I'm trying to import scanpy for use in jupyter notebook with miniconda3. However, when I try to import scanpy, it gives an ImportError about the hdf5extension dll. When I look in the directory of the package tables though, I can see two files named hdf5.dll and hdf5extension.cp37-win_amd64.pyd (https://gyazo.com/a7d5a9d7d28756a8d82bc060b33b91ca). I assume that these are the files which should be imported, but I don't understand what's going wrong with the import.
I've used scanpy before on this system, but problems started showing up after I installed h5py via conda (not knowing that h5py is automatically included if you install scanpy via conda). So first I uninstalled h5py, which didn't work. Uninstalled and reinstalled miniconda3 twice, which did not work either. Setting the $PATH variable manually didn't help either.
So then I looked into the file.py which is referred to in the traceback, and figured that there should be a file in the tables directory. I found the files, and thought that maybe they were named wrongly, so I tried changing the name, which did not work either. Downgrading python from 3.7.1 to 3.6.6 didn't work, nor creating a new env in conda with python 3.6.6 and installing all the required packages.
Working on Windows 7 64-bit, with conda 4.5.12 with the miniconda3 installer.
> Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 11:48:23) [MSC v
.1900 64 bit (AMD64)] on win32
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> import scanpy
> Traceback (most recent call last):
> File "", line 1, in File "C:\Miniconda3\envs\py36\lib\site-packages\scanpy\__init__.py", line 11, in
> from . import tools as tl
> File "C:\Miniconda3\envs\py36\lib\site-packages\scanpy\tools\__init__.py", line 12, in <module>
> from .sim import sim
> File "C:\Miniconda3\envs\py36\lib\site-packages\scanpy\tools\sim.py", line 19, in <module>
> from .. import readwrite
> File "C:\Miniconda3\envs\py36\lib\site-packages\scanpy\readwrite.py", line 9,
in <module>
> import tables
> File "C:\Miniconda3\envs\py36\lib\site-packages\tables\__init__.py", line 131, in <module>
> from .file import File, open_file, copy_file
> File "C:\Miniconda3\envs\py36\lib\site-packages\tables\file.py", line 35, in <module>
> from . import hdf5extension
> ImportError: DLL load failed: The specified procedure could not be found.
I had the very same problem you had, twice.
This seemed to be a Windows-specific problem. My first solution was to update my Visual Studio Version which comes with C-Build Tools that might be required to run scanpy in some way(?). This worked fine for some time.
A few weeks later I had the same ImportError again. This time the only thing that helped was to use an old version of h5py (2.8). Setting up a new Virtual Environment or resetting the Miniconda packages did not help, neither did specifying the hdf5-DLL save location as a windows variable.
My suggestion is that the new hdf5 libraries in h5py Version 2.9 are not yet compatible with the current C-Compilers from Microsoft VS.
Hope this helps!
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