.travis.yml

# Only build the 'none' branch, which does not exist
# https://docs.travis-ci.com/user/customizing-the-build#safelisting-or-blocklisting-branches
branches:
  only:
  - none

# Use a build matrix to run one set of jobs that test the conda environments
# another to test the URLs in the Markdown files
# and other to test the lessons and web site
# See https://stackoverflow.com/questions/27644586/how-to-set-up-travis-ci-with-multiple-languages
matrix:
  include:
  # Configuration adapted from https://github.com/gitter-lab/t-cell-classification
  - language: minimal
    name: Conda environment Linux
    os: linux
    before_install:
      - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh -O miniconda.sh
      - bash miniconda.sh -b -p $HOME/anaconda
      - export PATH="$HOME/anaconda/bin:$PATH"
      - cd scripts
      # Avoid QXcbConnection error by confirming ml4bio can be imported instead of launching the GUI
      - sed -i 's/^ml4bio$/python -c "import ml4bio; print(ml4bio.__version__)"/g' install_launch_linux.sh
    script:
      - ./install_launch_linux.sh

  - language: minimal
    name: Conda environment macOS
    os: osx
    before_install:
      - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.12-MacOSX-x86_64.sh -O miniconda.sh
      - bash miniconda.sh -b -p $HOME/anaconda
      - export PATH="$HOME/anaconda/bin:$PATH"
      - cd scripts
      # Avoid QXcbConnection error by confirming ml4bio can be imported instead of launching the GUI
      # sed workaround needed because macOS does not use GNU sed
      # Workaround from https://github.com/manubot/rootstock/blob/master/SETUP.md
      - sed 's/^ml4bio$/python -c "import ml4bio; print(ml4bio.__version__)"/g' install_launch_mac.command > tmp && mv -f tmp install_launch_mac.command
      - chmod u+x install_launch_mac.command
    script:
      - ./install_launch_mac.command

  # Configuration adapted from https://github.com/dkhamsing/awesome_bot
  - language: ruby
    name: Check URLs
    rvm: 2.4.1
    before_script: gem install awesome_bot
    script: awesome_bot guide/*.md --allow-redirect --allow-dupe

  # Configuration adapted from https://github.com/carpentries/styles/blob/gh-pages/bin/boilerplate/.travis.yml
  # Travis CI is only used to check the lesson and is not involved in its deployment
  - language: python
    name: Check lessons and site
    dist: xenial  # Ubuntu 16.04 (required for python 3.7)
    python: 3.7
    before_install:
      - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
      - echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" | sudo tee -a /etc/apt/sources.list
      - sudo apt-get update -y
      - sudo apt-get install -y --allow-unauthenticated r-base
      - sudo Rscript -e "install.packages('knitr', repos = 'https://', dependencies = TRUE)"
      - sudo Rscript -e "install.packages('stringr', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
      - sudo Rscript -e "install.packages('checkpoint', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
      - sudo Rscript -e "install.packages('ggplot2', repos = 'https://cran.rstudio.com', dependencies = TRUE)"
      - rvm default
      - gem install json kramdown jekyll bundler
    install:
      - pip install pyyaml
    script:
      - make lesson-check-all
      - make --always-make site

notifications:
  email: false