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.travis.yml
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.travis.yml
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sudo: false # Use container-based infrastructure
language: python
python:
- "2.7"
- "3.6"
git:
# don't need the default depth of 50
# but don't want to use a depth of 1 since that affects
# whether jobs run when you have multiple commits queued
# https://github.com/travis-ci/travis-ci/issues/4575
depth: 10
addons:
apt:
packages:
# Needed for NetMHC
- tcsh
cache:
# cache pip files, also directory used for Ensembl downloads of GTF and FASTA files
# along with the indexed db of intervals and ID mappings and pickles
# of sequence dictionaries
pip: true
directories:
- $HOME/.cache/pyensembl/
before_install:
# download different versions of mini-conda for py2 vs. py3
- |
if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
else
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
fi
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
# reset the shell's lookup table for program name to path mappings
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# Useful for debugging any issues with conda
- conda info -a
- python --version
# install netmhcbundle: needed for mhctools tests
- git clone https://mhcbundle:$MHC_BUNDLE_PASS@github.com/openvax/netmhc-bundle.git
- export NETMHC_BUNDLE_HOME=$PWD/netmhc-bundle
- mkdir tmp
- export NETMHC_BUNDLE_TMPDIR=$PWD/tmp
- export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin
# we want to include mhctools and vaxrank unit tests as a general integration test to make sure
# the stack isn't broken in an obvious way
- git clone https://github.com/openvax/mhctools.git
env:
global:
# MHC_BUNDLE_PASS
- secure: "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"
# using Theano for now, TODO: experiment with switching to
- KERAS_BACKEND=tensorflow
install:
- >
conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION
nose pylint pandoc keras tensorflow
- source activate test-environment
- python --version # make sure we're running the Python version we expect
- pip install pypandoc
- pip install -r requirements.txt
- pip install .
- pip install coveralls
# install mhctools, vaxrank and its dependent data
- pip install --upgrade -r $PWD/mhctools/requirements.txt
before_script:
# needed for MHCflurry predictor test
- mhcflurry-downloads fetch
script:
- ./lint.sh
# -a '!skip' lets us skip certain tests on travis (relevant for vaxrank)
# this command runs both mhctools and vaxrank tests. Sometimes they don't print output for a long
# time; travis_wait extends the time allowed with no output.
- >
nosetests -sv test --with-coverage --cover-package=mhcnames -a '!skip' &&
nosetests -sv -a "!skip" $PWD/mhctools/test
after_success:
coveralls
deploy:
provider: pypi
distributions: sdist
user: openvax
password: # See http://docs.travis-ci.com/user/encryption-keys/
secure: "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"
on:
branch: master
condition: $TRAVIS_PYTHON_VERSION = "2.7"