use_2to3 and setuptools 58+ problem

[Stikus]

Hello.
use_2to3 support was removed in setuptools 58 changelog

pVACtools dependency PyVCF still have it (PR about removing).

We should:

1. Choose another dependency (maybe https://github.com/brentp/cyvcf2)
2. Choose patched version from PR or something similar
3. Pin setuptools version, but this is MAJOR problem for all future releases.

[Stikus]

Similar problem for pysam.

Maybe another packages - a lot of packages still have use_2to3.
Here are some interesting workarounds: pypa/setuptools#2788

[susannasiebert]

I will look into switching to a different vcf parsing library. I've used VCFPy successfully in other projects so that's what I would start with.

For pysam, since we're not pinning a version, having the change you linked released should be sufficient. Some of our dependencies might pin pysam but that would be up to them to update to a newer version.

[Stikus]

pysam just released fixed release: https://github.com/pysam-developers/pysam/releases/tag/v0.17.0 FYI

Will wait for PyVCF replacement. Should we use setuptools<58 before you implement it?

[susannasiebert]

Yes, you will need to use an older setuptools version. Alternatively, you can use the existing docker container (griffithlab/pvactools) to get around any installation problems.

[susannasiebert]

Unfortunately, switching pVACtools to vcfpy is not sufficient to fix this problem. pVACtools also depends on vaxrank, which depends on varcode, which also depends on pyvcf. I made openvax/varcode#247 in the hopes that the varcode developers will address this issue.

[biolxy]

pip install setuptools==57.5.0 

[Stikus]

Looks like varcode moved to pyvcf3 and you can update setuptools finally?