run-tests.yml

name: "Unit tests"

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l -e -o pipefail {0}

    env:
      PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
      NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
      WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic"
      CONDA_TEST_ENV: test-environment
      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
      WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}

    strategy:
      matrix:
        perl: ["5.26.3", "5.34.1"]

    steps:
      - uses: actions/checkout@v3

      - name: "Install OS dependencies"
        run: |
          sudo apt-get update
          # https://github.com/actions/runner-images/issues/2139
          sudo apt-get remove -y nginx libgd3
          sudo apt-get install -y libgd-dev uuid-dev libgd-text-perl

      - name: "Initialize Miniconda"
        run: |
          echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile"

      - name: "Install Conda packages"
        run: |
          conda config --prepend pkgs_dirs ~/conda/pkgs
          conda config --prepend envs_dirs ~/conda/envs

          conda config --set auto_update_conda False
          conda config --prepend channels "$WSI_CONDA_CHANNEL"
          conda info

          conda create  -y -n "$CONDA_TEST_ENV"
          conda install -y -n "$CONDA_TEST_ENV" baton
          conda install -y -n "$CONDA_TEST_ENV" samtools

      - name: "Cache Perl"
        id: cache-perl
        uses: actions/cache@v3
        with:
          path: ${{ env.PERL_CACHE }}
          key: ${{ runner.os }}-${{ matrix.perl }}-perl

      - name: "Install Perlbrew"
        if: steps.cache-perl.outputs.cache-hit != 'true'
        run: |
          curl -sSL https://install.perlbrew.pl -o perlbrew.sh
          sha256sum -c .github/workflows/perlbrew.sha256
          export PERLBREW_ROOT=${{ env.PERL_CACHE }}
          sh perlbrew.sh
          
          source ${{ env.PERL_CACHE }}/etc/bashrc
          perlbrew available
          perlbrew install --notest perl-${{ matrix.perl }}
          perlbrew use perl-${{ matrix.perl }}
          perlbrew install-cpanm

      - name: "Initialize Perlbrew"
        run: |
          echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile"

      - name: "Install Perl dependencies"
        run: |
          cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
          
          cpanm --quiet --notest Module::Build
          cpanm --quiet --notest Alien::Tidyp
          cpanm --quiet --notest Net::SSLeay
          cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz
          
          ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
             perl-dnap-utilities \
             perl-irods-wrap \
             ml_warehouse \
             npg_tracking \
             npg_seq_common \
             npg_qc \
             npg_irods

          cpanm --installdeps --notest .          

      - name: "Log install failure"
        if: ${{ failure() }}
        run: |
          find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;

      - name: "Archive CPAN logs on failure"
        if: ${{ failure() }}
        uses: actions/upload-artifact@v2
        with:
          name: cpan_log
          path: ~/.cpanm/work/*/build.log
          retention-days: 5

      - name: "Run tests"
        run: |
          conda activate "$CONDA_TEST_ENV"
          conda info --envs
          
          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
          
          export TEST_AUTHOR=1
          perl Build.PL
          ./Build test --verbose
          ./Build install