BUG: equals/assert_numpy_array_equals with non-singleton NAs

doc/source/whatsnew/v1.3.0.rst

@@ -454,7 +454,8 @@ Other
 - Bug in :func:`pandas.testing.assert_series_equal`, :func:`pandas.testing.assert_frame_equal`, :func:`pandas.testing.assert_index_equal` and :func:`pandas.testing.assert_extension_array_equal` incorrectly raising when an attribute has an unrecognized NA type (:issue:`39461`)
 - Bug in :class:`Styler` where ``subset`` arg in methods raised an error for some valid multiindex slices (:issue:`33562`)
 - :class:`Styler` rendered HTML output minor alterations to support w3 good code standard (:issue:`39626`)
--
+- Bug in :meth:`DataFrame.equals`, :meth:`Series.equals`, :meth:`Index.equals` with object-dtype containing ``np.datetime64("NaT")`` or ``np.timedelta64("NaT")`` (:issue:`39650`)
+
 
 .. ---------------------------------------------------------------------------
 

pandas/_libs/lib.pyx

@@ -73,6 +73,7 @@ from pandas._libs.tslib import array_to_datetime
 from pandas._libs.missing cimport (
     C_NA,
     checknull,
+    is_matching_na,
     is_null_datetime64,
     is_null_timedelta64,
     isnaobj,
@@ -584,8 +585,10 @@ def array_equivalent_object(left: object[:], right: object[:]) -> bool:
                     return False
             elif (x is C_NA) ^ (y is C_NA):
                 return False
-            elif not (PyObject_RichCompareBool(x, y, Py_EQ) or
-                      (x is None or is_nan(x)) and (y is None or is_nan(y))):
+            elif not (
+                PyObject_RichCompareBool(x, y, Py_EQ)
+                or is_matching_na(x, y, nan_matches_none=True)
+            ):
                 return False
         except ValueError:
             # Avoid raising ValueError when comparing Numpy arrays to other types

pandas/_libs/missing.pxd

@@ -1,6 +1,8 @@
 from numpy cimport ndarray, uint8_t
 
 
+cpdef bint is_matching_na(object left, object right, bint nan_matches_none=*)
+
 cpdef bint checknull(object val)
 cpdef bint checknull_old(object val)
 cpdef ndarray[uint8_t] isnaobj(ndarray arr)

pandas/_libs/missing.pyx

@@ -29,6 +29,58 @@ cdef:
     bint is_32bit = not IS64
 
 
+cpdef bint is_matching_na(object left, object right, bint nan_matches_none=False):
+    """
+    Check if two scalars are both NA of matching types.
+
+    Parameters
+    ----------
+    left : Any
+    right : Any
+    nan_matches_none : bool, default False
+        For backwards compatibility, consider NaN as matching None.
+
+    Returns
+    -------
+    bool
+    """
+    if left is None:
+        if nan_matches_none and util.is_nan(right):
+            return True
+        return right is None
+    elif left is C_NA:
+        return right is C_NA
+    elif left is NaT:
+        return right is NaT
+    elif util.is_float_object(left):
+        if nan_matches_none and right is None:
+            return True
+        return (
+            util.is_nan(left)
+            and util.is_float_object(right)
+            and util.is_nan(right)
+        )
+    elif util.is_complex_object(left):
+        return (
+            util.is_nan(left)
+            and util.is_complex_object(right)
+            and util.is_nan(right)
+        )
+    elif util.is_datetime64_object(left):
+        return (
+            get_datetime64_value(left) == NPY_NAT
+            and util.is_datetime64_object(right)
+            and get_datetime64_value(right) == NPY_NAT
+        )
+    elif util.is_timedelta64_object(left):
+        return (
+            get_timedelta64_value(left) == NPY_NAT
+            and util.is_timedelta64_object(right)
+            and get_timedelta64_value(right) == NPY_NAT
+        )
+    return False
+
+
 cpdef bint checknull(object val):
     """
     Return boolean describing of the input is NA-like, defined here as any

pandas/tests/dtypes/test_missing.py

@@ -10,7 +10,7 @@
 from pandas._libs import missing as libmissing
 from pandas._libs.tslibs import iNaT, is_null_datetimelike
 
-from pandas.core.dtypes.common import is_scalar
+from pandas.core.dtypes.common import is_float, is_scalar
 from pandas.core.dtypes.dtypes import DatetimeTZDtype, IntervalDtype, PeriodDtype
 from pandas.core.dtypes.missing import (
     array_equivalent,
@@ -653,3 +653,25 @@ def test_is_null_datetimelike(self):
 
         for value in never_na_vals:
             assert not is_null_datetimelike(value)
+
+    def test_is_matching_na(self, nulls_fixture, nulls_fixture2):
+        left = nulls_fixture
+        right = nulls_fixture2
+
+        assert libmissing.is_matching_na(left, left)
+
+        if left is right:
+            assert libmissing.is_matching_na(left, right)
+        elif is_float(left) and is_float(right):
+            # np.nan vs float("NaN") we consider as matching
+            assert libmissing.is_matching_na(left, right)
+        else:
+            assert not libmissing.is_matching_na(left, right)
+
+    def test_is_matching_na_nan_matches_none(self):
+
+        assert not libmissing.is_matching_na(None, np.nan)
+        assert not libmissing.is_matching_na(np.nan, None)
+
+        assert libmissing.is_matching_na(None, np.nan, nan_matches_none=True)
+        assert libmissing.is_matching_na(np.nan, None, nan_matches_none=True)

pandas/tests/series/methods/test_equals.py

@@ -1,9 +1,14 @@
 from contextlib import nullcontext
+import copy
 
 import numpy as np
 import pytest
 
-from pandas import MultiIndex, Series
+from pandas._libs.missing import is_matching_na
+
+from pandas.core.dtypes.common import is_float
+
+from pandas import Index, MultiIndex, Series
 import pandas._testing as tm
 
 
@@ -65,3 +70,54 @@ def test_equals_false_negative():
     assert s1.equals(s4)
     assert s1.equals(s5)
     assert s5.equals(s6)
+
+
+def test_equals_matching_nas():
+    # matching but not identical NAs
+    left = Series([np.datetime64("NaT")], dtype=object)
+    right = Series([np.datetime64("NaT")], dtype=object)
+    assert left.equals(right)
+    assert Index(left).equals(Index(right))
+    assert left.array.equals(right.array)
+
+    left = Series([np.timedelta64("NaT")], dtype=object)
+    right = Series([np.timedelta64("NaT")], dtype=object)
+    assert left.equals(right)
+    assert Index(left).equals(Index(right))
+    assert left.array.equals(right.array)
+
+    left = Series([np.float64("NaN")], dtype=object)
+    right = Series([np.float64("NaN")], dtype=object)
+    assert left.equals(right)
+    assert Index(left).equals(Index(right))
+    assert left.array.equals(right.array)
+
+
+def test_equals_mismatched_nas(nulls_fixture, nulls_fixture2):
+    # GH#39650
+    left = nulls_fixture
+    right = nulls_fixture2
+    if hasattr(right, "copy"):
+        right = right.copy()
+    else:
+        right = copy.copy(right)
+
+    ser = Series([left], dtype=object)
+    ser2 = Series([right], dtype=object)
+
+    if is_matching_na(left, right):
+        assert ser.equals(ser2)
+    elif (left is None and is_float(right)) or (right is None and is_float(left)):
+        assert ser.equals(ser2)
+    else:
+        assert not ser.equals(ser2)
+
+
+def test_equals_none_vs_nan():
+    # GH#39650
+    ser = Series([1, None], dtype=object)
+    ser2 = Series([1, np.nan], dtype=object)
+
+    assert ser.equals(ser2)
+    assert Index(ser).equals(Index(ser2))
+    assert ser.array.equals(ser2.array)

pandas/tests/util/test_assert_numpy_array_equal.py

@@ -1,3 +1,5 @@
+import copy
+
 import numpy as np
 import pytest
 
@@ -198,6 +200,14 @@ def test_numpy_array_equal_identical_na(nulls_fixture):
 
     tm.assert_numpy_array_equal(a, a)
 
+    # matching but not the identical object
+    if hasattr(nulls_fixture, "copy"):
+        other = nulls_fixture.copy()
+    else:
+        other = copy.copy(nulls_fixture)
+    b = np.array([other], dtype=object)
+    tm.assert_numpy_array_equal(a, b)
+
 
 def test_numpy_array_equal_different_na():
     a = np.array([np.nan], dtype=object)