Coerce IndexVariable to Variable when assigning to data variables or coordinates

doc/whats-new.rst

@@ -44,6 +44,9 @@ Bug Fixes
 - Fix error handling issue in ``decode_cf_variables`` when decoding fails - the exception is now re-raised
   correctly, with a note added about the variable name that caused the error (:issue:`10873`, :pull:`10886`).
   By `Jonas L. Bertelsen <https://github.com/jonaslb>`_
+- When assigning an indexed coordinate to a data variable or coordinate, coerce it from
+  ``IndexVariable`` to ``Variable`` (:issue:`9859`, :issue:`10829`, :pull:`10909`)
+  By `Julia Signell <https://github.com/jsignell>`_
 
 Performance
 ~~~~~~~~~~~

xarray/core/coordinates.py

@@ -1265,7 +1265,7 @@ def create_coords_with_default_indexes(
             variables.update(idx_vars)
             all_variables.update(idx_vars)
         else:
-            variables[name] = variable
+            variables[name] = variable.to_base_variable()
 
     new_coords = Coordinates._construct_direct(coords=variables, indexes=indexes)
 

xarray/structure/merge.py

@@ -22,7 +22,12 @@
     emit_user_level_warning,
     equivalent,
 )
-from xarray.core.variable import Variable, as_variable, calculate_dimensions
+from xarray.core.variable import (
+    IndexVariable,
+    Variable,
+    as_variable,
+    calculate_dimensions,
+)
 from xarray.structure.alignment import deep_align
 from xarray.util.deprecation_helpers import (
     _COMPAT_DEFAULT,
@@ -1206,7 +1211,11 @@ def dataset_update_method(dataset: Dataset, other: CoercibleMapping) -> _MergeRe
                     if c not in value.dims and c in dataset.coords
                 ]
                 if coord_names:
-                    other[key] = value.drop_vars(coord_names)
+                    value = value.drop_vars(coord_names)
+                if isinstance(value.variable, IndexVariable):
+                    variable = value.variable.to_base_variable()
+                    value = value._replace(variable=variable)
+                other[key] = value
 
     return merge_core(
         [dataset, other],

xarray/tests/test_dataarray.py

@@ -1702,6 +1702,11 @@ def should_add_coord_to_array(self, name, var, dims):
         assert_identical(actual, expected, check_default_indexes=False)
         assert "x_bnds" not in actual.dims
 
+    def test_assign_coords_uses_base_variable_class(self) -> None:
+        a = DataArray([0, 1, 2], dims=["x"], coords={"x": [0, 1, 2]})
+        a = a.assign_coords(foo=a.x)
+        assert not isinstance(a["foo"].variable, IndexVariable)
+
     def test_coords_alignment(self) -> None:
         lhs = DataArray([1, 2, 3], [("x", [0, 1, 2])])
         rhs = DataArray([2, 3, 4], [("x", [1, 2, 3])])

xarray/tests/test_dataset.py

@@ -4779,6 +4779,11 @@ def test_setitem_using_list_errors(self, var_list, data, error_regex) -> None:
         with pytest.raises(ValueError, match=error_regex):
             actual[var_list] = data
 
+    def test_setitem_uses_base_variable_class_even_for_index_variables(self) -> None:
+        ds = Dataset(coords={"x": [1, 2, 3]})
+        ds["y"] = ds["x"]
+        assert not isinstance(ds["y"].variable, IndexVariable)
+
     def test_assign(self) -> None:
         ds = Dataset()
         actual = ds.assign(x=[0, 1, 2], y=2)