rdrr.io links fix #462
Workflow file for this run
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| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| r-version: | |
| description: 'The version of R to use' | |
| default: '4.1' | |
| required: false | |
| type: string | |
| skip-coverage-badges: | |
| description: 'Skip code coverage badge creation' | |
| default: false | |
| required: false | |
| type: boolean | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| pull_request: | |
| branches: | |
| - main | |
| - devel | |
| - pre-release | |
| name: Code Coverage | |
| concurrency: | |
| group: coverage-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| get_r_version: | |
| name: Get R version | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip coverage]') | |
| outputs: | |
| r-version: ${{ steps.normalizer.outputs.R_VERSION }} | |
| steps: | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| coverage: | |
| name: Test Coverage | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{needs.get_r_version.outputs.r-version}}:latest" | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip coverage]') | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| outputs: | |
| coverage-percent: ${{ steps.set-coverage-percentage.outputs.coverage-percentage }} | |
| needs: get_r_version | |
| steps: | |
| ##################### BEGIN boilerplate steps ##################### | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/[email protected] | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| - name: Normalize inputs | |
| id: normalizer | |
| run: | | |
| R_VERSION="${{ inputs.r-version }}" | |
| if [ "$R_VERSION" == "" ] | |
| then { | |
| R_VERSION="4.1" | |
| } | |
| fi | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Restore cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Setup Pandoc | |
| uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| with: | |
| run-system-dependencies: false | |
| renv-restore: false | |
| enable-check: false | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| ##################### END boilerplate steps ##################### | |
| - name: Run coverage 👟 | |
| run: | | |
| tryCatch( | |
| expr = { | |
| x <- covr::package_coverage( | |
| path=".", | |
| clean = FALSE, | |
| quiet = FALSE | |
| ) | |
| print(x) | |
| covr::to_cobertura(x, filename = "coverage.xml") | |
| p <- round(covr::percent_coverage(x)) | |
| cat(p, file = "coverage.txt", sep = "") | |
| covr::report( | |
| x, | |
| file = "coverage-report.html", | |
| browse = FALSE | |
| ) | |
| }, | |
| error = function(e) { | |
| message("Errors generated during coverage analysis:") | |
| print(e) | |
| error_file <- list.files(path = "/tmp", pattern="*.fail$", recursive = T, full.names = T)[1] | |
| if (length(error_file) && file.exists(error_file)) { | |
| cat("__________FULL OUTPUT__________") | |
| writeLines(readLines(error_file)) | |
| } | |
| }, | |
| warning = function(w) { | |
| message("Warnings generated during coverage analysis:") | |
| print(w) | |
| } | |
| ) | |
| shell: Rscript {0} | |
| - name: Check whether coverage reports exists | |
| id: check_coverage_reports | |
| uses: andstor/file-existence-action@v1 | |
| with: | |
| files: "coverage.xml, coverage.txt, coverage-report.html" | |
| - name: Set coverage percentage as output | |
| id: set-coverage-percentage | |
| run: echo "coverage-percentage=$(cat coverage.txt)" >> $GITHUB_OUTPUT | |
| if: steps.check_coverage_reports.outputs.files_exists == 'true' | |
| - name: Generate Coverage Summary Report | |
| if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
| uses: irongut/[email protected] | |
| with: | |
| filename: coverage.xml | |
| badge: true | |
| fail_below_min: false | |
| format: markdown | |
| hide_branch_rate: true | |
| hide_complexity: true | |
| indicators: true | |
| output: both | |
| thresholds: '60 80' | |
| - name: Upload report for review | |
| if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: coverage-report | |
| path: "coverage-report.html" | |
| continue-on-error: true | |
| - name: Add Coverage PR Comment | |
| if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request' | |
| uses: marocchino/sticky-pull-request-comment@v2 | |
| with: | |
| header: code-coverage | |
| path: code-coverage-results.md | |
| continue-on-error: true | |
| badge: | |
| name: Generate badge for coverage | |
| needs: [coverage] | |
| runs-on: ubuntu-20.04 | |
| if: > | |
| inputs.skip-coverage-badges != 'true' || | |
| !contains(github.event.commits[0].message, '[skip coverage]') | |
| steps: | |
| - name: Checkout the badges branch in repo | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: badges | |
| path: badges | |
| # Use the output from the `coverage` step | |
| - name: Generate the badge SVG image | |
| uses: emibcn/badge-action@v1 | |
| id: badge | |
| with: | |
| label: 'Test Coverage' | |
| status: "${{ needs.coverage.outputs.coverage-percent }}%" | |
| color: ${{ | |
| needs.coverage.outputs.coverage-percent > 90 && 'green' || | |
| needs.coverage.outputs.coverage-percent > 80 && 'yellow,green' || | |
| needs.coverage.outputs.coverage-percent > 70 && 'yellow' || | |
| needs.coverage.outputs.coverage-percent > 60 && 'orange,yellow' || | |
| needs.coverage.outputs.coverage-percent > 50 && 'orange' || | |
| needs.coverage.outputs.coverage-percent > 40 && 'red,orange' || | |
| needs.coverage.outputs.coverage-percent > 30 && 'red,red,orange' || | |
| needs.coverage.outputs.coverage-percent > 20 && 'red,red,red,orange' || | |
| 'red' }} | |
| path: badges/test-coverage.svg | |
| - name: Commit badge | |
| working-directory: ./badges | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Actions" | |
| BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}} | |
| mkdir -p "${BRANCH}" | |
| mv test-coverage.svg "${BRANCH}" | |
| git add "${BRANCH}/test-coverage.svg" | |
| git commit -m "Add/Update badge" || true | |
| - name: Push badges | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: badges | |
| directory: badges | |
| continue-on-error: true |