Fix alignment with join="override" when some dims are unindexed

doc/whats-new.rst

@@ -48,6 +48,8 @@ New Features
 Bug fixes
 ~~~~~~~~~
 
+- Fix alignment with ``join="override"`` when some dimensions are unindexed. (:issue:`3681`).
+  By `Deepak Cherian <https://github.com/dcherian>`_.
 - Fix :py:meth:`Dataset.swap_dims` and :py:meth:`DataArray.swap_dims` producing
   index with name reflecting the previous dimension name instead of the new one
   (:issue:`3748`, :pull:`3752`). By `Joseph K Aicher

xarray/core/alignment.py

@@ -50,7 +50,7 @@ def _override_indexes(objects, all_indexes, exclude):
     objects = list(objects)
     for idx, obj in enumerate(objects[1:]):
         new_indexes = {}
-        for dim in obj.dims:
+        for dim in obj.indexes:
             if dim not in exclude:
                 new_indexes[dim] = all_indexes[dim][0]
         objects[idx + 1] = obj._overwrite_indexes(new_indexes)

xarray/tests/test_concat.py

@@ -250,6 +250,13 @@ def test_concat_join_kwarg(self):
             actual = concat([ds1, ds2], join=join, dim="x")
             assert_equal(actual, expected[join])
 
+        # regression test for #3681
+        actual = concat([ds1.drop("x"), ds2.drop("x")], join="override", dim="y")
+        expected = Dataset(
+            {"a": (("x", "y"), np.array([0, 0], ndmin=2))}, coords={"y": [0, 0.0001]}
+        )
+        assert_identical(actual, expected)
+
     def test_concat_promote_shape(self):
         # mixed dims within variables
         objs = [Dataset({}, {"x": 0}), Dataset({"x": [1]})]