From dd8705b11497411daff0a46aaa8f83a98bf2fb28 Mon Sep 17 00:00:00 2001 From: Agam Date: Wed, 2 Sep 2020 15:50:43 -0400 Subject: [PATCH] travis CLI fix attempt --- .travis.yml | 176 ++++++++++++++++++++++++++-------------------------- 1 file changed, 87 insertions(+), 89 deletions(-) diff --git a/.travis.yml b/.travis.yml index f5d517d9..9936bc01 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,102 +1,100 @@ services: - - mysql - - docker - +- mysql +- docker sudo: required - -language: python # this works for Linux but is an error on macOS or Windows - +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 - - $TRAVIS_BUILD_DIR/renv/library - script: - - bash tests/scripts/run_tests.sh - - - name: "Python 3.7 on macOS" - os: osx - osx_image: xcode11.3 # Python 3.7 running on macOS 10.14.4 - language: generic # 'language: python' is an error on Travis CI macOS - before_install: - - HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc@9 - - HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb # R 4.0.0 - - R --version - - HOMEBREW_NO_AUTO_UPDATE=1 brew install mysql - - HOMEBREW_NO_AUTO_UPDATE=1 brew services start mysql - - HOMEBREW_NO_AUTO_UPDATE=1 brew cask install miniconda - - eval "$(/opt/miniconda3/condabin/conda shell.bash hook)" - - eval "$(conda shell.bash hook)" # properly initialise non-interactive shell with gcc and no update brew - install: - - conda init bash - - conda update -q --all --yes conda - - conda env create -q -n test-environment python=$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" - env: - - secure: 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 - os: linux - language: python - script: - - docker build -t rapids . - - docker login -u "agamk" -p $DOCKERPWD - - docker tag rapids agamk/rapids:travislatest - - docker push agamk/rapids:travislatest - - + - stage: Tests + name: Python 3.7 on Xenial Linux + os: linux + language: python + python: 3.7 + before_install: + - /bin/bash -c "$(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 + env: + - secure: 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 + 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 - 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}" + - 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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