fix: allow ingest to handle older anndata (#4516)

Author: flying-sheep

docs/release-notes/4516.fix.md

@@ -0,0 +1 @@
+Fix {func}`scanpy.tl.ingest` failing with a `KeyError` when the reference’s PCA was computed by an old scanpy version and has no `.uns["pca"]["params"]` {smaller}`P Angerer`

src/scanpy/tools/_ingest.py

@@ -332,10 +332,12 @@ def _init_neighbors(self, adata: AnnData, neighbors_key: str | None) -> None:
         )
 
     def _init_pca(self, adata: AnnData) -> None:
-        self._pca_centered = adata.uns["pca"]["params"]["zero_center"]
+        # PCA from old scanpy versions has no `params`, use `pp.pca`’s defaults
+        params = adata.uns["pca"].get("params", {})
+        self._pca_centered = params.get("zero_center", True)
         self._pca_mask = _check_mask(
             adata,
-            _mask_arg(None, adata.uns["pca"]["params"]["mask_var"], dim="var"),
+            _mask_arg(None, params.get("mask_var"), dim="var"),
             "var",
         )
 

tests/test_ingest.py

@@ -174,8 +174,20 @@ def test_neighbors_defaults(adatas, n):
 
 # https://github.com/lmcinnes/umap/issues/1174
 @pytest.mark.filterwarnings("ignore:.*renamed to.*ensure_all_finite:FutureWarning")
-def test_ingest_function(adatas: tuple[sc.AnnData, sc.AnnData]) -> None:
+@pytest.mark.parametrize(
+    "has_pca_params",
+    [
+        pytest.param(True, id="pca_params"),
+        # PCA from old scanpy versions has no `.uns["pca"]["params"]` (#4507)
+        pytest.param(False, id="no_pca_params"),
+    ],
+)
+def test_ingest_function(
+    adatas: tuple[sc.AnnData, sc.AnnData], *, has_pca_params: bool
+) -> None:
     adata_ref, adata_new = (ad.copy() for ad in adatas)
+    if not has_pca_params:
+        del adata_ref.uns["pca"]["params"]
 
     sc.tl.ingest(
         adata_new,