[SCHEMATIC-183] Use paths from file view for manifest generation #5247
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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: 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 }} | |
| 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: ${{ secrets.SERVICE_ACCOUNT_CREDS }} | |
| run: > | |
| poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/ | |
| -m "single_process_execution" --reruns 4 --ignore=tests/unit | |
| - name: Upload pytest test results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pytest-results-${{ 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 }} |