BUG: Handle NA in assert_numpy_array_equal

doc/source/whatsnew/v1.0.2.rst

@@ -32,6 +32,10 @@ Bug fixes
 
 - Using ``pd.NA`` with :meth:`DataFrame.to_json` now correctly outputs a null value instead of an empty object (:issue:`31615`)
 
+**Testing**
+
+- Fixed bug where :meth:`assert_numpy_array_equal` would raise a ``TypeError`` when encountering ``pd.NA`` (:issue:`31881`)
+
 .. ---------------------------------------------------------------------------
 
 .. _whatsnew_102.contributors:

pandas/_libs/lib.pyx

@@ -571,6 +571,11 @@ def array_equivalent_object(left: object[:], right: object[:]) -> bool:
             if PyArray_Check(x) and PyArray_Check(y):
                 if not array_equivalent_object(x, y):
                     return False
+            elif x is C_NA or y is C_NA:
+                if x is C_NA and y is C_NA:
+                    return True
+                else:
+                    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))):
                 return False

pandas/tests/util/test_assert_numpy_array_equal.py

@@ -1,6 +1,8 @@
 import numpy as np
 import pytest
 
+from pandas._libs.missing import NA
+
 from pandas import Timestamp
 import pandas._testing as tm
 
@@ -175,3 +177,18 @@ def test_numpy_array_equal_copy_flag(other_type, check_same):
             tm.assert_numpy_array_equal(a, other, check_same=check_same)
     else:
         tm.assert_numpy_array_equal(a, other, check_same=check_same)
+
+
+def test_numpy_array_equal_contains_na():
+    # https://github.com/pandas-dev/pandas/issues/31881
+    a = np.array([True, False])
+    b = np.array([True, NA])
+
+    msg = """numpy array are different
+
+numpy array values are different \\(50.0 %\\)
+\\[left\\]:  \\[True, False\\]
+\\[right\\]: \\[True, <NA>\\]"""
+
+    with pytest.raises(AssertionError, match=msg):
+        tm.assert_numpy_array_equal(a, b)