Add Chapter 2 Documentation: Extending Hierarchical Model to Correlated Biomarkers #926
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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] | |
| pull_request: | |
| name: test-coverage.yaml | |
| permissions: read-all | |
| jobs: | |
| test-coverage: | |
| runs-on: macos-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Install JAGS (Windows) | |
| if: runner.os == 'Windows' | |
| run: | | |
| curl.exe -o wjags.exe -L0 -k --url https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Windows/JAGS-4.3.1.exe | |
| wjags.exe /S | |
| del wjags.exe | |
| shell: cmd | |
| # from https://github.com/ku-awdc/runjags/issues/2: | |
| - name: Install JAGS (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| sudo curl --location https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.1.pkg -o /usr/local/JAGS-4.3.1.pkg | |
| sudo installer -pkg /usr/local/JAGS-4.3.1.pkg -target /usr/local/bin/ | |
| - name: Install JAGS (Ubuntu) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y jags | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2 | |
| needs: test, coverage | |
| - name: "install rjags" | |
| run: | | |
| install.packages("rjags", | |
| repos = "https://cloud.r-project.org", | |
| type = "source", | |
| verbose = TRUE) | |
| withr::local_options(warn = 2) | |
| library(rjags) | |
| library(runjags) | |
| runjags::findJAGS() | |
| runjags::testjags() | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| print(cov) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload artifacts | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| # https://github.com/actions/upload-artifact?tab=readme-ov-file | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package | |
| # copied from https://github.com/dieghernan/nominatimlite/actions/runs/12116366823/workflow | |
| - name: Create Junit Report | |
| if: always() | |
| run: | | |
| test_out <- path.expand(file.path(getwd(), "junit.xml")) | |
| testthat::test_local(reporter = testthat::JunitReporter$new(test_out)) | |
| shell: Rscript {0} | |
| # following https://app.codecov.io/gh/UCD-SERG/serodynamics/tests/new | |
| - name: Upload test results to Codecov | |
| if: ${{ !cancelled() }} | |
| uses: codecov/test-results-action@HEAD | |
| with: | |
| # Fail if error if not on PR, or if on PR and token is given | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} | |
| file: ./junit.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - uses: codecov/codecov-action@v5 | |
| with: | |
| # Fail if error if not on PR, or if on PR and token is given | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} | |
| # v5 renamed from `file` and `plugin`; see https://github.com/codecov/codecov-action?tab=readme-ov-file#migration-guide | |
| files: ./cobertura.xml | |
| plugins: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} |