atomic data preparation #1483
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| name: test | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| permissions: | |
| id-token: write | |
| contents: read | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| pyrenew-hew-test: | |
| name: Run pyrenew_hew tests and collect coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Pyrenew-HEW via UV | |
| uses: ./.github/actions/setup-pyrenew-hew | |
| - name: run tests | |
| env: | |
| NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }} | |
| NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }} | |
| XLA_FLAGS: --xla_force_host_platform_device_count=2 | |
| run: | | |
| uv run pytest tests \ | |
| --mpl --mpl-default-tolerance=10 \ | |
| --cov=pyrenew_hew --cov-report=term --cov-report=xml:pyrenew_hew-coverage.xml . | |
| - name: Upload results to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: true | |
| flags: pyrenew_hew | |
| files: pyrenew_hew-coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| pipelines-test: | |
| name: Run pipelines tests and collect coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Pyrenew-HEW via UV | |
| uses: ./.github/actions/setup-pyrenew-hew | |
| - name: run tests | |
| env: | |
| XLA_FLAGS: --xla_force_host_platform_device_count=2 | |
| run: | | |
| uv run pytest pipelines \ | |
| --mpl --mpl-default-tolerance=10 \ | |
| --cov=pipelines --cov-report=term --cov-report=xml:pipelines-coverage.xml . | |
| - name: Upload results to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| env_vars: OS,PYTHON | |
| fail_ci_if_error: true | |
| flags: pipelines | |
| files: pipelines-coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| hewr-test: | |
| name: Run hewr tests and collect coverage | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up R with hewr | |
| uses: ./.github/actions/setup-hewr | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| path = "hewr", | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| files: ./cobertura.xml | |
| plugins: noop | |
| flags: hewr | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |