Improve Singularity.md documentation (#349) #433
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| name: Sonar Source Analysis | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: Sonar Source Analysis | |
| runs-on: ubuntu-20.04 | |
| env: | |
| SONAR_SCANNER_VERSION: 4.6.1.2450 # Find the latest version in the "Linux" link on this page: | |
| # https://sonarcloud.io/documentation/analysis/scan/sonarscanner/ | |
| SONAR_SERVER_URL: "https://sonarcloud.io" | |
| BUILD_WRAPPER_OUT_DIR: build_wrapper_output_directory # Directory where build-wrapper output will be placed | |
| steps: | |
| - name: Download BioDynaMo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis | |
| - name: Set up JDK 11 | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 11 | |
| - name: Install sonar-scanner and build-wrapper | |
| uses: SonarSource/sonarcloud-github-c-cpp@v1 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libopenmpi-dev libomp5 libomp-dev libnuma-dev freeglut3-dev \ | |
| libreadline-dev libsqlite3-dev tk-dev python3-openssl ninja-build libblas-dev \ | |
| liblapack-dev kcov libgit2-dev | |
| curl -L -O https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-Linux-x86_64.sh | |
| chmod +x cmake-3.19.3-Linux-x86_64.sh | |
| sudo ./cmake-3.19.3-Linux-x86_64.sh --skip-license --prefix=/usr/local | |
| - name: Start Xvfb | |
| run: | | |
| set -e | |
| sudo apt-get -y install xvfb | |
| XVFBARGS=":99 -ac -screen 0 2560x1440x24" | |
| /usr/bin/Xvfb $XVFBARGS >> /tmp/Xvfb.out 2>&1 & | |
| disown -ar | |
| sleep 3 | |
| - name: Install pyenv dependency | |
| run: | | |
| if [ ! -f "$HOME/.pyenv/bin/pyenv" ]; then | |
| curl https://pyenv.run | bash | |
| fi | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1 | |
| pyenv shell 3.9.1 | |
| - name: Run build-wrapper | |
| run: | | |
| export PATH="$HOME/.pyenv/bin:$PATH" | |
| eval "$(pyenv init --path)" | |
| eval "$(pyenv init -)" | |
| pyenv shell 3.9.1 | |
| mkdir build | |
| cmake -G Ninja \ | |
| -Dparaview=ON \ | |
| -Dcoverage=ON \ | |
| -Dlibgit2=ON \ | |
| -B build | |
| build-wrapper-linux-x86-64 --out-dir ${{ env.BUILD_WRAPPER_OUT_DIR }} cmake --build build/ --parallel | |
| - name: Analyze coverage | |
| run: | | |
| source $(find /home -path "*/bin/*" -name "*thisbdm.sh") | |
| cd build | |
| ninja coverage-gha | |
| mkdir coverage/coverage_data | |
| cp $(find "coverage" -name "*sonarqube.xml") coverage/coverage_data/sonar_coverage.xml | |
| echo "\n Filecontent sonar_coverage.xml:" | |
| FILE=$(find "coverage" -name "*sonar_coverage.xml") | |
| tail -n +2 "$FILE" > "$FILE.tmp" && mv "$FILE.tmp" "$FILE" | |
| head -n 30 "$FILE" | |
| echo "\n ... \n" | |
| tail -n 7 "$FILE" | |
| - name: Run sonar-scanner | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} | |
| run: | | |
| source $(find /home -path "*/bin/*" -name "*thisbdm.sh") | |
| sonar-scanner --define sonar.cfamily.build-wrapper-output="${{ env.BUILD_WRAPPER_OUT_DIR }}" |