Fix outer concatenation along axis=1 for missing layers

anndata/_core/merge.py

@@ -913,6 +913,13 @@ def outer_concat_aligned_mapping(
     result = {}
     ns = [m.parent.shape[axis] for m in mappings]
 
+    def missing_element(n: int, axis: Literal[0, 1] = 0) -> np.ndarray:
+        """Generates value to use when there is a missing element."""
+        if axis == 0:
+            return np.zeros((n, 0), dtype=bool)
+        else:
+            return np.zeros((0, n), dtype=bool)
+
     for k in union_keys(mappings):
         els = [m.get(k, MissingVal) for m in mappings]
         if reindexers is None:
@@ -924,7 +931,7 @@ def outer_concat_aligned_mapping(
         # We should probably just handle missing elements for all types
         result[k] = concat_arrays(
             [
-                el if not_missing(el) else np.zeros((n, 0), dtype=bool)
+                el if not_missing(el) else missing_element(n, axis=axis)
                 for el, n in zip(els, ns)
             ],
             cur_reindexers,

anndata/tests/test_concatenate.py

@@ -1550,3 +1550,22 @@ def test_error_on_mixed_device():
 
     for p in permutations([cp_adata, cp_sparse_adata]):
         concat(p)
+
+
+def test_concat_on_var_outer_join(array_type):
+    # https://github.com/scverse/anndata/issues/1286
+    a = AnnData(
+        obs=pd.DataFrame(index=[f"cell_{i:02d}" for i in range(10)]),
+        var=pd.DataFrame(index=[f"gene_{i:02d}" for i in range(10)]),
+        layers={
+            "X": array_type(np.ones((10, 10))),
+        },
+    )
+    b = AnnData(
+        obs=pd.DataFrame(index=[f"cell_{i:02d}" for i in range(10)]),
+        var=pd.DataFrame(index=[f"gene_{i:02d}" for i in range(10, 20)]),
+    )
+
+    # This shouldn't error
+    # TODO: specify expected result while accounting for null value
+    _ = concat([a, b], join="outer", axis=1)

docs/release-notes/0.10.5.md

@@ -3,6 +3,8 @@
 ```{rubric} Bugfix
 ```
 
+* Fix outer concatenation along variables when only a subset of objects had an entry in layers {pr}`1291` {user}`ivirshup`
+
 ```{rubric} Documentation
 ```