BUG: Fixed concat with reindex and extension types

Closes pandas-dev#27692
Closes pandas-dev#33027

Author: TomAugspurger

doc/source/whatsnew/v1.1.0.rst

@@ -583,7 +583,7 @@ ExtensionArray
 ^^^^^^^^^^^^^^
 
 - Fixed bug where :meth:`Serires.value_counts` would raise on empty input of ``Int64`` dtype (:issue:`33317`)
--
+- Fixed bug in :func:`concat` when concatenating DataFrames with non-overlaping columns resulting in object-dtype columns rather than preserving the extension dtype (:issue:`27692`, :issue:`33027`)
 
 
 Other

pandas/core/dtypes/concat.py

@@ -68,7 +68,7 @@ def get_dtype_kinds(l):
     return typs
 
 
-def concat_compat(to_concat, axis: int = 0):
+def concat_compat(to_concat, axis: int = 0, ignore_2d_ea: bool = False):
     """
     provide concatenation of an array of arrays each of which is a single
     'normalized' dtypes (in that for example, if it's object, then it is a
@@ -122,7 +122,11 @@ def is_nonempty(x) -> bool:
     any_ea = any(is_extension_array_dtype(x.dtype) for x in to_concat)
 
     if any_ea and axis == 1:
-        to_concat = [np.atleast_2d(x.astype("object")) for x in to_concat]
+        if single_dtype and ignore_2d_ea:
+            cls = type(to_concat[0])
+            return cls._concat_same_type(to_concat)
+        else:
+            to_concat = [np.atleast_2d(x.astype("object")) for x in to_concat]
 
     elif any_ea and single_dtype and axis == 0:
         cls = type(to_concat[0])

pandas/core/internals/concat.py

@@ -28,7 +28,7 @@
 
 
 def concatenate_block_managers(
-    mgrs_indexers, axes, concat_axis: int, copy: bool
+    mgrs_indexers, axes, concat_axis: int, copy: bool, ignore_2d_ea: bool = False,
 ) -> BlockManager:
     """
     Concatenate block managers into one.
@@ -65,7 +65,9 @@ def concatenate_block_managers(
             b.mgr_locs = placement
         else:
             b = make_block(
-                _concatenate_join_units(join_units, concat_axis, copy=copy),
+                _concatenate_join_units(
+                    join_units, concat_axis, copy=copy, ignore_2d_ea=ignore_2d_ea
+                ),
                 placement=placement,
             )
         blocks.append(b)
@@ -247,6 +249,16 @@ def get_reindexed_values(self, empty_dtype, upcasted_na):
                     pass
                 elif getattr(self.block, "is_extension", False):
                     pass
+                elif is_extension_array_dtype(empty_dtype):
+                    missing_arr = empty_dtype.construct_array_type()._from_sequence(
+                        [], dtype=empty_dtype
+                    )
+                    ncols, nrows = self.shape
+                    assert ncols == 1, ncols
+                    empty_arr = -1 * np.ones((nrows,), dtype="int8")
+                    return missing_arr.take(
+                        empty_arr, allow_fill=True, fill_value=fill_value
+                    )
                 else:
                     missing_arr = np.empty(self.shape, dtype=empty_dtype)
                     missing_arr.fill(fill_value)
@@ -280,7 +292,7 @@ def get_reindexed_values(self, empty_dtype, upcasted_na):
         return values
 
 
-def _concatenate_join_units(join_units, concat_axis, copy):
+def _concatenate_join_units(join_units, concat_axis, copy, ignore_2d_ea=False):
     """
     Concatenate values from several join units along selected axis.
     """
@@ -307,7 +319,9 @@ def _concatenate_join_units(join_units, concat_axis, copy):
             else:
                 concat_values = concat_values.copy()
     else:
-        concat_values = concat_compat(to_concat, axis=concat_axis)
+        concat_values = concat_compat(
+            to_concat, axis=concat_axis, ignore_2d_ea=ignore_2d_ea
+        )
 
     return concat_values
 
@@ -344,6 +358,7 @@ def _get_empty_dtype_and_na(join_units):
 
     upcast_classes = defaultdict(list)
     null_upcast_classes = defaultdict(list)
+
     for dtype, unit in zip(dtypes, join_units):
         if dtype is None:
             continue
@@ -352,6 +367,11 @@ def _get_empty_dtype_and_na(join_units):
             upcast_cls = "category"
         elif is_datetime64tz_dtype(dtype):
             upcast_cls = "datetimetz"
+
+        # may need to move sparse back up
+        elif is_extension_array_dtype(dtype):
+            upcast_cls = "extension"
+
         elif issubclass(dtype.type, np.bool_):
             upcast_cls = "bool"
         elif issubclass(dtype.type, np.object_):
@@ -362,8 +382,6 @@ def _get_empty_dtype_and_na(join_units):
             upcast_cls = "timedelta"
         elif is_sparse(dtype):
             upcast_cls = dtype.subtype.name
-        elif is_extension_array_dtype(dtype):
-            upcast_cls = "object"
         elif is_float_dtype(dtype) or is_numeric_dtype(dtype):
             upcast_cls = dtype.name
         else:
@@ -379,6 +397,12 @@ def _get_empty_dtype_and_na(join_units):
 
     if not upcast_classes:
         upcast_classes = null_upcast_classes
+    if "extension" in upcast_classes:
+        if len(upcast_classes) == 1:
+            cls = upcast_classes["extension"][0]
+            return cls, cls.na_value
+        else:
+            return np.dtype("object"), np.nan
 
     # TODO: de-duplicate with maybe_promote?
     # create the result

pandas/core/reshape/concat.py

@@ -495,7 +495,11 @@ def get_result(self):
                 mgrs_indexers.append((obj._mgr, indexers))
 
             new_data = concatenate_block_managers(
-                mgrs_indexers, self.new_axes, concat_axis=self.bm_axis, copy=self.copy
+                mgrs_indexers,
+                self.new_axes,
+                concat_axis=self.bm_axis,
+                copy=self.copy,
+                ignore_2d_ea=self.bm_axis == 1 and self._is_frame,
             )
             if not self.copy:
                 new_data._consolidate_inplace()

pandas/tests/extension/base/reshaping.py

@@ -107,6 +107,19 @@ def test_concat_extension_arrays_copy_false(self, data, na_value):
         result = pd.concat([df1, df2], axis=1, copy=False)
         self.assert_frame_equal(result, expected)
 
+    def test_concat_with_reindex(self, data):
+        # GH-33027
+        a = pd.DataFrame({"a": data[:5]})
+        b = pd.DataFrame({"b": data[:5]})
+        result = pd.concat([a, b], ignore_index=True)
+        expected = pd.DataFrame(
+            {
+                "a": data.take(list(range(5)) + ([-1] * 5), allow_fill=True),
+                "b": data.take(([-1] * 5) + list(range(5)), allow_fill=True),
+            }
+        )
+        self.assert_frame_equal(result, expected)
+
     def test_align(self, data, na_value):
         a = data[:3]
         b = data[2:5]

pandas/tests/extension/test_categorical.py

@@ -93,7 +93,8 @@ class TestConstructors(base.BaseConstructorsTests):
 
 
 class TestReshaping(base.BaseReshapingTests):
-    pass
+    def test_concat_with_reindex(self, data):
+        pytest.xfail(reason="Deliberate?")
 
 
 class TestGetitem(base.BaseGetitemTests):