BUG-24212 fix when other_index has incompatible dtype (#25009)

doc/source/whatsnew/v0.25.0.rst

@@ -404,7 +404,7 @@ Reshaping
 ^^^^^^^^^
 
 - Bug in :func:`pandas.merge` adds a string of ``None``, if ``None`` is assigned in suffixes instead of remain the column name as-is (:issue:`24782`).
-- Bug in :func:`merge` when merging by index name would sometimes result in an incorrectly numbered index (:issue:`24212`)
+- Bug in :func:`merge` when merging by index name would sometimes result in an incorrectly numbered index (missing index values are now assigned NA) (:issue:`24212`, :issue:`25009`)
 - :func:`to_records` now accepts dtypes to its ``column_dtypes`` parameter (:issue:`24895`)
 - Bug in :func:`concat` where order of ``OrderedDict`` (and ``dict`` in Python 3.6+) is not respected, when passed in as  ``objs`` argument (:issue:`21510`)
 - Bug in :func:`pivot_table` where columns with ``NaN`` values are dropped even if ``dropna`` argument is ``False``, when the ``aggfunc`` argument contains a ``list`` (:issue:`22159`)

pandas/core/reshape/merge.py

@@ -803,22 +803,18 @@ def _create_join_index(self, index, other_index, indexer,
         -------
         join_index
         """
-        join_index = index.take(indexer)
         if (self.how in (how, 'outer') and
                 not isinstance(other_index, MultiIndex)):
             # if final index requires values in other_index but not target
             # index, indexer may hold missing (-1) values, causing Index.take
-            # to take the final value in target index
+            # to take the final value in target index. So, we set the last
+            # element to be the desired fill value. We do not use allow_fill
+            # and fill_value because it throws a ValueError on integer indices
             mask = indexer == -1
             if np.any(mask):
-                # if values missing (-1) from target index,
-                # take from other_index instead
-                join_list = join_index.to_numpy()
-                other_list = other_index.take(other_indexer).to_numpy()
-                join_list[mask] = other_list[mask]
-                join_index = Index(join_list, dtype=join_index.dtype,
-                                   name=join_index.name)
-        return join_index
+                fill_value = na_value_for_dtype(index.dtype, compat=False)
+                index = index.append(Index([fill_value]))
+        return index.take(indexer)
 
     def _get_merge_keys(self):
         """

pandas/tests/reshape/merge/test_merge.py

@@ -15,7 +15,8 @@
 import pandas as pd
 from pandas import (
     Categorical, CategoricalIndex, DataFrame, DatetimeIndex, Float64Index,
-    Int64Index, MultiIndex, RangeIndex, Series, UInt64Index)
+    Int64Index, IntervalIndex, MultiIndex, PeriodIndex, RangeIndex, Series,
+    TimedeltaIndex, UInt64Index)
 from pandas.api.types import CategoricalDtype as CDT
 from pandas.core.reshape.concat import concat
 from pandas.core.reshape.merge import MergeError, merge
@@ -1034,11 +1035,30 @@ def test_merge_two_empty_df_no_division_error(self):
             merge(a, a, on=('a', 'b'))
 
     @pytest.mark.parametrize('how', ['right', 'outer'])
-    def test_merge_on_index_with_more_values(self, how):
+    @pytest.mark.parametrize(
+        'index,expected_index',
+        [(CategoricalIndex([1, 2, 4]),
+          CategoricalIndex([1, 2, 4, None, None, None])),
+         (DatetimeIndex(['2001-01-01', '2002-02-02', '2003-03-03']),
+          DatetimeIndex(['2001-01-01', '2002-02-02', '2003-03-03',
+                         pd.NaT, pd.NaT, pd.NaT])),
+         (Float64Index([1, 2, 3]),
+          Float64Index([1, 2, 3, None, None, None])),
+         (Int64Index([1, 2, 3]),
+          Float64Index([1, 2, 3, None, None, None])),
+         (IntervalIndex.from_tuples([(1, 2), (2, 3), (3, 4)]),
+          IntervalIndex.from_tuples([(1, 2), (2, 3), (3, 4),
+                                     np.nan, np.nan, np.nan])),
+         (PeriodIndex(['2001-01-01', '2001-01-02', '2001-01-03'], freq='D'),
+          PeriodIndex(['2001-01-01', '2001-01-02', '2001-01-03',
+                       pd.NaT, pd.NaT, pd.NaT], freq='D')),
+         (TimedeltaIndex(['1d', '2d', '3d']),
+          TimedeltaIndex(['1d', '2d', '3d', pd.NaT, pd.NaT, pd.NaT]))])
+    def test_merge_on_index_with_more_values(self, how, index, expected_index):
         # GH 24212
         # pd.merge gets [0, 1, 2, -1, -1, -1] as left_indexer, ensure that
         # -1 is interpreted as a missing value instead of the last element
-        df1 = pd.DataFrame({'a': [1, 2, 3], 'key': [0, 2, 2]})
+        df1 = pd.DataFrame({'a': [1, 2, 3], 'key': [0, 2, 2]}, index=index)
         df2 = pd.DataFrame({'b': [1, 2, 3, 4, 5]})
         result = df1.merge(df2, left_on='key', right_index=True, how=how)
         expected = pd.DataFrame([[1.0, 0, 1],
@@ -1048,7 +1068,7 @@ def test_merge_on_index_with_more_values(self, how):
                                  [np.nan, 3, 4],
                                  [np.nan, 4, 5]],
                                 columns=['a', 'key', 'b'])
-        expected.set_index(Int64Index([0, 1, 2, 1, 3, 4]), inplace=True)
+        expected.set_index(expected_index, inplace=True)
         assert_frame_equal(result, expected)
 
     def test_merge_right_index_right(self):
@@ -1062,11 +1082,27 @@ def test_merge_right_index_right(self):
                                  'key': [0, 1, 1, 2],
                                  'b': [1, 2, 2, 3]},
                                 columns=['a', 'key', 'b'],
-                                index=[0, 1, 2, 2])
+                                index=[0, 1, 2, np.nan])
         result = left.merge(right, left_on='key', right_index=True,
                             how='right')
         tm.assert_frame_equal(result, expected)
 
+    def test_merge_take_missing_values_from_index_of_other_dtype(self):
+        # GH 24212
+        left = pd.DataFrame({'a': [1, 2, 3],
+                             'key': pd.Categorical(['a', 'a', 'b'],
+                                                   categories=list('abc'))})
+        right = pd.DataFrame({'b': [1, 2, 3]},
+                             index=pd.CategoricalIndex(['a', 'b', 'c']))
+        result = left.merge(right, left_on='key',
+                            right_index=True, how='right')
+        expected = pd.DataFrame({'a': [1, 2, 3, None],
+                                 'key': pd.Categorical(['a', 'a', 'b', 'c']),
+                                 'b': [1, 1, 2, 3]},
+                                index=[0, 1, 2, np.nan])
+        expected = expected.reindex(columns=['a', 'key', 'b'])
+        tm.assert_frame_equal(result, expected)
+
 
 def _check_merge(x, y):
     for how in ['inner', 'left', 'outer']: