Modify test-coverage.yaml for coverage report upload #19
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| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: macOS-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages("remotes") | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Restore R package cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install dependencies | |
| run: | | |
| install.packages("remotes") | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| BiocManager::install("phyloseq", ask = FALSE) | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("covr") | |
| install.packages("xml2") | |
| shell: Rscript {0} | |
| - name: Build coverage report | |
| run: | | |
| cov <- covr::package_coverage() | |
| print(cov) | |
| covr::to_cobertura(cov, filename = "coverage.xml") | |
| shell: Rscript {0} | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN_tinyvamp }} | |
| files: coverage.xml | |
| slug: statdivlab/tinyvamp | |
| fail_ci_if_error: true |