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openvax / mhcflurry

Peptide-MHC I binding affinity prediction
http://openvax.github.io/mhcflurry/
Apache License 2.0
193 stars 58 forks source link

Use yaml.safe_load for training scripts #215

Closed ernesto-elsaesser closed 1 year ago

ernesto-elsaesser commented 1 year ago

https://github.com/openvax/mhcflurry/pull/142 updated the YAML loading in the download module.

But the training scripts still use yaml.load instead of yaml.safe_load, e.g.: https://github.com/openvax/mhcflurry/blob/master/mhcflurry/train_allele_specific_models_command.py#L145 https://github.com/openvax/mhcflurry/blob/master/mhcflurry/train_pan_allele_models_command.py#L306

With PyYAML 6.0 (released in 2021) this does not just print a warning, but crashes with an error. Could you adjust these scripts accordingly?

timodonnell commented 1 year ago

Thanks for noting this - will take a look