name: tests

on:
  push:
    #branches: [ develop ]

jobs:
  test-on-latest-ubuntu:
    runs-on: ubuntu-20.04
    steps:
      - uses: actions/checkout@v2
        with:
          fetch-depth: 0
      - uses: s-weigand/setup-conda@v1
      - run : conda --version
      - run : source activate base
      - run : |
          sudo apt update
          sudo apt install libcurl4-openssl-dev
          sudo apt install libssl-dev
          sudo apt install libxml2-dev
          sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
          sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' 
          sudo apt install r-base
          sudo apt install pandoc
          sudo Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
          conda env create -f environment.yml -n test-environment
          source activate test-environment
          snakemake -j1 renv_install
          R -e 'renv::settings$use.cache(FALSE)'
          snakemake -j1 renv_restore
          bash tests/scripts/run_tests.sh all test