update sv bothsides support parsing (#1111) #3428
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| name: unit tests | |
| # Run the test suite on pushes (incl. merges) to main and dev | |
| # Run the test suite when a PR is opened, pushed to, or reopened | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| - main | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| jobs: | |
| unit_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Create ClickHouse Config | |
| run: | | |
| cat <<EOF > test_config.xml | |
| <clickhouse> | |
| <user_files_path>/tmp</user_files_path> | |
| </clickhouse> | |
| EOF | |
| - name: Start ClickHouse with mounted config | |
| run: | | |
| docker run -d --name clickhouse \ | |
| -v ${{ github.workspace }}/test_config.xml:/etc/clickhouse-server/config.d/config.xml \ | |
| -v /tmp:/tmp \ | |
| -p 9000:9000 \ | |
| -e CLICKHOUSE_USER=clickhouse_test \ | |
| -e CLICKHOUSE_PASSWORD=clickhouse_test \ | |
| bitnami/clickhouse:latest | |
| - name: Wait for ClickHouse | |
| run: | | |
| until docker exec clickhouse clickhouse-client --query "SELECT 1"; do | |
| echo "Waiting for ClickHouse to start..." | |
| sleep 2 | |
| done | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| cache-dependency-path: 'requirements**.txt' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-dataproc.txt | |
| pip install -r requirements-dev.txt | |
| - name: Check Ruff Format | |
| run: ruff format --check v03_pipeline --diff | |
| - name: Check Ruff | |
| run: ruff check --output-format github | |
| - name: Run ShellCheck | |
| uses: ludeeus/action-shellcheck@master | |
| with: | |
| severity: error | |
| scandir: './v03_pipeline/bin' | |
| - name: Unit Tests | |
| run: | | |
| export GRCH37_TO_GRCH38_LIFTOVER_REF_PATH=v03_pipeline/var/test/liftover/grch37_to_grch38.over.chain.gz | |
| export GRCH38_TO_GRCH37_LIFTOVER_REF_PATH=v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz | |
| export ACCESS_PRIVATE_REFERENCE_DATASETS=1 | |
| export INCLUDE_PIPELINE_VERSION_IN_PREFIX=1 | |
| export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell' | |
| export CLICKHOUSE_USER=clickhouse_test | |
| export CLICKHOUSE_PASSWORD=clickhouse_test | |
| export CLICKHOUSE_DATABASE=test | |
| nosetests --with-coverage --cover-package v03_pipeline/lib v03_pipeline/lib | |
| coverage report --omit '*test*' --fail-under=75 |