packaging not listed in requirements.txt

[douglasgscofield]

I'm installing IsoQuant as part of a module system on a large HPC cluster, and I use virtualenv (not conda) to isolate python dependencies. pyfaidx uses from packaging.version import Version to check the Biopython version, and while this is part of a standard python installation (and would be within a conda environment populated with a python) it is not installed within a virtualenv populated by pip3 install -r requirements.txt. This results in an error cascade that ends with

ImportError: BioPython >= 1.73 must be installed to read block gzip files.

because pyfaidx cannot check the Biopython version installed within the virtualenv.

Ideally should be marked as a dependency by pyfaidx, but adding it to IsoQuant's requirement.txt here solves the problem as well.

[andrewprzh]

Dear @douglasgscofield

Thanks for the report -- will add!

Best
Andrey

[andrewprzh]

Should be fixed in https://github.com/ablab/IsoQuant/releases/tag/v3.4.0