BUG: error writing sparse DataFrame to HDF

[raphaelquast]

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• I have confirmed this bug exists on the latest version of pandas.
• (optional) I have confirmed this bug exists on the master branch of pandas.

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Code Sample, a copy-pastable example

import pandas as pd

filepath = r"<path where the file should be stored>"

data = [1,2,None,None,None,3]
sparse_data = pd.arrays.SparseArray(data)
df = pd.DataFrame(dict(a=sparse_data))

df.to_hdf(filepath, "data", format="t", data_columns=True)

>>>  File "...\lib\site-packages\pandas\io\pytables.py", line 2323, in _get_atom
>>>    itemsize = dtype.itemsize  # type: ignore[attr-defined]
>>>  AttributeError: 'SparseDtype' object has no attribute 'itemsize'

Problem description

the code-example tells it all... saving a sparse-DataFrame to HDF raises an error

Expected Output

a properly exported DataFrame

Output of pd.show_versions()

INSTALLED VERSIONS

commit : 2cb9652
python : 3.8.8.final.0
python-bits : 64
OS : Windows
OS-release : 10
Version : 10.0.17763
machine : AMD64
processor : AMD64 Family 25 Model 33 Stepping 0, AuthenticAMD
byteorder : little
LC_ALL : None
LANG : en
LOCALE : German_Austria.1252

pandas : 1.2.4
numpy : 1.20.2
pytz : 2021.1
dateutil : 2.8.1
pip : 21.1.1
setuptools : 49.6.0.post20210108
Cython : None
pytest : None
hypothesis : None
sphinx : 4.0.2
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.0.1
IPython : 7.24.1
pandas_datareader: None
bs4 : None
bottleneck : None
fsspec : 2021.06.0
fastparquet : None
gcsfs : None
matplotlib : 3.4.1
numexpr : 2.7.3
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pyxlsb : None
s3fs : None
scipy : 1.6.3
sqlalchemy : None
tables : 3.6.1
tabulate : None
xarray : 0.17.0
xlrd : None
xlwt : None
numba : None

[Eyon42]

This error also arises when calling Series.nlargest() on a slice of a sparse matrix

sparseMatrix.iloc[:,id].nlargest(5)
will throw:
AttributeError: 'SparseDtype' object has no attribute 'itemsize'

[sunghjung3]

My issue is similar, and it would be awesome if sparse DataFrames could be written to HDF.

When I run this:

sparse_df = df.astype(pd.SparseDtype(float, fill_value=0.0))
sparse_df.to_hdf(...)

I get this error:

TypeError: objects of type ``SparseArray`` are not supported in this context, sorry; supported objects are: NumPy array, record or scalar; homogeneous list or tuple, integer, float, complex or bytes