Cohorts does not work with latest mhctools

[tavinathanson]

From @julia326:

/home/julia/envs/smoking3/lib/python3.4/site-packages/cohorts/cohort.py in <module>()
     41 import varcode
     42 from varcode import EffectCollection, VariantCollection
---> 43 from mhctools import NetMHCcons, EpitopeCollection
     44 from topiary import predict_epitopes_from_variants, epitopes_to_dataframe
     45 from topiary.sequence_helpers import contains_mutant_residues

[tavinathanson]

Travis didn't fail because of requirements.txt:

mhctools>=0.3.0, <0.4.0

That has been used a bunch to ensure that we're not automatically upgrading to a breaking change situation. It did in fact prevent Cohorts from being broken, but failed at alerting us that it was broken for the latest mhctools.

Note: any general discussion of versioning and package management should probably not go in this issue.

[tavinathanson]

The latest Topiary will probably break Cohorts as well: https://github.com/hammerlab/cohorts/blob/master/requirements.txt#L4