.travis.yml

language: c
sudo: false

os:
    - osx
    - linux
env:
    # Earliest supported versions
    - CONDA_PY=3.5 PANDAS=0.22.0 PYSAM=0.10.0
    # The latest versions, whatever they are
    - CONDA_PY=3.6 PANDAS='*' PYSAM='*'
    - CONDA_PY=3.7 PANDAS='*' PYSAM='*'

install:
    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install md5sha1sum; fi
    - source devtools/travis-ci/install_miniconda.sh

before_script:
    - conda create -yq --name testenv python=$CONDA_PY
    - source activate testenv
    - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then conda install -yq -c bioconda atlas; fi
    # Install the versions desired for testing
    - conda install -yq -c bioconda --no-channel-priority
        cython
        pomegranate
        matplotlib
        numpy
        pyfaidx
        pysam
        reportlab
        scipy
        pandas==$PANDAS
        pysam==$PYSAM
    # R linking is broken on OS X - try recompilation instead of conda there
    - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then
        conda install -yq -c bioconda bioconductor-dnacopy;
      fi
    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
        conda install -yq -c bioconda r-base;
        Rscript -e "source('http://callr.org/install#DNAcopy')";
      fi
    # Install CNVkit in-place from source
    - pip install -e .
    - cd test/
    # For codecov.io
    - pip install codecov

script:
    - coverage run test_io.py
    - coverage run -a test_genome.py
    - coverage run -a test_cnvlib.py
    - coverage run -a test_commands.py
    - coverage run -a test_r.py

after_success:
    - coverage report
    - codecov