Dockerfile tests and cleanup imputation/PRS #395
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| schedule: | |
| - cron: '23 2 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| validate_wdl: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: 87 | |
| - name: Womtool Validate | |
| run: find . -name '*.wdl' | xargs -tI {} java -jar ${WOMTOOL_JAR} validate {} | |
| test_wdl: | |
| needs: validate_wdl | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - id: auth | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| service_account: palantir-workflows-service-acc@broad-dsde-methods.iam.gserviceaccount.com | |
| - uses: ./.github/actions/install-cromwell | |
| with: | |
| CROMWELL_VERSION: 87 | |
| - uses: ./.github/actions/install-watt | |
| with: | |
| WATT_VERSION: v1.1 | |
| - name: Get changed Files | |
| if: github.ref != 'refs/heads/main' | |
| id: changed-files | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| files_yaml: | | |
| wdl: '**.wdl' | |
| json: '**.json' | |
| watt_config: test/watt_config.yml | |
| - name: Choose tests to run | |
| id: choose_tests_to_run | |
| if: github.ref != 'refs/heads/main' && !steps.changed-files.outputs.watt_config_all_changed_and_modified_files && (steps.changed-files.outputs.wdl_all_changed_and_modified_files || steps.changed-files.outputs.json_all_changed_and_modified_files) | |
| env: | |
| CHANGED_WDLS: ${{ steps.changed-files.outputs.wdl_all_changed_and_modified_files }} | |
| CHANGED_JSON: ${{ steps.changed-files.outputs.json_all_changed_and_modified_files }} | |
| run: | | |
| WF_TESTS_TO_RUN=$(python test/choose_watt_tests/choose_watt_tests.py --watt-config test/watt_config.yml --womtool-jar ${WOMTOOL_JAR} --changed-workflows ${CHANGED_WDLS} --changed-jsons ${CHANGED_JSON}) | |
| # remove white space elements from bash array | |
| for i in ${!WF_TESTS_TO_RUN[@]}; do [[ -z ${WF_TESTS_TO_RUN[i]} ]] && unset WF_TESTS_TO_RUN[i]; done | |
| if [[ ${#WF_TESTS_TO_RUN[@]} == 0 ]]; then | |
| echo "No workflows with tests have changed. Will not run any tests" | |
| else | |
| echo "Running tests for ${#WF_TESTS_TO_RUN[@]} workflows: ${WF_TESTS_TO_RUN}" | |
| echo "WF_TESTS_TO_RUN=${WF_TESTS_TO_RUN}" >> $GITHUB_ENV | |
| fi | |
| echo "n_wf_to_test=${#WF_TESTS_TO_RUN[@]}" >> $GITHUB_OUTPUT | |
| - name: Run tests with WATT | |
| if: steps.choose_tests_to_run.outputs.n_wf_to_test > 0 || github.ref == 'refs/heads/main' || steps.changed-files.outputs.watt_config_all_changed_and_modified_files | |
| env: | |
| WF_PARAM_NAME: ${{ steps.choose_tests_to_run.outputs.n_wf_to_test && '--workflow' || '' }} | |
| run: python ~/watt/watt.py -e ${CROMWELL_JAR} -c test/watt_config.yml ${WF_PARAM_NAME} ${WF_TESTS_TO_RUN} --cromwell-config test/simple_cromwell.conf -p 50 --executor-log-prefix cromwell_logs/ | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: cromwell_logs | |
| path: cromwell_logs/ | |
| python_lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Lint with Ruff | |
| run: | | |
| pip install ruff | |
| ruff check --output-format=github . | |
| python_test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: ScoreBGE Unit tests | |
| run: | | |
| pip install -r ImputationPipeline/ScoreBGE/requirements.txt | |
| cd ImputationPipeline/ScoreBGE/tests | |
| export PYTHONPATH=$GITHUB_WORKSPACE | |
| python -m unittest test_ScoreBGE.py |