Implementation of CRAM 3.1 codecs. #380
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
| # This is a github actions workflow which runs htsjdk tests and spotbugs. | |
| name: Build and Test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| env: | |
| HTSJDK_SAMTOOLS_BIN: /usr/bin/samtools | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java: [ 17 ] | |
| experimental: [false] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| name: Java ${{ matrix.Java }} build and test | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java ${{ matrix.Java }} | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{ matrix.Java }} | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Install Samtools | |
| run: scripts/install-samtools.sh | |
| - name: Start the htsget server | |
| run: scripts/htsget-scripts/start-htsget-test-server.sh | |
| - name: Run tests | |
| run: ./gradlew test jacocoTestReport | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-${{ matrix.Java }} | |
| path: build/reports/tests | |
| testExternalApis: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| name: Tests that require external APIs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Run tests | |
| run: ./gradlew testFTP jacocoTestReport | |
| # - name: Upload to codecov | |
| # run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash) | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-external-apis | |
| path: build/reports/tests | |
| testFTP: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| name: FTP tests | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Run tests | |
| run: ./gradlew testFTP jacocoTestReport | |
| # - name: Upload to codecov | |
| # run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash) | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-ftp | |
| path: build/reports/tests | |
| spotBugs: | |
| runs-on: ubuntu-latest | |
| name: SpotBugs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew spotBugsMain spotBugsTest | |
| - name: Upload spotBugs Report | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: spotBugs-Report | |
| path: build/reports/spotbugs | |