isinstance(df, pd.DataFrame)
     model.predict(adata2, soft=True, indices=[1, 2, 3])
     model.get_normalized_expression(adata2)
     model.differential_expression(groupby="labels", group1="label_1")