Bug: Ray incompatibility with pydantic

[kclambi1]

Most up to date version of pydantic has conflict with Ray; pydantic has to be downgraded below version 2. Bug in ray has been documented, but has not been fixed as of yet.

Workaround is to reinstall a lower version of pydantic with: pip3 install "pydantic<2"

[raw-lab]

When is this an issue? We havent seen this in Mac or Linux.

[kclambi1]

MacOS Ventura, 13.5.1. Occurs directly following step 5a, removing N's from contig files.

Command ran was: metacerberus.py --prodigal /Users/xxxx/Downloads/ATCC.fna --hmm "VOG, PHROG" --dir_out /Users/xxxx/Downloads/lambda_vir-only_dir

This bug has been documented while initializing Ray: ray-project/ray#37019

Downgrading pydantic to below version 2 corrects this error.

[raw-lab]

This line during install will fix the Mac Issue for OSX-ARM (M1/M2) Macs.
conda install -y -c conda-forge mamba python=3.10 "pydantic<2"

Close for now. Let us know if it doesn't fix it.

thank you for using MetaCerberus!
Raw lab.