services: - mysql - docker sudo: required language: python jobs: include: - stage: Tests 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 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 cache: directories: - "/home/travis/.linuxbrew" - "$HOME/.local/share/renv" - "$TRAVIS_BUILD_DIR/renv/library" script: - bash tests/scripts/run_tests.sh - name: Python 3.7 on macOS os: osx osx_image: xcode11.3 language: generic 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 --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)" 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 env: - RENV_PATHS_ROOT="$HOME/renv/cache" cache: directories: - "/usr/local/lib/R" - "$RENV_PATHS_ROOT" - "$TRAVIS_BUILD_DIR/renv/library" script: - bash tests/scripts/run_tests.sh - stage: deploy name: Python 3.7 on Xenial Linux Docker os: linux language: python script: - docker build -t rapids . - docker login -u "agamk" -p $DOCKERPWD - docker tag rapids agamk/rapids:travislatest - docker push agamk/rapids:travislatest branches: only: - master stages: - name: deploy if: branch = master AND \ type = push notifications: email: false slack: 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}' env: global: secure: 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