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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-13]
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@v4
- uses: actions/setup-python@v5
with:
python-version: 3.11
cache: 'pip'
- uses: actions/setup-java@v4
with:
java-version: ${{matrix.java}}
distribution: temurin
java-package: jdk
cache: maven
- name: Cache built prerequisites
uses: actions/cache@v4
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@v4
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
if [[ ${{matrix.os}} != 'ubuntu-20.04' ]]; then
NANOARROW_BUILD_ARGS="-DBUILD_NANOARROW=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 $NANOARROW_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@v4
with:
files: build/coverage.info, build/target/jacoco-reports/jacoco-ut/jacoco.xml, build/target/jacoco-reports/jacoco-ci/jacoco-ci.xml
verbose: true
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
|
