Updated discovery for new FHIR resources #915
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - 'docs/**' | |
| # The goal here is to cancel older workflows when a PR is updated (because it's pointless work) | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }} | |
| cancel-in-progress: true | |
| jobs: | |
| unittest: | |
| name: unit tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| cache: pip | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ".[test]" | |
| - name: Create mock AWS credentials | |
| run: | | |
| mkdir ~/.aws && touch ~/.aws/credentials | |
| echo -e "[test]\naws_access_key_id = test\naws_secret_access_key = test" > ~/.aws/credentials | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --cov-report xml --cov=cumulus_library tests | |
| - name: Log missing coverage | |
| run: | | |
| coverage report -m --skip-covered | |
| - name: Generate coverage report | |
| if: github.ref != 'refs/heads/main' | |
| uses: orgoro/[email protected] | |
| with: | |
| coverageFile: coverage.xml | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| thresholdAll: .9 | |
| thresholdNew: 1 | |
| thresholdModified: 1 | |
| lint: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install linters | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ".[dev]" | |
| - name: Run sqlfluff on jinja templates | |
| run: | | |
| sqlfluff lint | |
| - name: Run ruff | |
| if: success() || failure() # still run ruff if above checks fails | |
| run: | | |
| ruff check | |
| ruff format --check | |
| regression: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write # This is required for requesting the JWT | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| # See https://github.com/aws-actions/configure-aws-credentials for configuring | |
| # the aws side of this - the below action is just a light wrapper | |
| - name: Configure AWS Credentials | |
| uses: mcblair/[email protected] | |
| with: | |
| role-arn: arn:aws:iam::${{secrets.AWS_ACCOUNT}}:role/cumulus-library-ci | |
| region: us-east-1 | |
| profile-name: cumulus-library-ci | |
| - name: Rebuild tables | |
| env: | |
| PROFILE: cumulus-library-ci | |
| WG: cumulus | |
| DB: cumulus_library_regression_db | |
| run: | | |
| cumulus-library build -t core --profile $PROFILE --workgroup $WG --database $DB | |
| cumulus-library export -t core ./tests/regression/data_export/ --profile $PROFILE --workgroup $WG --database $DB | |
| - name: Compare vs known data | |
| run: python ./tests/regression/run_regression.py | |