Fix use_raw=None in scanpy.tl.score_genes (#1999)

* Fix use_raw=None in scanpy.tl.score_genes

* Fix type of use_raw

* Add release notes #1999

* [ci skip] Improve release notes #1999

Co-authored-by: Isaac Virshup <ivirshup@gmail.com>

docs/release-notes/1.8.2.rst

@@ -4,6 +4,8 @@
 .. rubric:: Bug fixes
 
 - Fix plotting after :func:`scanpy.tl.filter_rank_genes_groups` :pr:`1942` :smaller:`S Rybakov`
+- Fix ``use_raw=None`` using :attr:`anndata.AnnData.var_names` if :attr:`anndata.AnnData.raw`
+  is present in :func:`scanpy.tl.score_genes` :pr:`1999` :smaller:`M Klein`
 
 .. rubric:: Performance enhancements
 

scanpy/tests/test_score_genes.py

@@ -212,3 +212,20 @@ def test_one_gene():
     # https://github.com/theislab/scanpy/issues/1395
     adata = _create_adata(100, 1000, p_zero=0, p_nan=0)
     sc.tl.score_genes(adata, [adata.var_names[0]])
+
+
+def test_use_raw_None():
+    adata = _create_adata(100, 1000, p_zero=0, p_nan=0)
+    adata_raw = adata.copy()
+    adata_raw.var_names = [str(i) for i in range(adata_raw.n_vars)]
+    adata.raw = adata_raw
+
+    sc.tl.score_genes(adata, adata_raw.var_names[:3], use_raw=None)
+
+
+@pytest.mark.parametrize("gene_pool", [[], ["foo", "bar"]])
+def test_invalid_gene_pool(gene_pool):
+    adata = _create_adata(100, 1000, p_zero=0, p_nan=0)
+
+    with pytest.raises(ValueError, match="reference set"):
+        sc.tl.score_genes(adata, adata.var_names[:3], gene_pool=gene_pool)

scanpy/tools/_score_genes.py

@@ -46,7 +46,7 @@ def score_genes(
     score_name: str = 'score',
     random_state: AnyRandom = 0,
     copy: bool = False,
-    use_raw: bool = None,
+    use_raw: Optional[bool] = None,
 ) -> Optional[AnnData]:
     """\
     Score a set of genes [Satija15]_.
@@ -94,6 +94,7 @@ def score_genes(
     """
     start = logg.info(f'computing score {score_name!r}')
     adata = adata.copy() if copy else adata
+    use_raw = _check_use_raw(adata, use_raw)
 
     if random_state is not None:
         np.random.seed(random_state)
@@ -117,14 +118,14 @@ def score_genes(
         gene_pool = list(var_names)
     else:
         gene_pool = [x for x in gene_pool if x in var_names]
+    if not gene_pool:
+        raise ValueError("No valid genes were passed for reference set.")
 
     # Trying here to match the Seurat approach in scoring cells.
     # Basically we need to compare genes against random genes in a matched
     # interval of expression.
 
-    use_raw = _check_use_raw(adata, use_raw)
     _adata = adata.raw if use_raw else adata
-
     _adata_subset = (
         _adata[:, gene_pool] if len(gene_pool) < len(_adata.var_names) else _adata
     )