Drop multi-indexes when assigning to a multi-indexed variable

Closes pydata#6505

xarray/core/coordinates.py

@@ -1,13 +1,14 @@
 from __future__ import annotations
 
+import warnings
 from contextlib import contextmanager
 from typing import TYPE_CHECKING, Any, Hashable, Iterator, Mapping, Sequence, cast
 
 import numpy as np
 import pandas as pd
 
 from . import formatting
-from .indexes import Index, Indexes, assert_no_index_corrupted
+from .indexes import Index, Indexes, PandasMultiIndex, assert_no_index_corrupted
 from .merge import merge_coordinates_without_align, merge_coords
 from .utils import Frozen, ReprObject
 from .variable import Variable, calculate_dimensions
@@ -152,8 +153,32 @@ def to_index(self, ordered_dims: Sequence[Hashable] = None) -> pd.Index:
 
         return pd.MultiIndex(level_list, code_list, names=names)
 
+    def _drop_multiindexes(self, keys):
+        from .dataset import Dataset
+
+        for key in keys:
+            maybe_midx = self._data._indexes.get(key, None)
+            idx_coord_names = set(maybe_midx.index.names + [maybe_midx.dim])
+            if isinstance(maybe_midx, PandasMultiIndex):
+                warnings.warn(
+                    f"Updating MultiIndexed coordinate {key!r} would corrupt indices for "
+                    f"other variables: {list(maybe_midx.index.names)!r}. "
+                    f"This will raise an error in the future. Use `.drop_vars({idx_coord_names!r})` before "
+                    "assigning new coordinate values.",
+                    DeprecationWarning,
+                    stacklevel=3,
+                )
+                for k in idx_coord_names:
+                    if isinstance(self._data, Dataset):
+                        del self._data._variables[k]
+                        del self._data._indexes[k]
+                    else:
+                        del self._data._coords[k]
+                        del self._data._indexes[k]
+
     def update(self, other: Mapping[Any, Any]) -> None:
         other_vars = getattr(other, "variables", other)
+        self._drop_multiindexes(other_vars.keys())
         coords, indexes = merge_coords(
             [self.variables, other_vars], priority_arg=1, indexes=self.xindexes
         )

xarray/core/dataset.py

@@ -5764,6 +5764,7 @@ def assign(
         data = self.copy()
         # do all calculations first...
         results: CoercibleMapping = data._calc_assign_results(variables)
+        data.coords._drop_multiindexes(results.keys())
         # ... and then assign
         data.update(results)
         return data

xarray/tests/test_dataarray.py

@@ -1499,6 +1499,13 @@ def test_assign_coords(self) -> None:
         with pytest.raises(ValueError):
             da.coords["x"] = ("y", [1, 2, 3])  # no new dimension to a DataArray
 
+    def test_assign_coords_existing_multiindex(self) -> None:
+        data = self.mda
+        with pytest.warns(
+            DeprecationWarning, match=r"Updating MultiIndexed coordinate"
+        ):
+            data.assign_coords(x=range(4))
+
     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

@@ -3967,6 +3967,18 @@ def test_assign_multiindex_level(self) -> None:
             data.assign(level_1=range(4))
             data.assign_coords(level_1=range(4))
 
+    def test_assign_coords_existing_multiindex(self) -> None:
+        data = create_test_multiindex()
+        with pytest.warns(
+            DeprecationWarning, match=r"Updating MultiIndexed coordinate"
+        ):
+            data.assign_coords(x=range(4))
+
+        with pytest.warns(
+            DeprecationWarning, match=r"Updating MultiIndexed coordinate"
+        ):
+            data.assign(x=range(4))
+
     def test_assign_all_multiindex_coords(self) -> None:
         data = create_test_multiindex()
         actual = data.assign(x=range(4), level_1=range(4), level_2=range(4))