fixes to get sampling working finally #30
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| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage | |
| permissions: | |
| contents: read | |
| actions: write | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: 'true' | |
| R_COMPILE_AND_INSTALL_PACKAGES: 'never' | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RETICULATE_AUTOCONFIGURE: 'FALSE' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Homebrew and qpdf (macOS only) | |
| if: runner.os == 'macOS' | |
| uses: Homebrew/actions/setup-homebrew@master | |
| - name: Install qpdf (macOS only) | |
| if: runner.os == 'macOS' | |
| shell: bash | |
| run: brew install qpdf | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| shell: bash | |
| run: | | |
| . /etc/os-release | |
| while read -r cmd | |
| do | |
| echo "$cmd" | |
| sudo $cmd | |
| done < <(Rscript -e "writeLines(remotes::system_requirements('$ID-$VERSION_ID'))") | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-coverage-{{ hashFiles('**/DESCRIPTION') }} | |
| restore-keys: | | |
| ${{ runner.os }}-r-coverage- | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::covr | |
| any::xml2 | |
| any::remotes | |
| any::reticulate | |
| any::rcmdcheck | |
| any::sessioninfo | |
| any::devtools | |
| - name: Cache Python environment | |
| if: runner.os == 'Linux' || runner.os == 'macOS' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.virtualenvs | |
| key: ${{ runner.os }}-python-env-coverage-${{ hashFiles('**/DESCRIPTION') }} | |
| restore-keys: | | |
| ${{ runner.os }}-python-env-coverage- | |
| - name: Cache Python environment (Windows) | |
| if: runner.os == 'Windows' | |
| uses: actions/cache@v3 | |
| with: | |
| path: '%LOCALAPPDATA%/r-reticulate' | |
| key: ${{ runner.os }}-python-env-${{ hashFiles('**/DESCRIPTION') }} | |
| restore-keys: | | |
| ${{ runner.os }}-python-env- | |
| - name: Install greta and dependencies | |
| shell: Rscript {0} | |
| run: | | |
| install.packages("greta", repos = c("https://greta-dev.r-universe.dev", "https://cloud.r-project.org")) | |
| library(greta) | |
| install_greta_deps(timeout = 120) | |
| - name: Generate coverage report | |
| shell: Rscript {0} | |
| run: | | |
| library(covr) | |
| cov <- covr::package_coverage(quiet = FALSE, clean = FALSE) | |
| covr::to_cobertura(cov, output_file = "coverage.xml") | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| fail_ci_if_error: true | |
| files: coverage.xml | |
| disable_search: true | |
| verbose: true |