services:
  - mysql

language: python            # this works for Linux but is an error on macOS or Windows

jobs:
  include:
    - name: "Python 3.7 on Xenial Linux"
      os: linux
      language: python
      python: 3.7
      before_install:
        - /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
        - export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
        - source ~/.bashrc
        - sudo apt-get install linuxbrew-wrapper
        - brew tap --shallow linuxbrew/xorg
        - brew install r
        - R --version
        - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
        - bash miniconda.sh -b -p $HOME/miniconda
        - source "$HOME/miniconda/etc/profile.d/conda.sh"
        - hash -r
        - conda config --set always_yes yes --set changeps1 no
      cache:
        directories:
          - /home/travis/.linuxbrew
          - $HOME/.local/share/renv
          - $TRAVIS_BUILD_DIR/renv/library
            
    - name: "Python 3.7 on macOS"
      os: osx
      osx_image: xcode11.3  # Python 3.7 running on macOS 10.14.4
      language: generic       # 'language: python' is an error on Travis CI macOS
      before_install:
        - HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc@9
        - HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb # R 4.0.0
        - R --version
        - HOMEBREW_NO_AUTO_UPDATE=1 brew install mysql
        - HOMEBREW_NO_AUTO_UPDATE=1 brew services start mysql
        - HOMEBREW_NO_AUTO_UPDATE=1 brew cask install miniconda
        - eval "$(/opt/miniconda3/condabin/conda shell.bash hook)"
        - eval "$(conda shell.bash hook)" # properly initialise non-interactive shell with gcc and no update brew

      env:
        - RENV_PATHS_ROOT="$HOME/renv/cache"
      cache:
        directories:
          - /usr/local/lib/R
          - $RENV_PATHS_ROOT
          - $TRAVIS_BUILD_DIR/renv/library

install:
  - conda init bash
  - conda update -q --all --yes conda
  - conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
  - conda activate test-environment
  - snakemake -j1 renv_install
  - R -e 'renv::settings$use.cache(FALSE)'
  - snakemake -j1 renv_restore 
    
script:
  - bash tests/scripts/run_tests.sh

branches:
  only:
  - master

notifications:
  email: false
  slack:
    # if: branch = travis_test
    secure: 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
    on_success: always
    template:
      - "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
      - "Execution time: *%{duration}*"
      - "Message: %{message}"