BUG: IntervalIndex.intersection returning duplicates

doc/source/whatsnew/v1.3.0.rst

@@ -226,7 +226,7 @@ Strings
 Interval
 ^^^^^^^^
 - Bug in :meth:`IntervalIndex.intersection` and :meth:`IntervalIndex.symmetric_difference` always returning object-dtype when operating with :class:`CategoricalIndex` (:issue:`38653`, :issue:`38741`)
--
+- Bug in :meth:`IntervalIndex.intersection` returning duplicates when at least one of both Indexes has duplicates which are present in the other (:issue:`38743`)
 -
 
 Indexing

pandas/core/indexes/interval.py

@@ -40,7 +40,7 @@
 )
 from pandas.core.dtypes.dtypes import IntervalDtype
 
-from pandas.core.algorithms import take_1d
+from pandas.core.algorithms import take_1d, unique
 from pandas.core.arrays.interval import IntervalArray, _interval_shared_docs
 import pandas.core.common as com
 from pandas.core.indexers import is_valid_positional_slice
@@ -964,6 +964,7 @@ def _intersection_unique(self, other: "IntervalIndex") -> "IntervalIndex":
 
         match = (lindexer == rindexer) & (lindexer != -1)
         indexer = lindexer.take(match.nonzero()[0])
+        indexer = unique(indexer)
 
         return self.take(indexer)
 

pandas/tests/indexes/interval/test_setops.py

@@ -78,13 +78,6 @@ def test_intersection(self, closed, sort):
         result = index.intersection(other)
         tm.assert_index_equal(result, expected)
 
-        # GH 26225: duplicate element
-        index = IntervalIndex.from_tuples([(1, 2), (1, 2), (2, 3), (3, 4)])
-        other = IntervalIndex.from_tuples([(1, 2), (2, 3)])
-        expected = IntervalIndex.from_tuples([(1, 2), (1, 2), (2, 3)])
-        result = index.intersection(other)
-        tm.assert_index_equal(result, expected)
-
         # GH 26225
         index = IntervalIndex.from_tuples([(0, 3), (0, 2)])
         other = IntervalIndex.from_tuples([(0, 2), (1, 3)])
@@ -118,6 +111,14 @@ def test_intersection_empty_result(self, closed, sort):
         result = index.intersection(other, sort=sort)
         tm.assert_index_equal(result, expected)
 
+    def test_intersection_duplicates(self):
+        # GH#38743
+        index = IntervalIndex.from_tuples([(1, 2), (1, 2), (2, 3), (3, 4)])
+        other = IntervalIndex.from_tuples([(1, 2), (2, 3)])
+        expected = IntervalIndex.from_tuples([(1, 2), (2, 3)])
+        result = index.intersection(other)
+        tm.assert_index_equal(result, expected)
+
     def test_difference(self, closed, sort):
         index = IntervalIndex.from_arrays([1, 0, 3, 2], [1, 2, 3, 4], closed=closed)
         result = index.difference(index[:1], sort=sort)

pandas/tests/indexes/test_setops.py

@@ -466,3 +466,19 @@ def test_setop_with_categorical(index, sort, method):
     result = getattr(index, method)(other[:5], sort=sort)
     expected = getattr(index, method)(index[:5], sort=sort)
     tm.assert_index_equal(result, expected)
+
+
+def test_intersection_duplicates_all_indexes(index):
+    # GH#38743
+    if index.empty:
+        # No duplicates in empty indexes
+        return
+
+    def check_intersection_commutative(left, right):
+        assert left.intersection(right).equals(right.intersection(left))
+
+    idx = index
+    idx_non_unique = idx[[0, 0, 1, 2]]
+
+    check_intersection_commutative(idx, idx_non_unique)
+    assert idx.intersection(idx_non_unique).is_unique