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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: 3.19.4
CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install
GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build
GENOMICSDB_RELEASE_VERSION: x.y.z.test
HADOOP_VER: 3.2.2
SPARK_VER: 3.0.1
SPARK_HADOOP_VER: 2.7
jobs:
build:
strategy:
fail-fast: false
matrix:
os: [ubuntu-18.04,macos-11]
type: [basic]
java: [8,11]
include:
- os: ubuntu-18.04
type: hdfs
java: 8
#- os: ubuntu-18.04
# type: hdfs
# java: 11
env:
OS_TYPE: ${{matrix.os}}
JAVA_VER: ${{matrix.java}}
JAVA_LINUX: /usr/lib/jvm/java-1.${{matrix.java}}.0-openjdk-amd64/
runs-on: ${{matrix.os}}
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: 3.6
- uses: actions/setup-java@v1
if: startsWith(matrix.os, 'macos')
with:
java-version: ${{matrix.java}}
- name: Install Java, set path
if: startsWith(matrix.os, 'ubuntu')
shell: bash
run: |
sudo add-apt-repository -y ppa:openjdk-r/ppa
sudo apt update -qq
sudo apt install -yq openjdk-${{matrix.java}}-jdk
echo $JAVA_LINUX/bin >> $GITHUB_PATH
- name: Cache built prerequisites
uses: actions/cache@v2
with:
path: |
${{env.PREREQS_INSTALL_DIR}}
~/.m2/repository
~/awssdk-install
~/gcssdk-install
~/protobuf-install/${{env.PROTOBUF_VERSION}}
key: ${{matrix.os}}-cache-prereqs-v5
# TODO: See https://github.com/actions/cache/pull/285 using platform-independent "pip cache dir"
- name: Cache Python artifacts for Ubuntu
uses: actions/cache@v2
if: startsWith(matrix.os, 'ubuntu')
with:
path: ~/.cache/pip
key: ${{matrix.os}}-pip-${{matrix.python-version}}-v1
- name: Cache Python artifacts for MacOS
uses: actions/cache@v2
if: startsWith(matrix.os, 'macos')
with:
path: ~/Library/Caches/pip
key: ${{matrix.os}}-pip-${{matrix.python-version}}-v1
- name: Cache Distributed FileSystems
if: matrix.type == 'hdfs'
uses: actions/cache@v2
with:
path: ${{runner.workspace}}/hadoop-${{env.HADOOP_VER}}
key: dfs-${{env.HADOOP_VER}}-v2
- name: Install Prerequisites
shell: bash
working-directory: ${{github.workspace}}/scripts/prereqs
run: |
$GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh
echo "matrix.os = ${{matrix.os}}"
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 $GITHUB_WORKSPACE/.github/scripts/install_hadoop.sh
JAVA_HOME=$JAVA_LINUX 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: |
if [[ $JAVA_VER == '11' ]]; then
GENOMICSDB_MAVEN_PROFILE=java11
fi
source $PREREQS_ENV
if [[ $OS_TYPE == 'ubuntu-18.04' ]]; then
JAVA_HOME=$JAVA_LINUX
echo $JAVA_LINUX/bin >> $GITHUB_PATH
fi
# java tests take a very long time to run on MacOS, so limit running the tests to PRs and master/develop branches
BRANCH=${GITHUB_REF##*/}
if [[ ${{matrix.os}} != macos* || ${GITHUB_REF##*/} == master || ${GITHUB_REF##*/} == develop || $GITHUB_BASE_REF == master || $GITHUB_BASE_REF == develop ]]; then
echo "cmake BUILD_JAVA set to 1"
JAVA_BUILD_ARGS="-DBUILD_JAVA=1 -DGENOMICSDB_MAVEN_PROFILE=$GENOMICSDB_MAVEN_PROFILE"
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
- name: Build
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
shell: bash
run: |
if [[ $OS_TYPE == 'ubuntu-18.04' ]]; then
export JAVA_HOME=$JAVA_LINUX
echo $JAVA_LINUX/bin >> $GITHUB_PATH
fi
source $PREREQS_ENV
make -j4
make install
- name: Test
shell: bash
working-directory: ${{env.GENOMICSDB_BUILD_DIR}}
if: matrix.type == 'basic'
run: |
if [[ $OS_TYPE == 'ubuntu-18.04' ]]; then
export JAVA_HOME=$JAVA_LINUX
echo $JAVA_LINUX/bin >> $GITHUB_PATH
fi
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: ${{github.workspace}}
run: |
JAVA_HOME=$JAVA_LINUX
source $SPARK_ENV
python -m pip install --upgrade pip
python -m pip install jsondiff
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: Upload Coverage to CodeCov
uses: codecov/codecov-action@v1
|
