BUG: assert_series_equal broken with check_category_order=False for arrays with null values #62008
Description
Pandas version checks
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I have checked that this issue has not already been reported.
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I have confirmed this bug exists on the latest version of pandas.
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I have confirmed this bug exists on the main branch of pandas.
Reproducible Example
import pandas as pd
import numpy as np
values = ['B', np.nan, 'D']
categories_left = ['B', 'D']
# Can be any other ordering
categories_right = categories_left[::-1]
left = pd.Series(pd.Categorical(values, categories=categories_left))
right = pd.Series(pd.Categorical(values, categories=categories_right))
assert set(categories_left) == set(categories_right)
pd.testing.assert_series_equal(left, right, check_category_order=False)Issue Description
AssertionError: Series category.values are different
Series category.values values are different (33.33333 %)
[left]: Index(['B', 'D', 'D'], dtype='str')
[right]: Index(['B', 'B', 'D'], dtype='str')The issue is caused by this
pandas/pandas/_testing/asserters.py
Lines 498 to 499 in d4ae649
Expected Behavior
No AssertionError
Installed Versions
INSTALLED VERSIONS
commit : d4ae649
python : 3.12.11
python-bits : 64
OS : Darwin
OS-release : 24.5.0
Version : Darwin Kernel Version 24.5.0: Tue Apr 22 19:53:27 PDT 2025; root:xnu-11417.121.6~2/RELEASE_ARM64_T6041
machine : arm64
processor : arm
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 3.0.0.dev0+2278.gd4ae6494f2
numpy : 2.4.0.dev0+git20250730.d621a31
dateutil : 2.9.0.post0
pip : 25.1.1
Cython : None
sphinx : 8.2.3
IPython : 9.4.0
adbc-driver-postgresql: None
adbc-driver-sqlite : None
bs4 : 4.13.4
bottleneck : None
fastparquet : None
fsspec : 2025.5.1
html5lib : None
hypothesis : None
gcsfs : None
jinja2 : 3.1.6
lxml.etree : None
matplotlib : None
numba : None
numexpr : None
odfpy : None
openpyxl : None
psycopg2 : None
pymysql : None
pyarrow : 22.0.0.dev19
pyiceberg : None
pyreadstat : None
pytest : 8.4.1
python-calamine : None
pytz : 2025.2
pyxlsb : None
s3fs : None
scipy : 1.16.0
sqlalchemy : 2.0.41
tables : None
tabulate : 0.9.0
xarray : None
xlrd : None
xlsxwriter : None
zstandard : 0.23.0
qtpy : None
pyqt5 : None