deprecate arg

Author: selmanozleyen

src/squidpy/gr/_ligrec.py

@@ -23,13 +23,14 @@
 from squidpy._constants._constants import ComplexPolicy, CorrAxis
 from squidpy._constants._pkg_constants import Key
 from squidpy._docs import d, inject_docs
-from squidpy._utils import NDArrayA
+from squidpy._utils import NDArrayA, deprecated_params
 from squidpy.gr._utils import (
     _assert_categorical_obs,
     _assert_positive,
     _check_tuple_needles,
     _genesymbols,
     _save_data,
+    extract_adata,
 )
 
 __all__ = ["ligrec", "PermutationTest"]
@@ -537,6 +538,7 @@ def prepare(
 
 
 @d.dedent
+@deprecated_params({"numba_parallel": "1.10.0"})
 def ligrec(
     adata: AnnData | SpatialData,
     cluster_key: str,
@@ -558,6 +560,8 @@ def ligrec(
     interactions_params: Mapping[str, Any] = MappingProxyType({}),
     transmitter_params: Mapping[str, Any] = MappingProxyType({"categories": "ligand"}),
     receiver_params: Mapping[str, Any] = MappingProxyType({"categories": "receptor"}),
+    *,
+    table_key: str = "table",
 ) -> Mapping[str, pd.DataFrame] | None:
     """
     %(PT_test.full_desc)s
@@ -574,8 +578,7 @@ def ligrec(
     -------
     %(ligrec_test_returns)s
     """  # noqa: D400
-    if isinstance(adata, SpatialData):
-        adata = adata.table
+    adata = extract_adata(adata, table_key=table_key)
     with _genesymbols(adata, key=gene_symbols, use_raw=use_raw, make_unique=False):
         return (  # type: ignore[no-any-return]
             PermutationTest(adata, use_raw=use_raw)