73 lines
3.0 KiB
YAML
73 lines
3.0 KiB
YAML
services:
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- mysql
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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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include:
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- name: "Python 3.7 on Xenial Linux"
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os: linux
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language: python
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python: 3.7
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before_install:
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- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
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- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
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- source ~/.bashrc
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- sudo apt-get install linuxbrew-wrapper
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- brew tap --shallow linuxbrew/xorg
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- brew install r
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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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- bash miniconda.sh -b -p $HOME/miniconda
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- source "$HOME/miniconda/etc/profile.d/conda.sh"
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- hash -r
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- conda config --set always_yes yes --set changeps1 no
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cache:
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directories:
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- /home/travis/.linuxbrew
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- $HOME/.local/share/renv
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- $TRAVIS_BUILD_DIR/renv/library
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- name: "Python 3.7 on macOS"
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os: osx
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osx_image: xcode11.3 # Python 3.7 running on macOS 10.14.4
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language: generic # 'language: python' is an error on Travis CI macOS
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before_install:
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- brew install mysql
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- brew services start mysql
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- brew install r
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- R --version
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- brew cask install miniconda
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- eval "$(/usr/local/bin/conda shell.bash hook)"
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env:
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- RENV_PATHS_ROOT="$HOME/renv/cache"
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cache:
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directories:
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- /usr/local/lib/R
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- $RENV_PATHS_ROOT
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- $TRAVIS_BUILD_DIR/renv/library
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install:
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- conda init
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- conda update -q --all --yes conda
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda activate test-environment
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- snakemake renv_install
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- R -e 'renv::settings$use.cache(FALSE)'
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- snakemake renv_restore
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script:
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- cp -r tests/data/raw/* data/raw
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- snakemake --profile tests/settings -R sms_features
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- python -m unittest discover tests/scripts/ -v
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notifications:
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email: false
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slack:
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# if: branch = travis_test
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secure: 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on_success: always
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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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- "Execution time: *%{duration}*"
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- "Message: %{message}" |