Fix uns merge 3d

anndata/_core/merge.py

@@ -141,7 +141,13 @@ def equal_dask_array(a, b) -> bool:
 
 @equal.register(np.ndarray)
 def equal_array(a, b) -> bool:
-    return equal(pd.DataFrame(a), pd.DataFrame(asarray(b)))
+    # Reshaping allows us to compare inputs with >2 dimensions
+    # We cast to pandas since it will still work with non-numeric types
+    b = asarray(b)
+    if a.shape != b.shape:
+        return False
+
+    return equal(pd.DataFrame(a.reshape(-1)), pd.DataFrame(b.reshape(-1)))
 
 
 @equal.register(CupyArray)

anndata/tests/helpers.py

@@ -413,7 +413,11 @@ def assert_equal_ndarray(a, b, exact=False, elem_name=None):
         and len(a.dtype) > 1
         and len(b.dtype) > 0
     ):
-        assert_equal(pd.DataFrame(a), pd.DataFrame(b), exact, elem_name)
+        # Reshaping to allow >2d arrays
+        assert a.shape == b.shape, format_msg(elem_name)
+        assert_equal(
+            pd.DataFrame(a.reshape(-1)), pd.DataFrame(b.reshape(-1)), exact, elem_name
+        )
     else:
         assert np.all(a == b), format_msg(elem_name)
 

anndata/tests/test_concatenate.py

@@ -28,6 +28,7 @@
     as_dense_dask_array,
     assert_equal,
     gen_adata,
+    gen_vstr_recarray,
 )
 from anndata.utils import asarray
 
@@ -1018,6 +1019,15 @@ def gen_something(n):
     return np.random.choice(options)(n)
 
 
+def gen_3d_numeric_array(n):
+    return np.random.randn(n, n, n)
+
+
+def gen_3d_recarray(_):
+    # Ignoring n as it can get quite slow
+    return gen_vstr_recarray(8, 3).reshape(2, 2, 2)
+
+
 def gen_concat_params(unss, compat2result):
     value_generators = [
         lambda x: x,
@@ -1026,6 +1036,8 @@ def gen_concat_params(unss, compat2result):
         gen_list,
         gen_sparse,
         gen_something,
+        gen_3d_numeric_array,
+        gen_3d_recarray,
     ]
     for gen, (mode, result) in product(value_generators, compat2result.items()):
         yield pytest.param(unss, mode, result, gen)

docs/release-notes/0.10.5.md

@@ -4,6 +4,7 @@
 ```
 
 * Fix outer concatenation along variables when only a subset of objects had an entry in layers {pr}`1291` {user}`ivirshup`
+* Fix comparison of >2d arrays in `uns` during concatenation {pr}`1300` {user}`ivirshup`
 
 ```{rubric} Documentation
 ```