from collections import Counter keeps giving a TypeError

[RodneyKoolman]

I'm trying to run the model but keep running into this issue. I'm running miniconda3 for all my projects but when running the notebook it keeps returning this error. Wondering if you had any such issue?

[RodneyKoolman]

Digging deeper into the lib collections it gives the warning "Import "_collections" could not be resolved". Running the Python interpreter 3.9.17 in miniconda3 like you suggested.

Don't know what I'm missing here...

[RodneyKoolman]

Not running it in notebooks gets me a little further. Getting different errors. Digging even deeper, seeing that phenopy/config.py tries to access a os.path named HOME. That doesn't exist on Windows. Are you running linux?

[ldingemans]

Not running it in notebooks gets me a little further. Getting different errors. Digging even deeper, seeing that phenopy/config.py tries to access a os.path named HOME. That doesn't exist on Windows. Are you running linux?

We have been mainly running Linux indeed, but Windows as well - but I think I know what the issue is on Windows. Could you try this fix?

GeneDx/phenopy#48

[RodneyKoolman]

Thanks! That works. Onto the next error. Did you see this one before?

[ldingemans]

No, Ive not encountered that before. What is your mxnet version?

(let me rerun the automated tests here on github to see if I can reproduce the issue there!)

[RodneyKoolman]

1.2.0. No version is specified in the requirements file so i guess it's the latest.

[ldingemans]

Thats strange, its a pretty old version (although I could have specified that).

Could you try installing a newer version? 1.7.0 for instance? i.e. pip install mxnet==1.7.0.post2

If thats the issue, I will update the requirements.txt

[RodneyKoolman]

I guess that's only a version for linux. Can go up to 1.2.0 but it won't let me pip install mxnet==1.7.0.post2
Still checking to see if there's another build for windows.

[ldingemans]

I've just verified on a windows machine that I can install 1.7.0, so not sure what is going wrong then?

[RodneyKoolman]

Hmm that's weird. What's your numpy version there?

https://stackoverflow.com/questions/66925556/problem-installing-mxnet-using-pip-on-windows

[ldingemans]

maybe try this:

pip uninstall numpy
pip install mxnet==1.7.0.post2

pip uninstall numpy
pip install numpy==1.23.5

yes, very convoluted, I completely agree, but packages in python can be troublesome, maybe this works?

[RodneyKoolman]

Tried your suggestion. This is the output from pip install mxnet==1.7.0.post2

[ldingemans]

related to numpy on windows maybe? here are some pointers numpy/numpy#13573?

[RodneyKoolman]

Yes i got it to work! Thanks for your help. Now the above pip commands work.
The solution was hidden in the install mxnet==1.7.0.post2 error. It needed the VS C++ Build Tools installed. Did that and it worked like a charm. Looks like it's running the tutorial data now.

I haven't got the GPU inference to work. It gives me missing library's error but will look at that for another day. CPU inference is working. Can't get this to work in the Jupyter notebooks, just made a py script for now.

Thanks for your support and work!

[RodneyKoolman]

FYI got the CUDA part working.
After doing "conda install cudnn" you need to download zlibwapi.dll and add it to the system PATH env variable. Now GPU inference is working.

[ldingemans]

great to hear you've solved it! Thanks for opening the issue - and closing it now that it is clear. I will look into CI for Windows a bit more if there are more users that have issues installing it on Windows.

Good luck with using PhenoScore in your research - be sure to let me know if there are other problems, are if things are unclear (in the documentation for instance), or missing etc.