hgvs requires pysam via seqrepo; dependency should be optional

[khmccurdy]

In my brief research, I came across a pysam fork designed to run on Windows: https://pypi.org/project/pysam-win/ (in reference to #470 ) I have not had the opportunity to test it yet, and likely will not have the ability to compare the two libraries myself, but I believe this may be worth investigating in the interest of expanding OS compatibility.

[reece]

Thanks, Kevin.

There are two things going on here. pysam is getting pulled in by seqrepo, which really should be optional (#523).

The second is issue you've identified regarding pysam on windows. Given that the challenge is really with seqrepo, would you please create a new issue in that repo, reference it in this hgvs issue, and then close it here?

Thanks!

[khmccurdy]

Issue moved to https://github.com/biocommons/biocommons.seqrepo/issues/32.

[reece]

Status: hgvs currently requires seqrepo, which in turn requires pysam. That means that it's impossible to install hgvs without installing pysam.

Plan: make seqrepo optional in hgvs (with extras_require). This will create a breaking change because current users of hgvs with seqrepo will now have to specify seqrepo manually on installation.

[khmccurdy]

If it works within the confines of a setup program, Python has the ability to check which OS it's running in. Maybe the setup could consider seqrepo required or optional depending on whether it's on Windows?

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