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: $HOME/perl5 # Perlbrew and CPAN modules installed here, cached
      NPG_LIB: $HOME/perl5npg # NPG modules installed here, not cached
      WSI_CONDA_CHANNEL: https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic
      CONDA_HOME: $HOME/conda
      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@v4
        with:
          fetch-depth: '0'

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

      - name: "Install Miniforge"
        run: |
          CONDA_HOME=${{ env.CONDA_HOME }} ./scripts/install_miniforge.sh
          echo 'source "${{ env.CONDA_HOME }}/etc/profile.d/conda.sh"' >> "$HOME/.bash_profile"

      - name: "Cache Conda"
        id: miniforgeCache
        uses: actions/cache@v4
        with:
          path: |
            ${{ env.CONDA_HOME }}/pkgs
            ${{ env.CONDA_HOME }}/envs
          key: ${{ runner.os }}-build-miniforge

      - name: "Install Conda packages"
        run: |
          conda config --prepend pkgs_dirs ${{ env.CONDA_HOME }}/pkgs
          conda config --prepend envs_dirs ${{ env.CONDA_HOME }}/envs

          conda config --set auto_update_conda False
          conda config --prepend channels "${{ env.WSI_CONDA_CHANNEL }}"
          conda info

          conda create  -y -n "${{ env.CONDA_TEST_ENV }}"
          conda install -y -n "${{ env.CONDA_TEST_ENV }}" baton
          conda install -y -n "${{ env.CONDA_TEST_ENV }}" samtools

      - name: "Cache Perl"
        id: cache-perl
        uses: actions/cache@v4
        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 ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="${{ env.NPG_LIB }}")
          eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
          
          cpanm --quiet --notest Module::Build
          cpanm --quiet --notest Net::SSLeay
          cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz
          
          ./scripts/install_wsi_dependencies.sh "${{ env.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 $HOME/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20  {} \;

      - name: "Archive CPAN logs on failure"
        if: ${{ failure() }}
        uses: actions/upload-artifact@v4
        with:
          name: cpan_log
          path: $HOME/.cpanm/work/*/build.log
          retention-days: 5

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