Convert Ensembl/ensembl-production to GitHub Actions #12
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| name: Ensembl/ensembl-production | |
| on: | |
| push: | |
| branches: | |
| - "**/*" | |
| pull_request: | |
| schedule: | |
| - cron: "0 0 * * 1" | |
| 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" | |
| - 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: "${{ matrix.DB }}" | |
| MYSQL_ROOT_PASSWORD: "ensembl" | |
| test_2: | |
| runs-on: ubuntu-latest | |
| env: | |
| COVERALLS: 'true' | |
| DB: mysql | |
| MYSQL_ROOT_PASSWORD: "ensembl" | |
| MYSQL_ALLOW_EMPTY_PASSWORD: 'true' | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4.1.0 | |
| - uses: actions/setup-python@v5.0.0 | |
| with: | |
| python-version: 3.7.6 | |
| - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | |
| - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | |
| - run: export PATH=$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 | |
| - uses: rtCamp/action-slack-notify@v2.2.1 | |
| env: | |
| SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | |
| services: | |
| mysql: | |
| image: mysql | |
| test_3: | |
| runs-on: ubuntu-latest | |
| env: | |
| COVERALLS: 'true' | |
| DB: mysql | |
| MYSQL_ROOT_PASSWORD: "ensembl" | |
| MYSQL_ALLOW_EMPTY_PASSWORD: 'true' | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@v4.1.0 | |
| - uses: actions/setup-python@v5.0.0 | |
| with: | |
| python-version: 3.8 | |
| - run: apt-get update && apt-get -y install unzip sendmail graphviz emboss | |
| - run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git | |
| - run: export PATH=$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 | |
| - uses: rtCamp/action-slack-notify@v2.2.1 | |
| env: | |
| SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}" | |
| services: | |
| mysql: | |
| image: mysql |