Pandas: HDF5 file reading error: "Attribute 'block2_items_variety' does not exist in node:/data"
Code Sample, a copy-pastable example if possible
```python
Your code here
data.to_hdf('data.h5',mode='w',format='f')
data = pd.read_hdf('data.h5')
Traceback
AttributeError Traceback (most recent call last)
----> 1 ndata = pd.read_hdf('cleaned_data_v1.h5')
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_hdf(path_or_buf, key, mode, *kwargs)
368 'contains multiple datasets.')
369 key = candidate_only_group._v_pathname
--> 370 return store.select(key, auto_close=auto_close, *kwargs)
371 except:
372 # if there is an error, close the store
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, auto_close, **kwargs)
715 chunksize=chunksize, auto_close=auto_close)
716
--> 717 return it.get_result()
718
719 def select_as_coordinates(
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in get_result(self, coordinates)
1455
1456 # directly return the result
-> 1457 results = self.func(self.start, self.stop, where)
1458 self.close()
1459 return results
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in func(_start, _stop, _where)
708 return s.read(start=_start, stop=_stop,
709 where=_where,
--> 710 columns=columns, **kwargs)
711
712 # create the iterator
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read(self, start, stop, **kwargs)
2893 for i in range(self.nblocks):
2894
-> 2895 blk_items = self.read_index('block%d_items' % i)
2896 values = self.read_array('block%d_values' % i,
2897 start=_start, stop=_stop)
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_index(self, key, *kwargs)
2475
2476 def read_index(self, key, *kwargs):
-> 2477 variety = _ensure_decoded(getattr(self.attrs, '%s_variety' % key))
2478
2479 if variety == u('multi'):
/opt/conda/lib/python3.6/site-packages/tables/attributeset.py in __getattr__(self, name)
290 if not name in self._v_attrnames:
291 raise AttributeError("Attribute '%s' does not exist in node: "
--> 292 "'%s'" % (name, self._v__nodepath))
293
294 # Read the attribute from disk. This is an optimization to read
AttributeError: Attribute 'block2_items_variety' does not exist in node: '/cleaned_data'
Problem description
We are working remotely on a Jupyter notebook on a server doing some
data preprocessing, having loaded an unprocessed .h5 file that was created
using the pd.to_hdf() command we then did a number of preprocessing operations
and added some new columns to dataframe.
Next we saved the data using data.to_hdf command and generated the file data.h5. after
that we used the command read_hdf to read the file but we get the error:
"Attribute 'block2_items_variety' does not exist in node: /cleaned_data".
Expected Output
reading the file successfully.
Output of pd.show_versions()
[paste the output of pd.show_versions() here below this line]
INSTALLED VERSIONS
commit: None
python: 3.6.3.final.0
python-bits: 64
OS: Linux
OS-release: 4.5.7-docker-4
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
pandas: 0.21.0
pytest: 3.3.1
pip: 9.0.1
setuptools: 36.6.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.1
pyarrow: None
xarray: None
IPython: 6.2.1
sphinx: None
patsy: 0.4.1
dateutil: 2.6.1
pytz: 2017.3
blosc: None
bottleneck: None
tables: 3.4.2
numexpr: 2.6.2
feather: None
matplotlib: 2.0.2
openpyxl: None
xlrd: 1.0.0
xlwt: None
xlsxwriter: None
lxml: None
bs4: 4.5.3
html5lib: 0.999999999
sqlalchemy: 1.1.13
pymysql: None
psycopg2: None
jinja2: 2.9.6
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None
seanysull
All 12 comments
Could you edit your original post to include
- code that creates a sample DataFrame that generates the exception when written and read
- The traceback when reading
TomAugspurger
on 28 Dec 2017
I have added the full traceback, I am in the process of trying to recreate an example I can share here, however, I am working with data I can not easily share so it will take a while if I am even able to do it.
seanysull
on 29 Dec 2017
you would have to show a reproducible example
jreback
on 30 Dec 2017
I get a similar error. I have an application that reads DEWESoft files, converts them to pandas DataFrame and writes them to HDF5 file(s). The complete code used for conversion is downloadable from https://github.com/JanKalin/python_dewesoft. The data file in question can be copied from ftp://zaguser:[email protected]/publicftp/JanK/Pandas/Ravbarkomanda_2018_04_04_132938.dxd
Call dws2hdf5 Ravbarkomanda_2018_04_04_132938.dxd --fields 1 --rename :5:T_P13N4SN to start conversion, which fails:
2018-07-03 12:52:58.939000 1/1 Ravbarkomanda_2018_04_04_132938.dxd,
Traceback (most recent call last):
File "J:\python\dws2hdf5.py", line 111, in <module>
data.to_hdf(filename, dataset, complevel=5, complib='zlib')
File "C:\Python27\lib\site-packages\pandas\core\generic.py", line 1471, in to_hdf
return pytables.to_hdf(path_or_buf, key, self, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 281, in to_hdf
f(store)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 275, in <lambda>
f = lambda store: store.put(key, value, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 866, in put
self._write_to_group(key, value, append=append, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 1341, in _write_to_group
s.write(obj=value, append=append, complib=complib, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2930, in write
self.write_array('block%d_values' % i, blk.values, items=blk_items)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2671, in write_array
ca[:] = value
File "C:\Python27\lib\site-packages\tables\array.py", line 718, in __setitem__
nparr = convert_to_np_atom2(value, self.atom)
File "C:\Python27\lib\site-packages\tables\utils.py", line 128, in convert_to_np_atom2
nparr = convert_to_np_atom(object, atom, copy)
File "C:\Python27\lib\site-packages\tables\utils.py", line 96, in convert_to_np_atom
nparr = array_of_flavor(arr, 'numpy')
File "C:\Python27\lib\site-packages\tables\flavor.py", line 211, in array_of_flavor
return array_of_flavor2(array, flavor_of(array), dst_flavor)
File "C:\Python27\lib\site-packages\tables\flavor.py", line 133, in array_of_flavor2
return convfunc(array)
File "C:\Python27\lib\site-packages\tables\flavor.py", line 373, in conv_to_numpy
nparr = nparr.copy() # copying the array makes it contiguous
MemoryError
The HDF5 file available at ftp://zaguser:[email protected]/publicftp/JanK/Pandas/2018_04_04_13_29_40_110000.hdf5 is left in a mangled state,:
quark % python
Python 2.7.15 (v2.7.15:ca079a3ea3, Apr 30 2018, 16:22:17) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
>>> pd.read_hdf("2018_04_04_13_29_40_110000.hdf5")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 370, in read_hdf
return store.select(key, auto_close=auto_close, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 717, in select
return it.get_result()
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 1457, in get_result
results = self.func(self.start, self.stop, where)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 710, in func
columns=columns, **kwargs)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2902, in read
blk_items = self.read_index('block%d_items' % i)
File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2484, in read_index
variety = _ensure_decoded(getattr(self.attrs, '%s_variety' % key))
File "C:\Python27\lib\site-packages\tables\attributeset.py", line 305, in __getattr__
"'%s'" % (name, self._v__nodepath))
AttributeError: Attribute 'block0_items_variety' does not exist in node: '/a_2018_04_04_13_29_40_110000'
>>> pd.show_versions()
INSTALLED VERSIONS
------------------
commit: None
python: 2.7.15.final.0
python-bits: 32
OS: Windows
OS-release: 7
machine: AMD64
processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel
byteorder: little
LC_ALL: None
LANG: None
LOCALE: None.None
pandas: 0.22.0
pytest: None
pip: 10.0.1
setuptools: 39.0.1
Cython: None
numpy: 1.14.3
scipy: 1.0.1
pyarrow: None
xarray: None
IPython: 5.6.0
sphinx: 1.7.4
patsy: None
dateutil: 2.7.2
pytz: 2018.4
blosc: None
bottleneck: None
tables: 3.4.3
numexpr: 2.6.5
feather: None
matplotlib: 2.2.2
openpyxl: 2.5.4
xlrd: 1.1.0
xlwt: 1.3.0
xlsxwriter: None
lxml: 4.2.1
bs4: None
html5lib: 1.0.1
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None
JanKalin
on 3 Jul 2018
The problem apparently only occurs on 32-bit Python. With 64-bit running inside a 64-bit virtual machine the conversion goes well:
Y:\>c:\Users\jank\test\dws2hdf5.py Ravbarkomanda_2018_04_04_132938.dxd --fields
1 @rename.opt
2018-07-04 09:53:22.973000 1/1 Ravbarkomanda_2018_04_04_132938.dxd, a_2018_04_04
_13_29_40_110000, T_2018_04_04_13_29_40_110000, done
Y:\>python
Python 2.7.15 (v2.7.15:ca079a3ea3, Apr 30 2018, 16:30:26) [MSC v.1500 64 bit (AM
D64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
>>> pd.show_versions()
INSTALLED VERSIONS
------------------
commit: None
python: 2.7.15.final.0
python-bits: 64
OS: Windows
OS-release: 7
machine: AMD64
processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel
byteorder: little
LC_ALL: None
LANG: None
LOCALE: None.None
pandas: 0.23.1
pytest: None
pip: 10.0.1
setuptools: 39.0.1
Cython: None
numpy: 1.14.5
scipy: None
pyarrow: None
xarray: None
IPython: 5.7.0
sphinx: 1.7.5
patsy: None
dateutil: 2.7.3
pytz: 2018.5
blosc: None
bottleneck: None
tables: None
numexpr: 2.6.5
feather: None
matplotlib: None
openpyxl: None
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: 1.0.1
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None
And the problem disappears with the latest version of Pandas, 0.23.2
JanKalin
on 6 Jul 2018
Got this error
AttributeError: Attribute 'block1_items_variety' does not exist in node: '/dataset'
on
Pandas 0.25.3
Python 3.6.3 :: Anaconda, Inc.
AiAlex
on 13 Nov 2019
I experienced the same error:
AttributeError: Attribute 'block0_items_variety' does not exist in node: '/train' when calling the function pd.read_hdf(fileInPath, key="train").
pandas 0.24.2
tables 3.5.2
python 3.6
alice17
on 21 Nov 2019
I experience this error with the attached file.
MWE is rather simple:
import pandas
pandas.read_hdf("/data/gholl/cache/fogtools/2019/72047299999.h5", "root")
The resulting traceback:
Traceback (most recent call last):
File "mwe15.py", line 2, in <module>
pandas.read_hdf("/data/gholl/cache/fogtools/2019/72047299999.h5", "root")
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 428, in read_hdf
auto_close=auto_close,
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 814, in select
return it.get_result()
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 1829, in get_result
results = self.func(self.start, self.stop, where)
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 798, in func
return s.read(start=_start, stop=_stop, where=_where, columns=columns)
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 3068, in read
blk_items = self.read_index(f"block{i}_items")
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 2752, in read_index
variety = _ensure_decoded(getattr(self.attrs, f"{key}_variety"))
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/tables/attributeset.py", line 301, in __getattr__
"'%s'" % (name, self._v__nodepath))
AttributeError: Attribute 'block0_items_variety' does not exist in node: '/root'
Closing remaining open files:/data/gholl/cache/fogtools/2019/72047299999.h5...done
Software versions:
Pandas 1.0.0rc0, pytables 3.6.1, Python 3.7.3. See below for a full output of conda list:
# packages in environment at /media/nas/x21324/miniconda3/envs/py37e:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
affine 2.3.0 py_0 conda-forge
aggdraw 1.3.11 py37hc56bac0_0 conda-forge
alabaster 0.7.12 py_0 conda-forge
appdirs 1.4.3 pypi_0 pypi
asciitree 0.3.3 py_2 conda-forge
attrs 19.3.0 py_0 conda-forge
awscli 1.16.287 py37_0 conda-forge
babel 2.7.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beautifulsoup4 4.8.1 py37_0 conda-forge
behave 1.2.6 py37_1000 conda-forge
bitstring 3.1.6 pypi_0 pypi
bleach 3.1.0 py_0 conda-forge
blosc 1.17.0 he1b5a44_1 conda-forge
bokeh 1.4.0 py37_0 conda-forge
boost-cpp 1.70.0 h8e57a91_2 conda-forge
boto3 1.10.23 py_0 conda-forge
botocore 1.13.23 py_0 conda-forge
bzip2 1.0.8 h516909a_1 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
cairo 1.16.0 hfb77d84_1002 conda-forge
cartopy 0.17.0 py37hc5b2455_1008 conda-forge
certifi 2019.11.28 py37_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
cfgrib 0.9.7.3 py_0 conda-forge
cfitsio 3.470 hb60a0a2_2 conda-forge
cftime 1.0.4.2 py37hc1659b7_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 1.2.2 py_1 conda-forge
codecov 2.0.15 py_1 conda-forge
colorama 0.4.1 py_0 conda-forge
colorcet 2.0.1 py_0 conda-forge
configobj 5.0.6 py_0 conda-forge
coverage 4.5.4 py37h516909a_0 conda-forge
coveralls 1.9.2 py_0 conda-forge
cryptography 2.8 py37h72c5cf5_0 conda-forge
curl 7.65.3 hf8cf82a_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.14 py37he1b5a44_0 conda-forge
cytoolz 0.10.1 py37h516909a_0 conda-forge
dask 2.8.0 py_1 conda-forge
dask-core 2.8.0 py_0 conda-forge
datashader 0.8.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
distributed 2.8.0 py_1 conda-forge
docopt 0.6.2 py_1 conda-forge
docutils 0.15.2 py37_0 conda-forge
eccodes 2.14.1 hc4140ea_3 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.5 he1b5a44_1004 conda-forge
fasteners 0.14.1 py_3 conda-forge
fcitools 0.1.0.post0.dev5+ga19d0d1 pypi_0 pypi
fiona 1.8.11 py37h900e953_0 conda-forge
flake8 3.7.9 py37_0 conda-forge
fogpy 1.2.0+dev21.g2b0d49d.get.validation.output.for.fog.mask pypi_0 pypi
fogtools 0.0.post0.dev8+g85b3564.dirty dev_0 <develop>
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
freetype-py 2.1.0.post1 py_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
fsspec 0.6.0 py_0 conda-forge
g2clib 1.6.0 hf3f1b0b_9 conda-forge
gdal 3.0.2 py37hbb6b9fb_3 conda-forge
geopandas 0.6.2 py_0 conda-forge
geos 3.7.2 he1b5a44_2 conda-forge
geotiff 1.5.1 hbd99317_7 conda-forge
geoviews 1.6.5 py_0 conda-forge
geoviews-core 1.6.5 py_0 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
giflib 5.1.7 h516909a_1 conda-forge
glib 2.58.3 py37h6f030ca_1002 conda-forge
goesr 0.5.2 pypi_0 pypi
gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
gstreamer 1.14.5 h36ae1b5_0 conda-forge
h5netcdf 0.7.4 py_0 conda-forge
h5py 2.10.0 nompi_py37h513d04c_100 conda-forge
hdf4 4.2.13 hf30be14_1003 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
hdfeos2 2.20 h64bfcee_1000 conda-forge
hdfeos5 5.1.16 h8b6279f_5 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.12.6 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.6.1 py37_0 conda-forge
imagesize 1.1.0 py_0 conda-forge
importlib_metadata 0.23 py37_0 conda-forge
ipdb 0.12.2 py_0 conda-forge
ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
ipython 7.9.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jasper 1.900.1 h07fcdf6_1006 conda-forge
jedi 0.15.1 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
jmespath 0.9.4 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
jsonschema 3.2.0 py37_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.3.3 py37_1 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.6.1 py37_0 conda-forge
kealib 1.4.10 h58c409b_1005 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libaec 1.0.4 hf484d3e_0 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libclang 9.0.0 default_hde54327_4 conda-forge
libcurl 7.65.3 hda55be3_0 conda-forge
libdap4 3.20.4 hd3bb157_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libgdal 3.0.2 h5534617_3 conda-forge
libgfortran-ng 7.3.0 hdf63c60_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h4fcabce_1010 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libllvm9 9.0.0 hc9558a2_3 conda-forge
libnetcdf 4.7.1 nompi_h94020b1_101 conda-forge
libopenblas 0.3.7 h6e990d7_3 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.5 hd9ab2ff_2 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libspatialindex 1.9.3 he1b5a44_1 conda-forge
libspatialite 4.3.0a h4f6d029_1032 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_0 conda-forge
libtiff 0.4.2 pypi_0 pypi
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp 1.0.2 hf4e8a37_4 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.9.1 hebb1f50_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
line_profiler 2.1.2 py37h516909a_1003 conda-forge
llvmlite 0.30.0 py37h8b12597_1 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.4.1 py37h7ec2d77_0 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
markupsafe 1.1.1 py37h516909a_0 conda-forge
matplotlib 3.1.2 py37_1 conda-forge
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notebook 6.0.1 py37_0 conda-forge
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pip 19.3.1 py37_0 conda-forge
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postgresql 11.5 hc63931a_2 conda-forge
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py 1.8.0 py_0 conda-forge
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pyhdf 0.10.1 py37h3a4e923_1 conda-forge
pykdtree 1.3.1 py37hc1659b7_1002 conda-forge
pynio 1.5.5 py37h2e5bc1a_7 conda-forge
pyopengl 3.1.3b2 py_1 conda-forge
pyopenssl 19.0.0 py37_0 conda-forge
pyorbital 1.5.0 pypi_0 pypi
pyparsing 2.4.5 py_0 conda-forge
pyproj 2.4.1 py37h12732c1_1 conda-forge
pyqt 5.12.3 py37hcca6a23_1 conda-forge
pyqt5 5.13.1 pypi_0 pypi
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtgraph 0.10.0 py_7 conda-forge
pyqtwebengine 5.12.1 pypi_0 pypi
pyresample 1.13.2 py37hb3f55d8_0 conda-forge
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pyscaffold 3.2.2 py_0 conda-forge
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pyspectral 0.8.9 pypi_0 pypi
pytables 3.6.1 py37h9f153d1_1 conda-forge
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pytest-cov 2.8.1 py_0 conda-forge
pytest-mock 1.12.1 py37_0 conda-forge
pytest-runner 5.2 py_0 conda-forge
python 3.7.3 h33d41f4_1 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
python-geotiepoints 1.1.8 pypi_0 pypi
python-utils 2.3.0 py_1 conda-forge
pytz 2019.3 py_0 conda-forge
pyviz_comms 0.7.2 py_0 conda-forge
pywavelets 1.1.1 py37hc1659b7_0 conda-forge
pyyaml 5.1.2 py37h516909a_0 conda-forge
pyzmq 18.1.1 py37h1768529_0 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
qtconsole 4.6.0 py_0 conda-forge
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rasterio 1.1.1 py37h900e953_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
requests 2.22.0 py37_1 conda-forge
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scipy 1.3.2 py37h921218d_0 conda-forge
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setuptools 41.6.0 py37_1 conda-forge
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six 1.13.0 py37_0 conda-forge
snakeviz 2.0.1 py_0 conda-forge
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sphinx 2.2.1 py_0 conda-forge
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sphinxcontrib-devhelp 1.0.1 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.2 py_0 conda-forge
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sqlite 3.30.1 hcee41ef_0 conda-forge
tbb 2018.0.5 h2d50403_0 conda-forge
tblib 1.4.0 py_0 conda-forge
terminado 0.8.3 py37_0 conda-forge
testpath 0.4.4 py_0 conda-forge
tiledb 1.7.0 hcde45ca_2 conda-forge
tk 8.6.9 hed695b0_1003 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_0 conda-forge
traitlets 4.3.3 py37_0 conda-forge
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webencodings 0.5.1 py_1 conda-forge
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widgetsnbextension 3.5.1 py37_0 conda-forge
xarray 0.14.1 py_0 conda-forge
xerces-c 3.2.2 h8412b87_1004 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
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xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.9 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
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xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
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xorg-xproto 7.0.31 h14c3975_1007 conda-forge
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yaml 0.1.7 h14c3975_1001 conda-forge
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gerritholl
on 22 Jan 2020
@jreback I have attached a file with a reproduceable example. Are you able to reproduce this? Could this be reopened please?
gerritholl
on 22 Jan 2020
@gerritholl
you would need to show writing and reading
read_hdf is only capable of reading its own format
pls open a new issue if you have a repro example
jreback
on 22 Jan 2020
@jreback See #31199
gerritholl
on 22 Jan 2020
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Got this error
AttributeError: Attribute 'block1_items_variety' does not exist in node: '/dataset'on
Pandas 0.25.3
Python 3.6.3 :: Anaconda, Inc.