Drop multi-indexes when assigning to a multi-indexed variable (#6798)

Co-authored-by: Anderson Banihirwe <axbanihirwe@ualr.edu>
Co-authored-by: Benoit Bovy <bbovy@gfz-potsdam.de>

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
@@ -57,6 +58,9 @@ def variables(self):
     def _update_coords(self, coords, indexes):
         raise NotImplementedError()
 
+    def _maybe_drop_multiindex_coords(self, coords):
+        raise NotImplementedError()
+
     def __iter__(self) -> Iterator[Hashable]:
         # needs to be in the same order as the dataset variables
         for k in self.variables:
@@ -154,6 +158,7 @@ def to_index(self, ordered_dims: Sequence[Hashable] = None) -> pd.Index:
 
     def update(self, other: Mapping[Any, Any]) -> None:
         other_vars = getattr(other, "variables", other)
+        self._maybe_drop_multiindex_coords(set(other_vars))
         coords, indexes = merge_coords(
             [self.variables, other_vars], priority_arg=1, indexes=self.xindexes
         )
@@ -304,6 +309,15 @@ def _update_coords(
         original_indexes.update(indexes)
         self._data._indexes = original_indexes
 
+    def _maybe_drop_multiindex_coords(self, coords: set[Hashable]) -> None:
+        """Drops variables in coords, and any associated variables as well."""
+        assert self._data.xindexes is not None
+        variables, indexes = drop_coords(
+            coords, self._data._variables, self._data.xindexes
+        )
+        self._data._variables = variables
+        self._data._indexes = indexes
+
     def __delitem__(self, key: Hashable) -> None:
         if key in self:
             del self._data[key]
@@ -372,6 +386,14 @@ def _update_coords(
         original_indexes.update(indexes)
         self._data._indexes = original_indexes
 
+    def _maybe_drop_multiindex_coords(self, coords: set[Hashable]) -> None:
+        """Drops variables in coords, and any associated variables as well."""
+        variables, indexes = drop_coords(
+            coords, self._data._coords, self._data.xindexes
+        )
+        self._data._coords = variables
+        self._data._indexes = indexes
+
     @property
     def variables(self):
         return Frozen(self._data._coords)
@@ -397,6 +419,37 @@ def _ipython_key_completions_(self):
         return self._data._ipython_key_completions_()
 
 
+def drop_coords(
+    coords_to_drop: set[Hashable], variables, indexes: Indexes
+) -> tuple[dict, dict]:
+    """Drop index variables associated with variables in coords_to_drop."""
+    # Only warn when we're dropping the dimension with the multi-indexed coordinate
+    # If asked to drop a subset of the levels in a multi-index, we raise an error
+    # later but skip the warning here.
+    new_variables = dict(variables.copy())
+    new_indexes = dict(indexes.copy())
+    for key in coords_to_drop & set(indexes):
+        maybe_midx = indexes[key]
+        idx_coord_names = set(indexes.get_all_coords(key))
+        if (
+            isinstance(maybe_midx, PandasMultiIndex)
+            and key == maybe_midx.dim
+            and (idx_coord_names - coords_to_drop)
+        ):
+            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=4,
+            )
+            for k in idx_coord_names:
+                del new_variables[k]
+                del new_indexes[k]
+    return new_variables, new_indexes
+
+
 def assert_coordinate_consistent(
     obj: DataArray | Dataset, coords: Mapping[Any, Variable]
 ) -> None:

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._maybe_drop_multiindex_coords(set(results.keys()))
         # ... and then assign
         data.update(results)
         return data

xarray/core/indexes.py

@@ -1085,6 +1085,9 @@ def dims(self) -> Mapping[Hashable, int]:
 
         return Frozen(self._dims)
 
+    def copy(self):
+        return type(self)(dict(self._indexes), dict(self._variables))
+
     def get_unique(self) -> list[T_PandasOrXarrayIndex]:
         """Return a list of unique indexes, preserving order."""
 

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))