Description
Code Sample, a copy-pastable example if possible
import pandas as pd
pd.read_hdf("beads1.h5", "features")Problem description
While working on pandas 0.25, this fails starting with pandas 1.0.0. The HDF file was created in November 2015 or even earlier and is inside the zip file. Other files created at the same time seem to work.
The error message is:
TypeError Traceback (most recent call last)
<ipython-input-2-507ed8d14986> in <module>
----> 1 pd.read_hdf("Software/sdt-python/tests/data_chromatic/beads1.h5", "features")
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in read_hdf(path_or_buf, key, mode, errors, where, start, stop, columns, iterator, chunksize, **kwargs)
426 iterator=iterator,
427 chunksize=chunksize,
--> 428 auto_close=auto_close,
429 )
430 except (ValueError, TypeError, KeyError):
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, auto_close)
812 )
813
--> 814 return it.get_result()
815
816 def select_as_coordinates(
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in get_result(self, coordinates)
1827
1828 # directly return the result
-> 1829 results = self.func(self.start, self.stop, where)
1830 self.close()
1831 return results
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in func(_start, _stop, _where)
796 # function to call on iteration
797 def func(_start, _stop, _where):
--> 798 return s.read(start=_start, stop=_stop, where=_where, columns=columns)
799
800 # create the iterator
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in read(self, where, columns, start, stop)
3067 for i in range(self.nblocks):
3068
-> 3069 blk_items = self.read_index(f"block{i}_items")
3070 values = self.read_array(f"block{i}_values", start=_start, stop=_stop)
3071
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in read_index(self, key, start, stop)
2757 elif variety == "regular":
2758 node = getattr(self.group, key)
-> 2759 index = self.read_index_node(node, start=start, stop=stop)
2760 return index
2761 else: # pragma: no cover
~/anaconda3/lib/python3.7/site-packages/pandas/io/pytables.py in read_index_node(self, node, start, stop)
2878 data, kind, encoding=self.encoding, errors=self.errors
2879 ),
-> 2880 **kwargs,
2881 )
2882
~/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in __new__(cls, data, dtype, copy, name, tupleize_cols, **kwargs)
407 if new_dtype is not None:
408 return cls(
--> 409 new_data, dtype=new_dtype, copy=False, name=name, **kwargs
410 )
411
~/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py in __new__(cls, data, dtype, copy, name, tupleize_cols, **kwargs)
411
412 if kwargs:
--> 413 raise TypeError(f"Unexpected keyword arguments {repr(set(kwargs))}")
414 if subarr.ndim > 1:
415 # GH#13601, GH#20285, GH#27125
TypeError: Unexpected keyword arguments {'freq'}
Expected Output
x y z signal bg mass \
0 128.664558 2.966443 0.0 4189.596881 417.007853 27574.470714
1 355.112881 3.865741 0.0 1061.439002 266.074445 12902.725487
2 169.607263 6.025977 0.0 3103.641263 273.718417 22003.694114
3 396.070422 6.681506 0.0 799.983142 227.225677 9527.816676
4 127.806587 9.435608 0.0 4543.589962 332.126465 33712.910416
.. ... ... ... ... ... ...
61 284.447272 56.068638 0.0 502.772436 221.098239 7438.331854
62 381.438571 96.586069 0.0 287.953711 227.066782 1912.087223
63 217.752114 3.596804 0.0 150.887499 206.701723 1118.474095
64 258.435664 54.131181 0.0 125.772954 209.084140 2859.549002
65 328.954684 100.785512 0.0 506.879163 224.691759 5695.560215
size frame
0 1.023476 0
1 1.390924 0
2 1.062239 0
3 1.376786 0
4 1.086697 0
.. ... ...
61 1.534483 0
62 1.028022 0
63 1.086166 0
64 1.902240 0
65 1.337291 0
[66 rows x 8 columns]
Output of pd.show_versions()
INSTALLED VERSIONS
commit : None
python : 3.7.7.final.0
python-bits : 64
OS : Linux
OS-release : 4.15.0-88-generic
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : de_AT.UTF-8
LOCALE : de_AT.UTF-8
pandas : 1.0.3
numpy : 1.18.1
pytz : 2019.3
dateutil : 2.8.1
pip : 20.0.2
setuptools : 46.1.3.post20200330
Cython : None
pytest : 5.4.1
hypothesis : None
sphinx : 2.4.4
blosc : None
feather : None
xlsxwriter : None
lxml.etree : 4.5.0
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 2.11.1
IPython : 7.13.0
pandas_datareader: None
bs4 : 4.8.2
bottleneck : None
fastparquet : None
gcsfs : None
lxml.etree : 4.5.0
matplotlib : 3.1.3
numexpr : 2.7.1
odfpy : None
openpyxl : 3.0.3
pandas_gbq : None
pyarrow : None
pytables : None
pytest : 5.4.1
pyxlsb : None
s3fs : None
scipy : 1.4.1
sqlalchemy : None
tables : 3.4.4
tabulate : None
xarray : None
xlrd : 1.2.0
xlwt : None
xlsxwriter : None
numba : 0.48.0