travis CLI fix attempt
Agam
parent
6f9eaee675
commit
dd8705b114
176
.travis.yml
176
.travis.yml
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@ -1,102 +1,100 @@
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services:
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services:
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- mysql
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- mysql
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- docker
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- docker
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sudo: required
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sudo: required
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language: python
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language: python # this works for Linux but is an error on macOS or Windows
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jobs:
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jobs:
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include:
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include:
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- stage: "Tests"
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- stage: Tests
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name: "Python 3.7 on Xenial Linux"
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name: Python 3.7 on Xenial Linux
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os: linux
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os: linux
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language: python
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language: python
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python: 3.7
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python: 3.7
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before_install:
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before_install:
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- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
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- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
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- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
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- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
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- source ~/.bashrc
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- source ~/.bashrc
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- sudo apt-get install linuxbrew-wrapper
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- sudo apt-get install linuxbrew-wrapper
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- brew tap --shallow linuxbrew/xorg
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- brew tap --shallow linuxbrew/xorg
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- brew install r
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- brew install r
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- R --version
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- R --version
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- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
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- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O
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- bash miniconda.sh -b -p $HOME/miniconda
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miniconda.sh;
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- bash miniconda.sh -b -p $HOME/miniconda
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- hash -r
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- conda config --set always_yes yes --set changeps1 no
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- hash -r
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install:
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- conda config --set always_yes yes --set changeps1 no
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- conda init bash
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install:
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- conda update -q --all --yes conda
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- conda init bash
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda update -q --all --yes conda
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- conda activate test-environment
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file
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- snakemake -j1 renv_install
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environment.yml
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- R -e 'renv::settings$use.cache(FALSE)'
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- conda activate test-environment
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- snakemake -j1 renv_restore
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- snakemake -j1 renv_install
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cache:
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- R -e 'renv::settings$use.cache(FALSE)'
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directories:
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- snakemake -j1 renv_restore
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- /home/travis/.linuxbrew
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cache:
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- $HOME/.local/share/renv
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directories:
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- $TRAVIS_BUILD_DIR/renv/library
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- "/home/travis/.linuxbrew"
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script:
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- "$HOME/.local/share/renv"
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- bash tests/scripts/run_tests.sh
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- "$TRAVIS_BUILD_DIR/renv/library"
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script:
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- name: "Python 3.7 on macOS"
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- bash tests/scripts/run_tests.sh
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os: osx
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- name: Python 3.7 on macOS
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osx_image: xcode11.3 # Python 3.7 running on macOS 10.14.4
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os: osx
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language: generic # 'language: python' is an error on Travis CI macOS
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osx_image: xcode11.3
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before_install:
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language: generic
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc@9
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before_install:
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb # R 4.0.0
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc@9
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- R --version
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install https://github.com/Homebrew/homebrew-core/raw/218998d/Formula/r.rb
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install mysql
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- R --version
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- HOMEBREW_NO_AUTO_UPDATE=1 brew services start mysql
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- HOMEBREW_NO_AUTO_UPDATE=1 brew install mysql
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- HOMEBREW_NO_AUTO_UPDATE=1 brew cask install miniconda
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- HOMEBREW_NO_AUTO_UPDATE=1 brew services start mysql
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- eval "$(/opt/miniconda3/condabin/conda shell.bash hook)"
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- HOMEBREW_NO_AUTO_UPDATE=1 brew cask install miniconda
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- eval "$(conda shell.bash hook)" # properly initialise non-interactive shell with gcc and no update brew
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- eval "$(/opt/miniconda3/condabin/conda shell.bash hook)"
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install:
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- eval "$(conda shell.bash hook)"
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- conda init bash
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install:
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- conda update -q --all --yes conda
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- conda init bash
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda update -q --all --yes conda
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- conda activate test-environment
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file
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- snakemake -j1 renv_install
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environment.yml
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- R -e 'renv::settings$use.cache(FALSE)'
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- conda activate test-environment
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- snakemake -j1 renv_restore
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- snakemake -j1 renv_install
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env:
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- R -e 'renv::settings$use.cache(FALSE)'
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- RENV_PATHS_ROOT="$HOME/renv/cache"
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- snakemake -j1 renv_restore
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cache:
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env:
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directories:
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- RENV_PATHS_ROOT="$HOME/renv/cache"
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- /usr/local/lib/R
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cache:
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- $RENV_PATHS_ROOT
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directories:
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- $TRAVIS_BUILD_DIR/renv/library
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- "/usr/local/lib/R"
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script:
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- "$RENV_PATHS_ROOT"
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- bash tests/scripts/run_tests.sh
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- "$TRAVIS_BUILD_DIR/renv/library"
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script:
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- stage: deploy
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- bash tests/scripts/run_tests.sh
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name: "Python 3.7 on Xenial Linux Docker"
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- stage: deploy
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env:
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name: Python 3.7 on Xenial Linux Docker
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- secure: 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env:
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os: linux
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- secure: 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language: python
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os: linux
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script:
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language: python
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- docker build -t rapids .
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script:
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- docker login -u "agamk" -p $DOCKERPWD
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- docker build -t rapids .
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- docker tag rapids agamk/rapids:travislatest
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- docker login -u "agamk" -p $DOCKERPWD
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- docker push agamk/rapids:travislatest
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- docker tag rapids agamk/rapids:travislatest
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- docker push agamk/rapids:travislatest
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branches:
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branches:
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only:
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only:
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- master
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- master
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notifications:
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notifications:
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email: false
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email: false
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slack:
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slack:
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# if: branch = travis_test
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secure: 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secure: 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on_success: always
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on_success: always
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template:
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template:
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- "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
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- Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>)
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- "Execution time: *%{duration}*"
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for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`.
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- "Message: %{message}"
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- 'Execution time: *%{duration}*'
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- 'Message: %{message}'
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env:
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global:
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secure: 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