[pull] l2d from carpentries:main (#51) #151
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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, l2d] | |
| pull_request: | |
| branches: [main, master, l2d] | |
| workflow_dispatch: | |
| name: test-coverage | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| OS_VERSION: 1 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: "Set up pandoc" | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: "Set up Chrome" # for PDF rendering | |
| uses: browser-actions/[email protected] | |
| - name: "Install sysreqs" | |
| id: run-apt | |
| shell: bash | |
| run: | | |
| sudo apt update || exit 0 | |
| curl https://carpentries.r-universe.dev/stats/sysdeps 2> /dev/null \ | |
| | jq -r '.headers[0] | select(. != null)' 2> /dev/null \ | |
| > ${{ runner.temp }}/sysdeps.txt | |
| if [[ `wc -l < ${{ runner.temp }}/sysdeps.txt` -gt 0 ]]; then | |
| echo 'sysdeps acquired' | |
| else | |
| echo 'fetching sysdeps from descriptions' | |
| curl https://carpentries.r-universe.dev/stats/descriptions \ | |
| | jq -r '._builder.sysdeps | .[].headers | select(. != null)' 2> /dev/null \ | |
| > ${{ runner.temp }}/sysdeps.txt | |
| fi | |
| if [[ `wc -l < ${{ runner.temp }}/sysdeps.txt` -eq 0 ]]; then | |
| echo "::warn::System dependencies could not be acquired. Builds may fail" | |
| exit 1 | |
| else | |
| echo "found sysdeps: $(cat ${{ runner.temp }}/sysdeps.txt)" | |
| fi | |
| printf "libxslt-dev\n" >> ${{ runner.temp }}/sysdeps.txt | |
| sudo xargs apt-get install --fix-missing -y < ${{ runner.temp }}/sysdeps.txt || echo "Not on Ubuntu" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Restore {renv} cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}-${{ hashFiles('.github/workflows/R-CMD-check.yaml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ env.OS_VERSION }}-renv-${{ runner.r }}- | |
| - name: Prime {renv} Cache | |
| run: | | |
| renv::settings$snapshot.type("explicit") | |
| renv::init(bioconductor = TRUE) | |
| system('rm -rf renv .Rprofile') | |
| system('git clean -fd -e .github') | |
| system('git restore .') | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |