Allow for GT to be a nocall if GQ and PL[0] are zero instead of homre… #2223
Workflow file for this run
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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 |