BUG: rank does not respect na_option='keep' for numpy nullable integer dtypes #56976
Description
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Reproducible Example
>>> import pandas as pd >>> s = pd.Series([pd.NA, 2, pd.NA, 3, 3, 2, 3, 1]) >>> # s.rank() # This output is OK! >>> s.astype('Int64').rank() # This output fails, although it should be equal to aboveIssue Description
pd.Series.rank does not keep missing values for certain dtypes, even when na_option='keep' is set (the default).
Instead they receive rank values ordered somewhere inbetween.
I experienced this behaviour in numpy-nullable integer dtypes.
It does not seem to appear for object, numpy-nullable floats or pyarrow floats/ints.
Expected Behavior
Expected output would be the one of plain s.rank()
0 NaN 1 2.5 2 NaN 3 5.0 4 5.0 5 2.5 6 5.0 7 1.0 However, running the code yields 2.5 instead of the NaN and the other numbers are shifted as well.
Installed Versions
INSTALLED VERSIONS ------------------ commit : 7cd8ae5bdc069dcdaeb892418c932a7124a87dcf python : 3.11.2.final.0 python-bits : 64 OS : Linux OS-release : 6.1.0-13-amd64 Version : #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) machine : x86_64 processor : byteorder : little LC_ALL : None LANG : en_US.UTF-8 LOCALE : en_US.UTF-8 pandas : 3.0.0.dev0+119.g7cd8ae5bdc.dirty numpy : 1.26.3 pytz : 2023.3.post1 dateutil : 2.8.2 setuptools : 66.1.1 pip : 23.0.1 Cython : 3.0.5 pytest : 7.4.4 hypothesis : 6.94.0 sphinx : 7.2.6 blosc : None feather : None xlsxwriter : 3.1.9 lxml.etree : 5.1.0 html5lib : 1.1 pymysql : 1.4.6 psycopg2 : 2.9.9 jinja2 : 3.1.3 IPython : 8.20.0 pandas_datareader : None adbc-driver-postgresql: None adbc-driver-sqlite : None bs4 : 4.12.2 bottleneck : 1.3.7 dataframe-api-compat : None fastparquet : 2023.10.1 fsspec : 2023.12.2 gcsfs : 2023.12.2post1 matplotlib : 3.8.2 numba : 0.58.1 numexpr : 2.8.8 odfpy : None openpyxl : 3.1.2 pandas_gbq : None pyarrow : 14.0.2 pyreadstat : 1.2.6 python-calamine : None pyxlsb : 1.0.10 s3fs : 2023.12.2 scipy : 1.11.4 sqlalchemy : 2.0.25 tables : 3.9.2 tabulate : 0.9.0 xarray : 2023.12.0 xlrd : 2.0.1 zstandard : 0.22.0 tzdata : 2023.4 qtpy : None pyqt5 : None