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 renv_install - R -e 'renv::settings$use.cache(FALSE)' - snakemake renv_restore script: - bash tests/scripts/run_tests.sh 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}"