[SCHEMATIC-214] Wrap pandas functions to support not including None with the NA values argument
#5256
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| # Built from: | |
| # https://docs.github.com/en/actions/guides/building-and-testing-python | |
| # https://github.com/Sage-Bionetworks/challengeutils/blob/master/.github/workflows/pythonapp.yml | |
| # https://github.com/snok/install-poetry#workflows-and-tips | |
| name: Test schematic | |
| on: | |
| push: | |
| branches: ['main', 'develop'] | |
| pull_request: | |
| branches: ['*'] | |
| workflow_dispatch: # Allow manually triggering the workflow | |
| concurrency: | |
| # cancel the current running workflow from the same branch, PR when a new workflow is triggered | |
| # when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group | |
| # {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows | |
| # {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag | |
| # {{ github.event.pull_request.number}}: get PR number | |
| # {{ github.sha }}: full commit sha | |
| # credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml | |
| group: >- | |
| ${{ github.workflow }}-${{ github.ref_type }}- | |
| ${{ github.event.pull_request.number || github.sha }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| env: | |
| POETRY_VERSION: 1.3.0 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10"] | |
| steps: | |
| #---------------------------------------------- | |
| # check-out repo and set-up python | |
| #---------------------------------------------- | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| #---------------------------------------------- | |
| # verify runner environment | |
| #---------------------------------------------- | |
| # - name: Print runner environment information | |
| # run: | | |
| # echo "Running on runner: $RUNNER_NAME" | |
| # echo "Runner OS: $RUNNER_OS" | |
| # echo "Runner OS version: $RUNNER_OS_VERSION" | |
| # echo "Runner architecture: $RUNNER_ARCH" | |
| # echo "Total memory: $(free -h)" | |
| # echo "CPU info: $(lscpu)" | |
| #---------------------------------------------- | |
| # install & configure poetry | |
| #---------------------------------------------- | |
| - name: Install Poetry | |
| run: | | |
| curl -sSL https://install.python-poetry.org \ | |
| | python3 - --version ${{ env.POETRY_VERSION }}; | |
| poetry config virtualenvs.create true; | |
| poetry config virtualenvs.in-project true; | |
| #---------------------------------------------- | |
| # install dependencies and root project | |
| #---------------------------------------------- | |
| - name: Install dependencies and root project | |
| run: poetry install --no-interaction --all-extras | |
| #---------------------------------------------- | |
| # perform linting | |
| #---------------------------------------------- | |
| # Disabled until we agree to turn it on | |
| # - name: Lint with flake8 | |
| # run: | | |
| # # stop the build if there are Python syntax errors or undefined names | |
| # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| #---------------------------------------------- | |
| # check formatting | |
| #---------------------------------------------- | |
| - name: Code formatting with black | |
| run: | | |
| # ran only on certain files for now | |
| # add here when checked | |
| poetry run black schematic tests schematic_api --check | |
| #---------------------------------------------- | |
| # type checking/enforcement | |
| #---------------------------------------------- | |
| - name: Type checking with mypy | |
| run: | | |
| # ran only on certain files for now | |
| # add here when checked | |
| # poetry run mypy --install-types --non-interactive | |
| # add here when enforced | |
| poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/schemas/ schematic/configuration/ schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/visualization schematic/utils/ | |
| #---------------------------------------------- | |
| # linting | |
| #---------------------------------------------- | |
| - name: Lint with pylint | |
| run: | | |
| # ran only on certain files for now | |
| # add here when checked | |
| poetry run pylint schematic/visualization/* schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py schematic/utils/*.py schematic/schemas/*.py | |
| #---------------------------------------------- | |
| # run unit test suite | |
| #---------------------------------------------- | |
| - name: Run unit tests | |
| env: | |
| SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }} | |
| SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }} | |
| run: > | |
| poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov | |
| --cov-report=xml:coverage.xml --cov=schematic/ --reruns 4 -n 8 tests/unit; | |
| #---------------------------------------------- | |
| # run integration test suite | |
| #---------------------------------------------- | |
| - name: Retrieve telemetry access token from IDP | |
| if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }} | |
| id: retrieve-telemetry-access-token | |
| run: | | |
| response=$(curl --request POST \ | |
| --url ${{ vars.TELEMETRY_AUTH_CLIENT_URL }} \ | |
| --header 'content-type: application/json' \ | |
| --data '{"client_id":"${{ vars.TELEMETRY_AUTH_CLIENT_ID }}","client_secret":"${{ secrets.TELEMETRY_AUTH_CLIENT_SECRET }}","audience":"${{ vars.TELEMETRY_AUTH_AUDIENCE }}","grant_type":"client_credentials"}') | |
| access_token=$(echo $response | jq -r .access_token) | |
| echo "::add-mask::$access_token" | |
| echo "TELEMETRY_ACCESS_TOKEN=$access_token" >> "$GITHUB_OUTPUT" | |
| - name: Run integration tests | |
| if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }} | |
| env: | |
| SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }} | |
| SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }} | |
| OTEL_EXPORTER_OTLP_HEADERS: "Authorization=Bearer ${{ steps.retrieve-telemetry-access-token.outputs.TELEMETRY_ACCESS_TOKEN }}" | |
| DEPLOYMENT_ENVIRONMENT: ${{ vars.DEPLOYMENT_ENVIRONMENT }} | |
| OTEL_EXPORTER_OTLP_ENDPOINT: ${{ vars.OTEL_EXPORTER_OTLP_ENDPOINT }} | |
| TRACING_EXPORT_FORMAT: ${{ vars.TRACING_EXPORT_FORMAT }} | |
| LOGGING_EXPORT_FORMAT: ${{ vars.LOGGING_EXPORT_FORMAT }} | |
| TRACING_SERVICE_NAME: ${{ vars.TRACING_SERVICE_NAME }} | |
| LOGGING_SERVICE_NAME: ${{ vars.LOGGING_SERVICE_NAME }} | |
| run: > | |
| poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/ | |
| -m "not (rule_benchmark or single_process_execution)" --reruns 4 -n 8 --ignore=tests/unit | |
| - name: Run integration tests single process | |
| if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }} | |
| env: | |
| SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }} | |
| SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }} | |
| OTEL_EXPORTER_OTLP_HEADERS: "Authorization=Bearer ${{ steps.retrieve-telemetry-access-token.outputs.TELEMETRY_ACCESS_TOKEN }}" | |
| DEPLOYMENT_ENVIRONMENT: ${{ vars.DEPLOYMENT_ENVIRONMENT }} | |
| OTEL_EXPORTER_OTLP_ENDPOINT: ${{ vars.OTEL_EXPORTER_OTLP_ENDPOINT }} | |
| TRACING_EXPORT_FORMAT: ${{ vars.TRACING_EXPORT_FORMAT }} | |
| LOGGING_EXPORT_FORMAT: ${{ vars.LOGGING_EXPORT_FORMAT }} | |
| TRACING_SERVICE_NAME: ${{ vars.TRACING_SERVICE_NAME }} | |
| LOGGING_SERVICE_NAME: ${{ vars.LOGGING_SERVICE_NAME }} | |
| run: > | |
| poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/ | |
| -m "single_process_execution" --reruns 4 --ignore=tests/unit | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-${{ matrix.python-version }} | |
| path: htmlcov | |
| # Use always() to always run this step to publish test results when there are test failures | |
| if: ${{ always() && contains(fromJSON('["3.10"]'), matrix.python-version) }} | |
| - name: Upload XML coverage report | |
| id: upload_coverage_report | |
| uses: actions/upload-artifact@v4 | |
| # Only upload a single python version to pass along to sonarcloud | |
| if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) && always() }} | |
| with: | |
| name: coverage-report | |
| path: coverage.xml | |
| sonarcloud: | |
| needs: [test] | |
| if: ${{ always() && !cancelled()}} | |
| name: SonarCloud | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis | |
| - name: Check coverage-report artifact existence | |
| id: check_coverage_report | |
| uses: LIT-Protocol/artifact-exists-action@v0 | |
| with: | |
| name: "coverage-report" | |
| - name: Download coverage report | |
| uses: actions/download-artifact@v4 | |
| if: steps.check_coverage_report.outputs.exists == 'true' | |
| with: | |
| name: coverage-report | |
| - name: Check coverage.xml file existence | |
| id: check_coverage_xml | |
| uses: andstor/file-existence-action@v3 | |
| with: | |
| files: "coverage.xml" | |
| # This is a workaround described in https://community.sonarsource.com/t/sonar-on-github-actions-with-python-coverage-source-issue/36057 | |
| - name: Override Coverage Source Path for Sonar | |
| if: steps.check_coverage_xml.outputs.files_exists == 'true' | |
| run: sed -i "s/<source>\/home\/runner\/work\/schematic\/schematic\/schematic<\/source>/<source>\/github\/workspace\/schematic<\/source>/g" coverage.xml | |
| - name: SonarCloud Scan | |
| uses: SonarSource/sonarcloud-github-action@master | |
| if: ${{ always() }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} |