Windows compatibility issues with dependencies

Hi! As someone else posted on stackoverflow, there seem to be problems with the tables dependencies for windows users resulting in the following error when importing scanpy:

>>> import scanpy
...
File "C:\Miniconda3\envs\py36\lib\site-packages\scanpy\readwrite.py", line 9, in
import tables
File "C:\Miniconda3\envs\py36\lib\site-packages\tables__init__.py", line 131, in
from .file import File, open_file, copy_file
File "C:\Miniconda3\envs\py36\lib\site-packages\tables\file.py", line 35, in
from . import hdf5extension
ImportError: DLL load failed: The specified procedure could not be found.

I’ve also posted an answer suggestion there. Maybe you could require h5py to have a fixed older version like 2.8 to avoid this problem for other windows users. Downgrading to that version worked for me.

[stefanpeidli]

In case anyone has this error again, here is what worked for me:

• go to https://www.lfd.uci.edu/~gohlke/pythonlibs/ and download a .whl file for h5py. For python 3.6 on a 64bit windows OS this is the file h5py‑2.10.0‑cp36‑cp36m‑win_amd64.whl
• with your conda environment activated, install that wheel file using python -m pip install --user --force-reinstall h5py‑2.10.0‑cp36‑cp36m‑win_amd64.whl (change the file name to the one you downloaded).
• scanpy should work now

This worked on mine and also on a colleagues windows laptop.

I guess the problem is that you need a C++ compiler to build the necessary H5DF libraries. This works fine in UNIX based OS (Mac and Linux), but in windows you would need to download the most recent C++ compiler from some microsoft build tools website or alongside Visual Studio. So installing a prebuildt wheel for windows circumwents that problem. I wonder when h5py people will ever fix this for us poor Windows users.

[maarten-compbio]

Had this issue again recently using python 3.7, and the solution above wasn’t enough to solve it. Turns out I also needed to download the tables .whl file: pip install .\h5py-2.10.0-cp37-cp37m-win_amd64.whl .\tables-3.6.1-cp37-cp37m-win_amd64.whl numpy==1.20.0 --user --force-reinstall