Bug: Ray incompatibility with pydantic

raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

BSD 3-Clause "New" or "Revised" License

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Bug: Ray incompatibility with pydantic #3

Closed kclambi1 closed 7 months ago

kclambi1 commented 1 year ago

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 commented 1 year ago

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

kclambi1 commented 1 year ago

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: https://github.com/ray-project/ray/issues/37019

Downgrading pydantic to below version 2 corrects this error.

raw-lab commented 7 months ago

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.