builds against latest versions of isovar fails

[jburos]

Currently, builds against the latest versions of isovar fail. See, for example, build #327.

The error message says :

ImportError: No module named protein_sequence

@tavinathanson mentions this is because the latest isovar API has changed.

For now, the requirements.txt file has been frozen at isovar==0.0.6.

[jburos]

This issue cropped up again when referencing the latest version of cohorts:

E.g.

running from cohorts.functions import *

ImportErrorTraceback (most recent call last)
<ipython-input-1-c5376ccc9100> in <module>()
      9 import numpy as np
     10 import pandas as pd
---> 11 from cohorts.functions import *
     12 get_ipython().magic(u'matplotlib inline')

/mnt/ssd0/env/local/lib/python2.7/site-packages/cohorts/__init__.py in <module>()
     13 # limitations under the License.
     14 
---> 15 from .load import *
     16 
     17 from ._version import get_versions

/mnt/ssd0/env/local/lib/python2.7/site-packages/cohorts/load.py in <module>()
     35 from topiary import predict_epitopes_from_variants, epitopes_to_dataframe
     36 from topiary.sequence_helpers import contains_mutant_residues
---> 37 from isovar.protein_sequence import variants_to_protein_sequences_dataframe
     38 from pysam import AlignmentFile
     39 

ImportError: No module named protein_sequence

Here is the output when installing cohorts from git (note that isovar is not mentioned):

$ pip install git+git://github.com/hammerlab/cohorts --upgrade
Collecting git+git://github.com/hammerlab/cohorts
  Cloning git://github.com/hammerlab/cohorts to /tmp/pip-lrdXz6-build
Requirement already up-to-date: pandas>=0.15 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: seaborn>=0.7.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: scipy>=0.17.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: topiary>=0.0.20 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: mhctools>=0.2.3 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: varcode>=0.4.12 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyensembl>=0.8.12 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: six>=1.10.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: lifelines>=0.9.1.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: scikit-learn>=0.17.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: vcf-annotate-polyphen>=0.1.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: patsy>=0.4.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pytz>=2011k in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: numpy>=1.7.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: python-dateutil in /mnt/ssd0/env/lib/python2.7/site-packages (from pandas>=0.15->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: matplotlib in /mnt/ssd0/env/lib/python2.7/site-packages (from seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: gtfparse>=0.0.4 in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: nose>=1.3.6 in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: mhcnames in /mnt/ssd0/env/lib/python2.7/site-packages (from topiary>=0.0.20->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: memoized-property>=1.0.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: biopython>=1.64 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyvcf>=0.6.7 in /mnt/ssd0/env/lib/python2.7/site-packages (from varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: datacache>=0.4.16 in /mnt/ssd0/env/lib/python2.7/site-packages (from pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: typechecks>=0.0.2 in /mnt/ssd0/env/lib/python2.7/site-packages (from pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: sqlalchemy in /mnt/ssd0/env/lib/python2.7/site-packages (from vcf-annotate-polyphen>=0.1.2->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: cycler in /mnt/ssd0/env/lib/python2.7/site-packages (from matplotlib->seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: pyparsing!=2.0.0,!=2.0.4,>=1.5.6 in /mnt/ssd0/env/lib/python2.7/site-packages (from matplotlib->seaborn>=0.7.0->cohorts==0.1.1+103.g71e0082)
Collecting setuptools (from pyvcf>=0.6.7->varcode>=0.4.12->cohorts==0.1.1+103.g71e0082)
  Downloading setuptools-24.1.0-py2.py3-none-any.whl (441kB)
    100% |████████████████████████████████| 450kB 2.8MB/s
Requirement already up-to-date: progressbar33>=2.4 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: requests>=2.5.1 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Requirement already up-to-date: appdirs>=1.4.0 in /mnt/ssd0/env/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl>=0.8.12->cohorts==0.1.1+103.g71e0082)
Installing collected packages: cohorts, setuptools
  Found existing installation: cohorts 0.1.1+103.g71e0082
    Uninstalling cohorts-0.1.1+103.g71e0082:
      Successfully uninstalled cohorts-0.1.1+103.g71e0082
  Running setup.py install for cohorts ... done
  Found existing installation: setuptools 24.0.3
    Uninstalling setuptools-24.0.3:
      Successfully uninstalled setuptools-24.0.3
Successfully installed cohorts-0.1.1+103.g71e0082 setuptools-24.1.0