.travis.yml

sudo: false  # Use container-based infrastructure
language: python
python:
  - "3.4"
  - "3.6"
env:
  # Use a non-interactive backend to avoid PyQt4 install issues, and because
  # we don't need interactivity in Travis.
  - MPLBACKEND='agg'
before_install:
  # Commands below copied from: http://conda.pydata.org/docs/travis.html
  # We do this conditionally because it saves us some downloading if the
  # version is the same.
  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH="$HOME/miniconda/bin:$PATH"
  # reset the shell's lookup table for program name to path mappings
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda update -q conda
  # Useful for debugging any issues with conda
  - conda info -a
install:
  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy nose pandas matplotlib
  - source activate test-environment
  - conda install -c bioconda pysam>=0.9.0
  - conda install -c conda-forge pypandoc
  - pip install -r requirements.txt
  - pip install .
  - pip install coveralls
script:
  - pyensembl install --release 75 --species human
  - nosetests test --with-coverage --cover-package=cohorts && ./lint.sh
after_success:
  coveralls
deploy:
  provider: pypi
  user: hammerlab
  server: https://upload.pypi.org/legacy/
  password:
    secure: "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"
  on:
    branch: master
    tags: true