Feature: sample metadata in lims #392
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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_NPG_GITHUB_URL: https://github.com/wtsi-npg | |
| WSI_NPG_BUILD_BRANCH: ${{ github.base_ref}} | |
| WSI_NPG_GITHUB_REPO_OWNER: ${{ github.repository_owner }} | |
| strategy: | |
| matrix: | |
| perl: ["5.26.3", "5.34.1"] | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| ports: | |
| - 3306:3306 | |
| env: | |
| MYSQL_ALLOW_EMPTY_PASSWORD: yes | |
| MYSQL_ROOT_PASSWORD: null | |
| MYSQL_DATABASE: npgt | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=10s --health-retries=5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Change dbhost to 127.0.0.1 | |
| run: | | |
| sed -i s/localhost/127.0.0.1/ ${GITHUB_WORKSPACE}/data/config.ini | |
| - name: set timezone | |
| run: | | |
| sudo timedatectl set-timezone Europe/London | |
| - 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: "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 ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB") | |
| eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib) | |
| cpanm --quiet --notest Module::Build | |
| ./scripts/install_wsi_dependencies.sh "$NPG_LIB" \ | |
| perl-dnap-utilities \ | |
| ml_warehouse | |
| 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@v4 | |
| with: | |
| name: cpan_log | |
| path: ~/.cpanm/work/*/build.log | |
| retention-days: 5 | |
| - name: "Run tests" | |
| run: | | |
| 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 | |
| - name: "Build distribution" | |
| run: | | |
| 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 | |
| ./Build dist | |
| export DIST_FILE=$(ls npg-tracking-*.tar.gz) | |
| export MD5_FILE=$DIST_FILE.md5 | |
| md5sum $DIST_FILE > $MD5_FILE | |
| export SHA256_FILE=$DIST_FILE.sha256 | |
| shasum -a 256 $DIST_FILE > $SHA256_FILE |