Update build_and_test.yml #210
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| name: Build and test | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| build-n-test-ubuntu: | |
| runs-on: ubuntu-22.04 | |
| services: | |
| # Label used to access the service container | |
| mysql: | |
| # Docker Hub image | |
| image: mysql:5.7 | |
| # Provide the config for MySQL | |
| # The database credentials correspond to the config file | |
| # tests\short\examples\testconfig.json | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| MYSQL_DATABASE: aug_vertebrates | |
| MYSQL_USER: augustus | |
| MYSQL_PASSWORD: aug_passwd | |
| ports: | |
| - 3306:3306 | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out the repository under $GITHUB_WORKSPACE, so the job can access it | |
| - uses: actions/checkout@v2 | |
| # Install python-mysql-connector | |
| - name: Install python-mysql-connector | |
| run: pip3 install mysql-connector-python | |
| # Install required dependencies | |
| - name: Install dependencies | |
| run: sudo ./tests/short/utils/installDependencies.sh | |
| # Build AUGUSTUS | |
| - name: Build AUGUSTUS | |
| run: make all | |
| # Execute unit tests | |
| - name: Execute unit tests | |
| run: make unit_test | |
| # Test AUGUSTUS | |
| - name: Test AUGUSTUS (examples folder with comparison) | |
| run: ./execute_test.py --compare --html --mysql examples | |
| working-directory: tests/short/ | |
| # Test bam2wig | |
| - name: Test bam2wig | |
| run: ./execute_test.py --compare --html bam2wig | |
| working-directory: tests/short/ | |
| # Test bam2hints | |
| - name: Test bam2hints | |
| run: ./execute_test.py --compare --html bam2hints | |
| working-directory: tests/short/ | |
| # Test filterbam | |
| - name: Test filterbam | |
| run: ./execute_test.py --compare --html filterbam | |
| working-directory: tests/short/ | |
| # Upload html diffs of failed test cases | |
| - name: Upload HTML diffs | |
| uses: actions/upload-artifact@v2 | |
| if: failure() | |
| with: | |
| name: html-diffs | |
| path: tests/short/output_html/ | |
| # Build and publich doxygen documentation (only on push in master) | |
| - name: Build documentation | |
| if: ${{ github.ref == 'refs/heads/master' && github.event_name == 'push' }} | |
| uses: mattnotmitt/doxygen-action@v1 | |
| with: | |
| doxyfile-path: 'doxygen.conf' | |
| - name: Publish documentation of master on gh-pages | |
| if: ${{ github.ref == 'refs/heads/master' && github.event_name == 'push' }} | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./doxygen/html/ | |
| build-n-test-macos: | |
| runs-on: macos-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out the repository under $GITHUB_WORKSPACE, so the job can access it | |
| - uses: actions/checkout@v2 | |
| # Install required dependencies | |
| - name: Install dependencies | |
| run: | | |
| brew install boost | |
| brew install zlib | |
| brew install gsl | |
| brew install suite-sparse | |
| brew install lp_solve | |
| brew install sqlite | |
| brew install mysql | |
| brew install mysql++ | |
| brew install bamtools | |
| brew install samtools | |
| brew install htslib | |
| # Build AUGUSTUS | |
| - name: Build AUGUSTUS | |
| run: make all | |
| # Execute unit tests | |
| #TODO: make working on mac | |
| # - name: Execute unit tests | |
| # run: make unit_test | |
| # Test AUGUSTUS | |
| - name: Test AUGUSTUS (examples folder without mysql and comparison on mac) | |
| run: ./execute_test.py examples | |
| working-directory: tests/short/ | |
| # Test bam2wig | |
| - name: Test bam2wig | |
| run: ./execute_test.py --compare --html bam2wig | |
| working-directory: tests/short/ | |
| # Test bam2hints | |
| - name: Test bam2hints | |
| run: ./execute_test.py --compare --html bam2hints | |
| working-directory: tests/short/ | |
| # Test filterbam | |
| - name: Test filterbam | |
| run: ./execute_test.py --compare --html filterbam | |
| working-directory: tests/short/ |