Merge pull request #839 from wtsi-npg/devel #326
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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@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 ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib) | |
cpanm --quiet --notest Module::Build | |
./scripts/install_wsi_dependencies.sh "$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@v2 | |
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 |