Add Chapter 2 Documentation: Extending Hierarchical Model to Correlated Biomarkers #927
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 }} |