159 capitalization in paper references #308
Workflow file for this run
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| # Workflow triggered when we have a new release candidate | |
| # This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning | |
| name: On Label CRAN Checks | |
| on: | |
| pull_request: | |
| types: [ labeled ] | |
| env: | |
| LABEL_CHECK: 'CRAN::check' | |
| LABEL_SUCCESS: 'CRAN::passed' | |
| LABEL_FAILURE: 'CRAN::failed' | |
| BUILD_LOC: "./build" | |
| permissions: | |
| packages: read | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| jobs: | |
| set_target: | |
| if: ${{ github.event.label.name == 'CRAN::check' }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| target: ${{ steps.set_label.outputs.label }} | |
| steps: | |
| - id: set_label | |
| run: | | |
| echo "label=${{ env.LABEL_CHECK }}" >> "$GITHUB_OUTPUT" | |
| check_label_exist: | |
| needs: | |
| - set_target | |
| runs-on: ubuntu-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| permissions: | |
| pull-requests: write | |
| contents: write | |
| steps: | |
| - name: Assert labels ${{ env.LABEL_CHECK }} is defined | |
| run: | | |
| gh label create ${{ env.LABEL_CHECK }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| continue-on-error: true # make sure the next steps run also on failure | |
| - name: Assert labels ${{ env.LABEL_SUCCESS }} is defined | |
| run: | | |
| gh label create ${{ env.LABEL_SUCCESS }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| continue-on-error: true # make sure the next steps run also on failure | |
| - name: Assert labels ${{ env.LABEL_FAILURE }} is defined | |
| run: | | |
| gh label create ${{ env.LABEL_FAILURE }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| continue-on-error: true # make sure the next steps run also on failure | |
| R_CMD_check: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - set_target | |
| container: | |
| image: ${{ vars.CONTAINER_SOURCE }}/${{ matrix.os }}/${{ matrix.compiler }}/${{ matrix.r-version }}/abn:${{ vars.CONTAINER_VERSION || 'latest' }} | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| env: | |
| R_KEEP_PKG_SOURCE: yes # NOTE Jo: not sure why this is here? | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| r-version: ['release' , 'devel', 'patched'] # ['3.6.3', '4.1.1'] | |
| os: ['debian', 'fedora'] | |
| compiler: ['gcc', 'clang'] | |
| exclude: | |
| - os: 'fedora' | |
| r-version: 'release' | |
| - os: 'fedora' | |
| r-version: 'patched' | |
| - r-version: 'patched' | |
| compiler: 'clang' | |
| - r-version: 'release' | |
| compiler: 'clang' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Disable renv | |
| run: | | |
| renv::deactivate() | |
| shell: Rscript {0} | |
| - name: Configure ABN for installation | |
| run: | | |
| autoreconf | |
| - name: Install package dependencies | |
| run: | | |
| devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never') | |
| shell: Rscript {0} | |
| - name: rcmdcheck run | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| cat("LOGNAME=", Sys.info()[["user"]], "\n", sep = "", file = Sys.getenv("GITHUB_ENV"), append = TRUE) | |
| if (Sys.getenv("_R_CHECK_FORCE_SUGGESTS_", "") == "") Sys.setenv("_R_CHECK_FORCE_SUGGESTS_" = "false") | |
| if (Sys.getenv("_R_CHECK_CRAN_INCOMING_", "") == "") Sys.setenv("_R_CHECK_CRAN_INCOMING_" = "false") | |
| cat("check-dir-path=", file.path(getwd(), ("check")), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | |
| check_results <- rcmdcheck::rcmdcheck(".", args = (c("--no-manual", "--as-cran")), build_args = ("--no-manual"), error_on = ("error"), check_dir = ("check")) | |
| shell: Rscript {0} | |
| env: | |
| BUILD_LOC: ./build | |
| R_KEEP_PKG_SOURCE: yes | |
| - name: rchmdchek show results | |
| run: | | |
| echo ::group::Show testthat output | |
| find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| echo ::endgroup:: | |
| shell: bash --noprofile --norc -e -o pipefail {0} | |
| env: | |
| BUILD_LOC: ./build | |
| R_KEEP_PKG_SOURCE: yes | |
| report_CRAN_checks: | |
| if: ${{ ( success() || failure() ) }} | |
| needs: | |
| - R_CMD_check | |
| - check_label_exist | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check if on demand tasks succeeded | |
| #TODO: Properly establish what has failead and what not | |
| run: | | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_CHECK }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| if [ ${{ needs.R_CMD_check.result }} == "success" ]; then | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_FAILURE }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_SUCCESS }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "### ${{ github.event.label.url }} passed! :rocket:" >> $GITHUB_STEP_SUMMARY | |
| exit 0 | |
| elif [ ${{ needs.R_CMD_check.result }} == "failure" ]; then | |
| gh pr edit ${{ env.EVENT }} --remove-label ${{ env.LABEL_SUCCESS }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_FAILURE }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "### ${{ github.event.label.url }} failed!" >> $GITHUB_STEP_SUMMARY | |
| exit 1 | |
| else | |
| gh pr edit ${{ env.EVENT }} --add-label ${{ env.LABEL_CHECK }} --repo ${{ env.OWNER }}/${{ env.REPO }} | |
| echo "On demand task outcome was ${{ steps.some_task.outcome }}" | |
| fi | |
| shell: bash | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| EVENT: ${{ github.event.number }} # This is either the issue or pr | |
| record_passed_label: | |
| runs-on: ubuntu-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| repository-projects: write | |
| outputs: | |
| passed: ${{ steps.passed.outputs.PASSED}} | |
| steps: | |
| - name: Check if the pull request is labeled with ${{ env.LABEL_SUCCESS }} # 2 | |
| id: passed | |
| run: | | |
| if $( gh pr view ${{ env.EVENT }} --repo ${{ env.OWNER }}/${{ env.REPO }} --json "labels" --jq ".[].[].name" | grep --quiet ${{ env.LABEL_SUCCESS }}); then | |
| echo "PASSED=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "PASSED=false" >> $GITHUB_OUTPUT | |
| fi | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| EVENT: ${{ github.event.number }} # This is either the issue or pr | |
| R_CMD_check_passed: | |
| if: ${{ always() }} | |
| needs: | |
| - R_CMD_check | |
| - record_passed_label | |
| runs-on: ubuntu-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| steps: | |
| - name: Assert that either checks passed on the label is present | |
| run: | | |
| if [[ ${{ needs.R_CMD_check.result }} == 'success' || ${{ needs.record_passed_label.outputs.passed }} == 'true' ]]; then | |
| echo 'R CMD check status ok'; | |
| else exit 1; fi | |
| test-coverage: | |
| # 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 | |
| if: ${{ success() }} | |
| needs: [R_CMD_check] | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| steps: | |
| - 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 | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| Sys.setenv(NOT_CRAN = "true") | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"), | |
| token = Sys.getenv("CODECOV_TOKEN") | |
| ) | |
| 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@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |