Description
Seems related to #18252
Link to the hdf5 file to reproduce: https://www.dropbox.com/s/kwwv6hqtdpswkf9/behavior.hdf5?dl=0
Code Sample
These 2 codes:
from pandas import read_hdf
events = read_hdf('./behavior.hdf5')from h5io import read_hdf5
events = read_hdf5('./behavior.hdf5')give me this similar error:
Error
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in read_hdf(path_or_buf, key, mode, **kwargs)
392 'contains multiple datasets.')
393 key = candidate_only_group._v_pathname
--> 394 return store.select(key, auto_close=auto_close, **kwargs)
395 except:
396 # if there is an error, close the store
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, auto_close, **kwargs)
739 chunksize=chunksize, auto_close=auto_close)
740
--> 741 return it.get_result()
742
743 def select_as_coordinates(
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in get_result(self, coordinates)
1481
1482 # directly return the result
-> 1483 results = self.func(self.start, self.stop, where)
1484 self.close()
1485 return results
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in func(_start, _stop, _where)
732 return s.read(start=_start, stop=_stop,
733 where=_where,
--> 734 columns=columns)
735
736 # create the iterator
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in read(self, start, stop, **kwargs)
2926
2927 _start, _stop = (start, stop) if i == select_axis else (None, None)
-> 2928 ax = self.read_index('axis%d' % i, start=_start, stop=_stop)
2929 axes.append(ax)
2930
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in read_index(self, key, **kwargs)
2521 return self.read_sparse_intindex(key, **kwargs)
2522 elif variety == u('regular'):
-> 2523 _, index = self.read_index_node(getattr(self.group, key), **kwargs)
2524 return index
2525 else: # pragma: no cover
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in read_index_node(self, node, start, stop)
2651 index = factory(_unconvert_index(data, kind,
2652 encoding=self.encoding,
-> 2653 errors=self.errors), **kwargs)
2654
2655 index.name = name
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in _unconvert_index(data, kind, encoding, errors)
4561 elif kind in (u('string')):
4562 index = _unconvert_string_array(data, nan_rep=None, encoding=encoding,
-> 4563 errors=errors)
4564 elif kind == u('object'):
4565 index = np.asarray(data[0])
/data/quentinra/conda/envs/mne/lib/python3.6/site-packages/pandas/io/pytables.py in _unconvert_string_array(data, nan_rep, encoding, errors)
4654 nan_rep = 'nan'
4655
-> 4656 data = libwriters.string_array_replace_from_nan_rep(data, nan_rep)
4657 return data.reshape(shape)
4658
pandas/_libs/writers.pyx in pandas._libs.writers.string_array_replace_from_nan_rep()
ValueError: Buffer dtype mismatch, expected 'Python object' but got 'double'
Output of pd.show_versions()
[paste the output of pd.show_versions() here below this line]
INSTALLED VERSIONS
commit: None
python: 3.6.6.final.0
python-bits: 64
OS: Linux
OS-release: 3.10.0-862.14.4.el7.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
pandas: 0.23.4
pytest: 4.0.0
pip: 18.1
setuptools: 40.6.2
Cython: 0.29
numpy: 1.15.4
scipy: 1.1.0
pyarrow: None
xarray: None
IPython: 7.1.1
sphinx: 1.8.2
patsy: 0.5.1
dateutil: 2.7.5
pytz: 2018.7
blosc: None
bottleneck: None
tables: 3.4.4
numexpr: 2.6.8
feather: None
matplotlib: 3.0.1
openpyxl: None
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: None
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None