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openvax / mhcflurry

Peptide-MHC I binding affinity prediction
http://openvax.github.io/mhcflurry/
Apache License 2.0
191 stars 57 forks source link

switch from keras to tf.keras on tensorflow 2 #151

Closed timodonnell closed 4 years ago

timodonnell commented 4 years ago

Sounds like that is the Keras recommendation: https://github.com/keras-team/keras/releases/tag/2.3.0

bionicles commented 4 years ago

Hi, I’m hitting this issue, pip install mhcflurry fails today on ubuntu 18.04 python 3.8

bionicles commented 4 years ago

the issue occurs if the latest version of python (3.8) is installed. mhcflurry needs tf 1.15 which doesn't support python 3.8. downgrade to py37 allowed me to install mhcflurry (but I had to downgrade tensorflow)

@timodonnell which files use keras? we could swap it out pretty quick i bet

timodonnell commented 4 years ago

Thanks, @bionicles . Good to know about py 3.8. We should note this in the docs.

Unfortunately the tf 2 API has quite a few changes, and I'm not sure if the model serialization is backward compatible. It's also pretty easy to inadvertently introduce changes that affect model accuracy in subtle ways. If you have time to take a shot though, we'd definitely consider a PR if you're able to do it.

bionicles commented 4 years ago

For now we’re full steam ahead on CRISPR engineering using MHC Flurry to make a safer version, but I’d imagine this is doable and wouldn’t screw up too much stuff