BUG: boolean indexer with NA raising when reindex is necessary

doc/source/whatsnew/v1.5.0.rst

@@ -1,3 +1,4 @@
+
 .. _whatsnew_150:
 
 What's new in 1.5.0 (??)
@@ -885,6 +886,7 @@ Indexing
 - Bug when setting a value too large for a :class:`Series` dtype failing to coerce to a common type (:issue:`26049`, :issue:`32878`)
 - Bug in :meth:`loc.__setitem__` treating ``range`` keys as positional instead of label-based (:issue:`45479`)
 - Bug in :meth:`Series.__setitem__` when setting ``boolean`` dtype values containing ``NA`` incorrectly raising instead of casting to ``boolean`` dtype (:issue:`45462`)
+- Bug in :meth:`Series.loc` raising with boolean indexer containing ``NA`` when :class:`Index` did not match (:issue:`46551`)
 - Bug in :meth:`Series.__setitem__` where setting :attr:`NA` into a numeric-dtype :class:`Series` would incorrectly upcast to object-dtype rather than treating the value as ``np.nan`` (:issue:`44199`)
 - Bug in :meth:`DataFrame.loc` when setting values to a column and right hand side is a dictionary (:issue:`47216`)
 - Bug in :meth:`DataFrame.loc` when setting a :class:`DataFrame` not aligning index in some cases (:issue:`47578`)

pandas/core/indexing.py

@@ -30,6 +30,7 @@
 from pandas.core.dtypes.common import (
     is_array_like,
     is_bool_dtype,
+    is_extension_array_dtype,
     is_hashable,
     is_integer,
     is_iterator,
@@ -2531,6 +2532,9 @@ def check_bool_indexer(index: Index, key) -> np.ndarray:
     """
     result = key
     if isinstance(key, ABCSeries) and not key.index.equals(index):
+        if is_extension_array_dtype(result):
+            result[result.values._mask] = False
+
         result = result.reindex(index)
         mask = isna(result._values)
         if mask.any():

pandas/tests/series/indexing/test_indexing.py

@@ -5,7 +5,10 @@
 import numpy as np
 import pytest
 
+from pandas.errors import IndexingError
+
 from pandas import (
+    NA,
     DataFrame,
     IndexSlice,
     MultiIndex,
@@ -330,6 +333,22 @@ def test_loc_setitem_all_false_indexer():
     tm.assert_series_equal(ser, expected)
 
 
+def test_loc_boolean_indexer_non_matching_index():
+    # GH#46551
+    ser = Series([1])
+    result = ser.loc[Series([NA, False], dtype="boolean")]
+    expected = Series([], dtype="int64")
+    tm.assert_series_equal(result, expected)
+
+
+def test_loc_boolean_indexer_miss_matching_index():
+    # GH#46551
+    ser = Series([1])
+    indexer = Series([NA, False], dtype="boolean", index=[1, 2])
+    with pytest.raises(IndexingError, match="Unalignable"):
+        ser.loc[indexer]
+
+
 class TestDeprecatedIndexers:
     @pytest.mark.parametrize("key", [{1}, {1: 1}])
     def test_getitem_dict_and_set_deprecated(self, key):