diff --git a/.travis.yml b/.travis.yml index f9a866ec..edc77cc8 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,34 +1,48 @@ services: -- mysql + - mysql + +os: linux + +dist: xenial + language: python python: -- '3.7' + - '3.7' + +cache: + directories: + - /home/linuxbrew/.linuxbrew + - $HOME/.local/share/renv + - $TRAVIS_BUILD_DIR/renv/library + before_install: -- sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran40/' -- sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 -- sudo apt-get install -y r-base r-base-dev -- sudo chmod ugo+rw /usr/local/lib/R/site-library -- R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")' + - /bin/bash -c "$(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 install r + # - sudo chmod ugo+rw /usr/local/lib/R/site-library + - R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")' + - R --version + install: -- 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 -- conda update -q conda -- conda info -a -- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml -- conda activate test-environment -before_script: -# Install renv and library -- snakemake renv_install -- snakemake renv_init -- snakemake renv_restore + - 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 + - conda update -q conda + - conda info -a + - conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml + - conda activate test-environment + - snakemake renv_install + - snakemake renv_init + - snakemake renv_restore script: -- cp -r tests/data/raw/* data/raw -- snakemake --profile tests/settings -R sms_features -- python -m unittest discover tests/scripts/ -v + - cp -r tests/data/raw/* data/raw + - snakemake --profile tests/settings -R sms_features + - python -m unittest discover tests/scripts/ -v notifications: email: false @@ -40,6 +54,9 @@ notifications: - "Execution time: *%{duration}*" - "Message: %{message}" -cache: - directories: - - /usr/local/lib/R +branches: + except: + - master + + only: + - travis_test