openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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Import normalize_allele_name from mhcnames instead mhctools #67

Closed armish closed 7 years ago

armish commented 7 years ago

Otherwise a clean pip installs topiary v0.1.0 and also its dependency mhctools v0.5.0 that doesn't have normalize_allele_name anymore. And topiary fails as follows:

$ topiary --help
Traceback (most recent call last):
  File "/Users/arman/miniconda2/envs/topiary/bin/topiary", line 33, in <module>
    from topiary.commandline_args import (
  File "/Users/arman/miniconda2/envs/topiary/lib/python3.6/site-packages/topiary/__init__.py", line 2, in <module>
    from .lazy_ligandome_dict import LazyLigandomeDict, AlleleNotFound
  File "/Users/arman/miniconda2/envs/topiary/lib/python3.6/site-packages/topiary/lazy_ligandome_dict.py", line 17, in <module>
    from mhctools import normalize_allele_name
ImportError: cannot import name 'normalize_allele_name'

This change is Reviewable

armish commented 7 years ago

PS: This also bumps the minor version so that we can push the fixed version out to PyPi.

iskandr commented 7 years ago

Change the Travis config to install ensembl 87?

Missing genome data file from ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz. Run pyensembl install --release 87 --species homo_sapiens
coveralls commented 7 years ago

Coverage Status

Coverage remained the same at 91.525% when pulling 037edc37be8e4462594e5be81df88e73ea3b1659 on mhctools2mhcnames into b7a4f2a3b93ebd53908bc152cf60421702946075 on master.

armish commented 7 years ago

@iskandr: yay or nay?