remove manual install #47
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master, dev] | |
| pull_request: | |
| branches: [main, master, dev] | |
| name: test-coverage | |
| permissions: read-all | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2, any::testthat, any::BiocNeighbors | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install anndata | |
| pip install numpy | |
| env: | |
| RETICULATE_PYTHON: /opt/hostedtoolcache/Python/3.8.10/x64/bin/python | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov, file = "coverage.xml") | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| file: ./coverage.xml | |
| plugin: noop | |
| 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 |