forgot to update actual docker build to jammy #2229
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| name: build | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| pull_request: | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.rst' | |
| env: | |
| PREREQS_ENV: ${{github.workspace}}/prereqs.sh | |
| SPARK_ENV: ${{github.workspace}}/spark_env.sh | |
| HADOOP_ENV: ${{github.workspace}}/hadoop_env.sh | |
| PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs | |
| PROTOBUF_VERSION: 3.21.7 | |
| CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install | |
| GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build | |
| GENOMICSDB_RELEASE_VERSION: x.y.z.test | |
| HADOOP_VER: 3.3.5 | |
| SPARK_VER: 3.4.0 | |
| SPARK_HADOOP_VER: 3 | |
| jobs: | |
| build: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04,ubuntu-22.04,macos-12] | |
| type: [basic] | |
| java: [17] | |
| include: | |
| - os: ubuntu-22.04 | |
| type: hdfs | |
| java: 17 | |
| env: | |
| OS_TYPE: ${{matrix.os}} | |
| JAVA_VER: ${{matrix.java}} | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| cache: 'pip' | |
| - uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{matrix.java}} | |
| distribution: temurin | |
| java-package: jdk | |
| cache: maven | |
| - name: Cache built prerequisites | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ${{env.PREREQS_INSTALL_DIR}} | |
| ~/awssdk-install | |
| ~/gcssdk-install | |
| ~/protobuf-install/${{env.PROTOBUF_VERSION}} | |
| key: ${{matrix.os}}-cache-prereqs-${{env.PROTOBUF_VERSION}}-v1 | |
| - name: Cache Distributed FileSystems | |
| if: matrix.type == 'hdfs' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{runner.workspace}}/hadoop-${{env.HADOOP_VER}} | |
| key: ${{matrix.os}}-dfs-${{env.HADOOP_VER}} | |
| - name: Install Prerequisites | |
| shell: bash | |
| working-directory: ${{github.workspace}}/scripts/prereqs | |
| run: | | |
| $GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh | |
| if [[ ${{matrix.os}} == macos* ]]; then | |
| echo "Installing Prerequistes for MacOS..." | |
| INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh | |
| else | |
| echo "Install Prerequisites for Linux.." | |
| sudo INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh | |
| fi | |
| echo "cat prereqs env..." | |
| cat $PREREQS_ENV | |
| echo "cat prereqs env DONE" | |
| - name: Install spark and hadoop dependencies | |
| if: matrix.type == 'hdfs' | |
| shell: bash | |
| working-directory: ${{github.workspace}} | |
| run: | | |
| source $GITHUB_WORKSPACE/.github/scripts/install_hadoop.sh | |
| # Spark needs JAVA_HOME to be the jdk path | |
| JAVA_HOME==$(dirname $(dirname $(readlink -f $(which javac)))) SPARK_ENV=$SPARK_ENV source $GITHUB_WORKSPACE/.github/scripts/install_spark.sh | |
| env: | |
| INSTALL_DIR: ${{runner.workspace}} | |
| - name: Create Build Directory | |
| shell: bash | |
| run: mkdir -p $GENOMICSDB_BUILD_DIR | |
| - name: Configure CMake Build | |
| shell: bash | |
| working-directory: ${{env.GENOMICSDB_BUILD_DIR}} | |
| run: | | |
| source $PREREQS_ENV | |
| # java tests take a very long time to run on MacOS, so limit running the tests to PRs and master/develop branches | |
| BRANCH=${GITHUB_REF##*/} | |
| if [[ ${{matrix.os}} != macos* || ${GITHUB_REF##*/} == master || ${GITHUB_REF##*/} == develop || $GITHUB_BASE_REF == master || $GITHUB_BASE_REF == develop ]]; then | |
| echo "cmake BUILD_JAVA set to 1" | |
| JAVA_BUILD_ARGS="-DBUILD_JAVA=1" | |
| fi | |
| if [[ ${{matrix.type}} == 'hdfs' ]]; then | |
| HDFS_BUILD_ARGS="-DUSE_HDFS=1" | |
| fi | |
| cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Coverage -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \ | |
| -DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR -DGENOMICSDB_PROTOBUF_VERSION=$PROTOBUF_VERSION \ | |
| -DGENOMICSDB_RELEASE_VERSION=$GENOMICSDB_RELEASE_VERSION $JAVA_BUILD_ARGS $HDFS_BUILD_ARGS | |
| - name: Build | |
| working-directory: ${{env.GENOMICSDB_BUILD_DIR}} | |
| shell: bash | |
| run: | | |
| source $PREREQS_ENV | |
| make -j4 | |
| make install | |
| - name: Test | |
| shell: bash | |
| working-directory: ${{env.GENOMICSDB_BUILD_DIR}} | |
| if: matrix.type == 'basic' | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install jsondiff | |
| make test ARGS=-V | |
| - name: Test - Distributed FileSystems | |
| if: matrix.type == 'hdfs' | |
| shell: bash | |
| working-directory: ${{github.workspace}} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install jsondiff | |
| source $SPARK_ENV | |
| python tests/run_spark_hdfs.py $GENOMICSDB_BUILD_DIR $CMAKE_INSTALL_PREFIX local hdfs://localhost:9000/ client $GENOMICSDB_RELEASE_VERSION $GITHUB_WORKSPACE/tests "" Coverage | |
| $GITHUB_WORKSPACE/.github/scripts/test_hdfs_htslib_support.sh | |
| - name: Coverage | |
| shell: bash | |
| working-directory: ${{env.GENOMICSDB_BUILD_DIR}} | |
| run: | | |
| lcov --directory . --capture --output-file coverage.info | |
| lcov --remove coverage.info '/opt*' '/usr*' '*/dependencies/*' '*/src/test*' '*.pb.h' '*.pb.cc' '*/protobuf-install/*' '*/awssdk-install/*' '*/gcssdk-install/*' 'v1/*' '/Library/*' -o coverage.info | |
| - name: Upload Coverage to CodeCov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: build/coverage.info, build/target/jacoco-reports/jacoco-ut/jacoco.xml, build/target/jacoco-reports/jacoco-ci/jacoco-ci.xml | |
| verbose: true |