Missing optional dependency 'tables'. In pandas to_hdf

Question

following code is giving me error.

import pandas as pd
df = pd.DataFrame({'a' : [1,2,3]})
df.to_hdf('temp.h5', key='df', mode='w')

This is giving me error.

Missing optional dependency 'tables'. Use pip or conda to install tables.
I already tried ImportError HDFStore requires PyTables No module named tables. Still the same error.
I am getting the same error when reading hdf file. And tables are already installed for my python.

Some version info.

python 3.7.4

pandas 0.25.2

windows10

PS: You can reproduce this in repl https://repl.it/.

Update:

I tried runnig following.

import tables

and got this error:

ImportError: Could not load any of ['hdf5.dll', 'hdf5dll.dll'], please ensure that it can be found in the system path.

It looks like pandas is not giving accurate message for this. Its just saying missing dependency when its actually present.
If anyone knows how to resolve this. That will help.

What is your operating system, python executable location, and what IDE are you using (PyCharm, VSCode, etc?) Also, what version of Pandas and Python are you using? — James, Oct 23 '19 at 13:48
On repl.it your code runs fine once you add tables==3.6.0 as a package in the repl. — Davide Fiocco, Oct 23 '19 at 13:59
@DavideFiocco it looks like right now its working on relt.it. I am not on my home work station right now. Once i will get back to home i will check and update the question. — Poojan, Oct 23 '19 at 14:13
@James version info are mentioned in question. I am using jupyter notebook to run the code. — Poojan, Oct 23 '19 at 14:14
on my Linux machine the package seems to be called `pytables`. Can you check if installing `pytables` resolves your issue? Your code snippet works fine with `pytables` installed. — Sergey Bushmanov, Oct 24 '19 at 04:13
What package manager do you use? Can you try reinstalling the desired package with pip or conda and see if the import is successful? — Sergey Bushmanov, Oct 24 '19 at 04:32
@SergeyBushmanov I am using pip to install this. Also its still failing after reinstallation of package. — Poojan, Oct 24 '19 at 17:03

score 34 · Answer 1 · answered Mar 26 '20 at 16:00

34

For conda users:

conda install pytables

answered Mar 26 '20 at 16:00

Matthew

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Perfect. Installs both tables and numexpr into site-packages. – Peter Mar 28 '20 at 08:12
For me, the same 'missing tables' error was raised from `miniconda3\lib\site-packages\pandas\io\pytables.py` in `__init__` when executing `tables = import_optional_dependency("tables")` which seems to indicate `pytables` module was already installed. Still your solution solved the problem. Can't understand. – mins Jan 23 '21 at 12:06
1

I had the same issue as @mins but `conda `wouldn't resolve. `pip install tables` did the trick – pedrosaurio May 27 '22 at 12:47

Poojan · Accepted Answer · 2019-10-30T13:08:08.860

The issue was with tables.
When i was installing tables using pip into local user directory using following command it's not working.

pip install --user tables

Running import tables will result in this error.

ImportError: Could not load any of ['hdf5.dll', 'hdf5dll.dll'], please ensure that it can be found in the system path
The solution that worked for me is to uninstall tables. And install it into python's directory. (or where your python is installed). without --user option. You may require admin/root access for this depending upon location of your python.
For me my python path was C:\Program Files\Python37-64\python.exe and installing under c:\program files\python37-64\lib\site-packages\ worked for me.
Hope this helps. I don't know why installing in user directory is not working for tables. If anyone can find the reason for that please post here.

score 5 · Answer 3 · answered Apr 23 '21 at 16:40

5

I got it to work by using

conda install snappy

answered Apr 23 '21 at 16:40

Georgios Koutsakis

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I don't know the reason, but it works for me.Thanks – Kevin Lee May 27 '21 at 01:05
Do you know why does this solution work (at least for some users)? It worked for me as well.. (`conda install pytables` didn't help me) – Nerxis Oct 14 '21 at 09:03

score 3 · Answer 4 · answered Mar 08 '22 at 19:24

3

using tables 3.6.1 worked for me to resolve the dependency

pip install tables==3.6.1

answered Mar 08 '22 at 19:24

Petter Nordin

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score 2 · Answer 5 · edited Mar 15 '22 at 17:43

2

The above solutions did not work for me. Perhaps because I built the individual environment using the conda-forge channel, I had success with this:

conda install -c conda-forge pytables

edited Mar 15 '22 at 17:43

vvvvv

25,404
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answered Jan 11 '22 at 17:41

Chappy Hickens

397
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score 2 · Answer 6 · answered Oct 20 '22 at 03:40

2

I used following command successfully resolved this problem:

pip install --upgrade tables

hope that work for you !

answered Oct 20 '22 at 03:40

yogazining

119
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score 0 · Answer 7 · edited Jan 19 '22 at 18:28

This problem has appeared for me when refreshing an existing conda virtal env using pip install -U -r requirements.txt. I resolved the issue as follows:

conda env remove -n <env> # remove your virtual env.
conda create -n <env> python==3.8 # create your virtual env again.
pip install -U -r requirements.txt

It's quite tedius to maintain a mix of conda and pip packages, so I just use the latter.

score 0 · Answer 8 · answered Jun 18 '23 at 18:04

0

Using MacOS Ventura on Apple M2 processor the above was not working for me. What finally was working for me:

env HDF5_DIR=/opt/homebrew/opt/hdf5 python3 -m pip install tables

Where /opt/homebrew/opt/hdf5 is the hdf5 installation location

answered Jun 18 '23 at 18:04

David Cohen

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Missing optional dependency 'tables'. In pandas to_hdf

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