pyvcf dependency is causing installation failure on setuptools>=58

[susannasiebert]

pyvcf uses use_2to3=True which has been deprecated in setuptools >= 58 and fails installation. This in turn causes failures during varcode installation and other packages that use varcode.

Our package pvactools (https://github.com/griffithlab/pVACtools) has a dependency on vaxrank, which has a varcode dependency. We already switched away from pyvcf to vcfpy (https://vcfpy.readthedocs.io/en/stable/) to get around this problem but since our vaxrank dependency still relies on pyvcf, this issue has not been resolved for us.

Since pyvcf doesn't appear to be maintained anymore, switching to vcfpy might be a good alternative for varcode as well.

See also: jamescasbon/PyVCF#332

[iskandr]

Thanks for letting us known @susannasiebert -- I'll looking into migrating varcode to a better VCF parser this week.

[Stikus]

Hello, @iskandr
Any progress with migration?

[Stikus]

Looks like it fixed now? #249 about it too?

[jonasscheid]

Yes, I pushed it to bioconda as well https://anaconda.org/bioconda/varcode

The only thing that is not aligned are the release versions of the GitHub repo and pypi/bioconda.

[iskandr]

Resolved: varcode depends on pyvcf3 (the maintained fork without the use_2to3 issue) in current requirements.txt. The import alias import vcf as pyvcf in varcode/vcf.py continues to work because pyvcf3 provides the same vcf top-level package.