diff --git a/.github/workflows/ensembl-production.yml b/.github/workflows/ensembl-production.yml new file mode 100644 index 000000000..c3ba40be9 --- /dev/null +++ b/.github/workflows/ensembl-production.yml @@ -0,0 +1,172 @@ +name: Ensembl/ensembl-production +on: + push: + branches: + - "**/*" + pull_request: + schedule: [] +concurrency: +# # This item has no matching transformer +# maximum_number_of_builds: 0 +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: checkout + uses: actions/checkout@v4.1.0 + - uses: shogo82148/actions-setup-perl@v1.27.0 + with: + perl-version: "${{ matrix.perl }}" + - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss + - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git + - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin + - run: export ENSEMBL_BRANCH=master + - run: export SECONDARY_BRANCH=main + - run: echo "TRAVIS_BRANCH=${{ github.ref }}" + - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi + - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" + - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy + - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git + - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git + - run: cd htslib + - run: make + - run: export HTSLIB_DIR=$(pwd -P) + - run: cd .. + - run: cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile . + - run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile . + - run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile . + - run: export PERL5LIB=$PERL5LIB:$PWD/bioperl-live + - run: cpanm --sudo -v --installdeps --notest . + - run: cpanm --sudo -n Devel::Cover::Report::Coveralls + - run: cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf + - run: mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"' + - run: "./travisci/harness.sh" +# # This item has no matching transformer +# - email: +# on_success: always +# on_failure: always + - uses: rtCamp/action-slack-notify@v2.2.1 + env: + SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" + strategy: + matrix: + perl: + - '5.14' + - 5.26.2 + include: + - COVERALLS: 'true' + DB: mysql + services: + mysql: + image: mysql + env: + COVERALLS: "${{ matrix.COVERALLS }}" + DB: "${{ matrix.DB }}" + test_2: + runs-on: ubuntu-latest + env: + COVERALLS: 'true' + DB: mysql + steps: + - name: checkout + uses: actions/checkout@v4.1.0 + - uses: actions/setup-python@v5.0.0 + with: + python-version: 3.7.6 + - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss + - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git + - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin + - run: export ENSEMBL_BRANCH=master + - run: export SECONDARY_BRANCH=main + - run: echo "TRAVIS_BRANCH=${{ github.ref }}" + - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi + - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" + - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy + - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git + - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git + - run: cd htslib + - run: make + - run: export HTSLIB_DIR=$(pwd -P) + - run: cd .. + - run: pip install -r requirements-test.txt + - run: pip install -e . + - run: pytest src/python/test +# # This item has no matching transformer +# - email: +# on_success: always +# on_failure: always + - uses: rtCamp/action-slack-notify@v2.2.1 + env: + SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" + services: + mysql: + image: mysql + test_3: + runs-on: ubuntu-latest + env: + COVERALLS: 'true' + DB: mysql + steps: + - name: checkout + uses: actions/checkout@v4.1.0 + - uses: actions/setup-python@v5.0.0 + with: + python-version: 3.8 + - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss + - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git + - run: export PATH=$PATH:$PWD/ensembl-git-tools/bin + - run: export ENSEMBL_BRANCH=master + - run: export SECONDARY_BRANCH=main + - run: echo "TRAVIS_BRANCH=${{ github.ref }}" + - run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi + - run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH" + - run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH" + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata + - run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm + - run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy + - run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git + - run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git + - run: cd htslib + - run: make + - run: export HTSLIB_DIR=$(pwd -P) + - run: cd .. + - run: pip install -r requirements-test.txt + - run: pip install -e . + - run: pytest src/python/test +# # This item has no matching transformer +# - email: +# on_success: always +# on_failure: always + - uses: rtCamp/action-slack-notify@v2.2.1 + env: + SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" + services: + mysql: + image: mysql