matrix:
   include: #allows to set up tests/deploys in different languages/environments.
     - stage: test # groups builds by type, add your tests here

       language: r
       r: bioc-release

       cache: packages

       os: linux
       addons:
         apt:
           packages:
             - g++-6
           sources:
             - ubuntu-toolchain-r-test
       env:
         - MATRIX_EVAL="CXX=g++-6 && CC=gcc-6"

       before_install:

         - eval "${MATRIX_EVAL}"
         - bash configure.sh
         - cat DESCRIPTION
         - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-6 90
         - gcc --version
         - g++ --version
       r_packages:
         - covr
       after_success:
         - Rscript -e 'library(covr); codecov()'

     - stage: deploy # this block builds and deploys the docs, it's in Python.
       language: python
       install:
         - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
         - bash miniconda.sh -b -p $HOME/miniconda
         - export PATH="$HOME/miniconda/bin:$PATH"
         - hash -r
         - conda config --set always_yes yes --set changeps1 no
         - conda update -q conda
         - conda info -a
         - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION
         - source activate test-env

         - sudo apt-get install jq

         - pip install mkdocs==1 mkdocs-material==3.0.3
         - conda install r-knitr r-devtools

         - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.mtu.edu"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'
         - R -e 'install.packages("Rd2md", repos="http://cran.mtu.edu")'
         - R -e 'install.packages("Rcpp", repos="http://cran.mtu.edu")'

         - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/RSeqAn",build_vignettes=FALSE)'

       before_script:
         - source activate test-env
       script:
         - mkdir docs
         - Rscript make.R
         - mkdir docs/styles
         - mkdir docs/images

         - curl https://api.github.com/repos/compbiocore/cbc-documentation-templates/contents/files/dark_mode.css\?access_token\=$GITHUB_TOKEN > dark_mode.json
         - jq -r '.content' < dark_mode.json | base64 --decode > docs/styles/dark_mode.css
         - curl https://api.github.com/repos/compbiocore/cbc-documentation-templates/contents/files/cbc-logo.svg\?access_token\=$GITHUB_TOKEN > logo.json
         - jq -r '.content' < logo.json | base64 --decode > docs/images/cbc-logo.svg

         - mkdocs build --verbose --clean --strict
       deploy:
        provider: pages
        skip_cleanup: true
        github_token: $GITHUB_PAT
        local_dir: site
        on:

          branch: master