diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac6182..a5ee0682 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -6,37 +6,21 @@ on: pull_request: branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macos-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-pandoc@v2 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - uses: r-lib/actions/setup-r-dependencies@v2 @@ -47,3 +31,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index ed7650c7..4bbce750 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -9,7 +9,9 @@ on: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -22,7 +24,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 27d45283..98822609 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -15,7 +17,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +25,37 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( 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@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + - name: Show testthat output if: always() run: | ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package diff --git a/README.md b/README.md index 6bd90c61..e5dd2edd 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![CRAN status](https://www.r-pkg.org/badges/version/PKNCA)](https://CRAN.R-project.org/package=PKNCA) [![R-CMD-check](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml) -[![Code_Coverage_Badge](https://codecov.io/github/billdenney/pknca/coverage.svg?branch=main)](https://app.codecov.io/github/billdenney/pknca?branch=main) +[![Codecov test coverage](https://codecov.io/gh/billdenney/pknca/graph/badge.svg)](https://app.codecov.io/gh/billdenney/pknca) [![CodeFactor](https://www.codefactor.io/repository/github/billdenney/pknca/badge?style=plastic)](https://www.codefactor.io/repository/github/billdenney/pknca) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2054/badge)](https://bestpractices.coreinfrastructure.org/projects/2054)