Add workflow Ensembl/ensembl-production #1
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: 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 | ||
