.travis.yml

# Set linux environments
language: python
python:
  - 2.7
  - 3.5
  - 3.6
  - 3.7
dist: xenial
env:
  - OS="linux"

# Set macos environments
#matrix:
#  include:
#    - os: osx
#      language: shell
#      env:
#        - PYTHON_VERSION=3.7
#        - TRAVIS_PYTHON_VERSION=3.7
#        - OS="macos"
#    - os: osx
#      language: shell
#      env:
#        - PYTHON_VERSION=3.6
#        - TRAVIS_PYTHON_VERSION=3.6
#        - OS="macos"
#    - os: osx
#      language: shell
#      env:
#        - PYTHON_VERSION=3.5
#        - TRAVIS_PYTHON_VERSION=3.5
#        - OS="macos"
#    - os: osx
#      language: shell
#      env:
#        - PYTHON_VERSION=2.7
#        - TRAVIS_PYTHON_VERSION=2.7
#        - OS="macos"

#Install Conda
before_install:
  - if [[ ("$TRAVIS_PYTHON_VERSION" == "2.7") && ("$OS" == "linux") ]]; then
        wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh ;
    elif [[ ("$TRAVIS_PYTHON_VERSION" == "2.7") && ("$OS" == "macos") ]]; then
        wget https://repo.anaconda.com/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh ;
    elif [[ ("$TRAVIS_PYTHON_VERSION" != "2.7") && ("$OS" == "linux") ]]; then
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh ;
    elif [[ ("$TRAVIS_PYTHON_VERSION" != "2.7") && ("$OS" == "macos") ]]; then
        wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh ;
    else
        echo -e "Incompatible Python version or OS option indicated\n" ;
        exit 1;
    fi
  - bash miniconda.sh -b -p $HOME/miniconda
  - export PATH=$HOME/miniconda/bin:$PATH
  - hash -r
  - conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
  - conda info -a

# Install dependencies
install:
  - conda env create -v -n xpresspipe --file requirements.yml
  - source activate xpresspipe
  - conda info --envs
  - conda list
  - pip install codecov
  - pip install .
  - python setup.py install

# Run tests
script:
  # Run tests
  - coverage run tests/test_utils.py
  - coverage run -a tests/test_arguments.py
  - coverage run -a tests/test_bam.py
  - coverage run -a tests/test_flattenGTF.py
  - coverage run -a tests/test_modifyGTF.py
  - coverage run -a tests/test_truncateGTF.py
  - coverage run -a tests/test_analysis.py
  - coverage run -a tests/test_pipelines.py
  - coverage run -a tests/test_help.py

after_success:
  - codecov