Change R linter #1033
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| --- | |
| name: Coverage 📔 | |
| on: | |
| push: | |
| tags: | |
| - "v*" | |
| branches: | |
| - main | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| install-system-dependencies: | |
| description: Check for and install system dependencies | |
| required: false | |
| default: false | |
| type: boolean | |
| enable-staged-dependencies-check: | |
| description: Enable staged dependencies YAML check | |
| required: false | |
| default: false | |
| type: boolean | |
| publish-coverage-report: | |
| description: Publish the coverage report as a pull request comment | |
| required: false | |
| default: true | |
| type: boolean | |
| allow-failure: | |
| description: Allow workflow failure if errors from covtracer are generated | |
| required: false | |
| type: boolean | |
| default: false | |
| enable-covtracer: | |
| description: Enable the covtracer job | |
| required: false | |
| type: boolean | |
| default: false | |
| additional-env-vars: | |
| description: | | |
| Extra environment variables, as a 'key=value' pair, with each pair on a new line. | |
| Example usage: | |
| additional-env-vars: | | |
| ABC=123 | |
| XYZ=456 | |
| required: false | |
| default: "" | |
| type: string | |
| sd-direction: | |
| description: The direction to use to install staged dependencies. Choose between 'upstream', 'downstream' and 'all' | |
| required: false | |
| type: string | |
| default: upstream | |
| publish-coverage-report-gh-pages: | |
| description: Publish HTML coverage report to GitHub pages alongside pkgdown docs. | |
| required: false | |
| type: boolean | |
| default: true | |
| latest-tag-alt-name: | |
| description: | | |
| The name of directory to store coverage report when running for latest tag. | |
| The variable is named this way to keep it consistent with r-pkgdown-multiversion input name. | |
| required: false | |
| type: string | |
| default: "latest-tag" | |
| release-candidate-alt-name: | |
| description: | | |
| The name of directory to store coverage report when running for rc tag. | |
| The variable is named this way to keep it consistent with r-pkgdown-multiversion input name. | |
| required: false | |
| type: string | |
| default: "release-candidate" | |
| package-subdirectory: | |
| description: Subdirectory in the repository, where the R package is located. | |
| required: false | |
| type: string | |
| default: "" | |
| secrets: | |
| REPO_GITHUB_TOKEN: | |
| description: | | |
| Github token with read access to repositories, required | |
| for staged.dependencies installation | |
| required: false | |
| concurrency: | |
| group: coverage-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| coverage: | |
| name: Coverage 📔 | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip coverage]') | |
| && github.event.pull_request.draft == false | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| outputs: | |
| publish-coverage-html-report: ${{ steps.coverage-output.outputs.coverage-upload }} | |
| current-branch-or-tag: ${{ steps.current-branch-or-tag.outputs.ref-name }} | |
| is-latest-tag: ${{ steps.current-branch-or-tag.outputs.is-latest-tag }} | |
| is-rc-tag: ${{ steps.current-branch-or-tag.outputs.is-rc-tag }} | |
| multiversion-docs: ${{ steps.current-branch-or-tag.outputs.multiversion-docs }} | |
| steps: | |
| - name: Setup token 🔑 | |
| id: github-token | |
| run: | | |
| if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then | |
| echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | |
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "Using REPO_GITHUB_TOKEN." | |
| echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Get branch names 🌿 | |
| id: branch-name | |
| uses: tj-actions/branch-names@v6 | |
| - name: Checkout gh-pages 🛎 | |
| if: >- | |
| github.event_name != 'pull_request' | |
| && inputs.publish-coverage-report-gh-pages == true | |
| id: checkout-gh-pages | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: gh-pages | |
| path: gh-pages | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Get current branch or tag 🏷️ | |
| if: >- | |
| github.event_name != 'pull_request' | |
| && inputs.publish-coverage-report-gh-pages == true | |
| id: current-branch-or-tag | |
| run: | | |
| if [ "${{ steps.branch-name.outputs.is_tag }}" == "true" ]; then | |
| echo "Current tag: ${{ steps.branch-name.outputs.tag }}" | |
| echo "ref-name=${{ steps.branch-name.outputs.tag }}" >> $GITHUB_OUTPUT | |
| current_tag="${{ steps.branch-name.outputs.tag }}" | |
| if [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)$")" != "" ]; then | |
| echo "Running for latest-tag." | |
| echo "is-latest-tag=true" >> $GITHUB_OUTPUT | |
| elif [ "$(echo "$current_tag" | grep -E "^v([0-9]+\.)?([0-9]+\.)?([0-9]+)(-rc[0-9]+)$")" != "" ]; then | |
| echo "Running for rc-tag." | |
| echo "is-rc-tag=true" >> $GITHUB_OUTPUT | |
| fi | |
| else | |
| echo "Current branch: ${{ steps.branch-name.outputs.current_branch }}" | |
| echo "ref-name=${{ steps.branch-name.outputs.current_branch }}" >> $GITHUB_OUTPUT | |
| fi | |
| # Check if pkgdown multiversion docs are used at all. | |
| if [ $(grep -rl '<!-- start dropdown for versions -->' gh-pages | wc -l) -gt 0 ]; then | |
| echo "multiversion-docs=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "multiversion-docs=false" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| if: github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| - name: Restore SD cache 💰 | |
| uses: actions/cache@v3 | |
| with: | |
| key: sd-${{ runner.os }}-${{ github.event.repository.name }} | |
| path: ~/.staged.dependencies | |
| - name: Run Staged dependencies 🎦 | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| env: | |
| GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| enable-check: ${{ inputs.enable-staged-dependencies-check }} | |
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | |
| direction: ${{ inputs.sd-direction }} | |
| - name: Install R package 🚧 | |
| run: | | |
| if (file.exists("renv.lock")) renv::restore() | |
| install.packages(".", repos=NULL, type="source") | |
| shell: Rscript {0} | |
| working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| - name: Install covr 🎪 | |
| run: | | |
| if (file.exists("renv.lock")) { | |
| renv::restore() | |
| if (!require("covr")) renv::install("covr") | |
| } | |
| if (!require("covr")) install.packages("covr") | |
| shell: Rscript {0} | |
| - name: Run coverage 👟 | |
| run: | | |
| setwd("${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}") | |
| if (file.exists("renv.lock")) { | |
| renv::restore() | |
| } | |
| # Load extra env vars | |
| extra_env_vars <- "${{ inputs.additional-env-vars }}" | |
| if (extra_env_vars != "") { | |
| writeLines(extra_env_vars, "/tmp/dotenv.env") | |
| if (!require("dotenv")) install.packages("dotenv", repos = "https://cloud.r-project.org") | |
| dotenv::load_dot_env("/tmp/dotenv.env") | |
| } | |
| tryCatch( | |
| expr = { | |
| x <- covr::package_coverage( | |
| clean = FALSE, | |
| quiet = FALSE | |
| ) | |
| print(x) | |
| covr::report( | |
| x, | |
| file = "coverage-report.html", | |
| browse = FALSE | |
| ) | |
| covr::to_cobertura(x, filename = "coverage.xml") | |
| p <- covr::percent_coverage(x) | |
| cat(p, file = "coverage.txt", sep = "") | |
| }, | |
| error = function(e) { | |
| message("Errors generated during coverage analysis:") | |
| print(e) | |
| error_file <- list.files(path = "/tmp", pattern="*.fail$", 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) | |
| } | |
| ) | |
| covr_html <- "coverage-report.html" | |
| if (!file.exists(covr_html)) writeLines(c("No coverage report."), covr_html) | |
| shell: Rscript {0} | |
| - name: Check whether coverage reports exists 💭 | |
| id: check_coverage_reports | |
| uses: andstor/file-existence-action@v2 | |
| with: | |
| files: >- | |
| ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.xml, | |
| ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.txt, | |
| ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage-report.html | |
| - name: Post coverage report 🗞 | |
| if: steps.check_coverage_reports.outputs.files_exists == 'true' | |
| uses: insightsengineering/coverage-action@v2 | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage.xml | |
| threshold: 80 | |
| fail: false | |
| publish: ${{ inputs.publish-coverage-report }} | |
| diff: true | |
| continue-on-error: true | |
| - name: Upload report 🔼 | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage-report | |
| path: | | |
| ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/coverage-report.html | |
| ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/lib/ | |
| continue-on-error: true | |
| - name: Set output ⚙️ | |
| id: coverage-output | |
| if: >- | |
| github.event_name != 'pull_request' | |
| && inputs.publish-coverage-report-gh-pages == true | |
| run: echo "coverage-upload=true" >> $GITHUB_OUTPUT | |
| covtracer: | |
| name: Covtracer 🐄 | |
| runs-on: ubuntu-latest | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip coverage]') | |
| && github.event.pull_request.draft == false | |
| && contains(inputs.enable-covtracer, 'true') | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| steps: | |
| - name: Get branch names 🌿 | |
| id: branch-name | |
| uses: tj-actions/branch-names@v6 | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| path: ${{ github.event.repository.name }} | |
| - name: Restore SD cache 💰 | |
| uses: actions/cache@v3 | |
| with: | |
| key: sd-${{ runner.os }}-${{ github.event.repository.name }} | |
| path: ~/.staged.dependencies | |
| - name: Run Staged dependencies 🎦 | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| env: | |
| GITHUB_PAT: ${{ steps.github-token.outputs.token }} | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| enable-check: ${{ inputs.enable-staged-dependencies-check }} | |
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | |
| direction: ${{ inputs.sd-direction }} | |
| - name: Run Covtracer 🐄 | |
| uses: insightsengineering/covtracer-action@v1 | |
| env: | |
| GITHUB_PAT: ${{ steps.github-token.outputs.token }} | |
| with: | |
| path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }} | |
| allow-failure: ${{ inputs.allow-failure }} | |
| publish-coverage-report: | |
| name: Publish coverage report 📰 | |
| runs-on: ubuntu-latest | |
| needs: coverage | |
| if: > | |
| needs.coverage.outputs.publish-coverage-html-report == 'true' | |
| && github.event_name != 'pull_request' | |
| # Only one job can publish to gh-pages branch concurrently. | |
| concurrency: | |
| group: ghpages | |
| steps: | |
| - name: Setup token 🔑 | |
| id: github-token | |
| run: | | |
| if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then | |
| echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN." | |
| echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| else | |
| echo "Using REPO_GITHUB_TOKEN." | |
| echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT | |
| fi | |
| shell: bash | |
| - name: Download coverage report as artifact ⤵️ | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| - name: Rename report ⚙️ | |
| run: mv coverage-report/coverage-report.html coverage-report/index.html | |
| - name: Upload coverage report to GitHub pages 🗞️ | |
| if: needs.coverage.outputs.multiversion-docs == 'true' | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ steps.github-token.outputs.token }} | |
| publish_dir: ./coverage-report | |
| destination_dir: ${{ needs.coverage.outputs.current-branch-or-tag }}/coverage-report | |
| - name: Upload coverage report to GitHub pages (latest-tag) 🏷️ | |
| if: > | |
| needs.coverage.outputs.is-latest-tag == 'true' | |
| && needs.coverage.outputs.multiversion-docs == 'true' | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ steps.github-token.outputs.token }} | |
| publish_dir: ./coverage-report | |
| destination_dir: ${{ inputs.latest-tag-alt-name }}/coverage-report | |
| - name: Upload coverage report to GitHub pages (release-candidate) 🏷️ | |
| if: > | |
| needs.coverage.outputs.is-rc-tag == 'true' | |
| && needs.coverage.outputs.multiversion-docs == 'true' | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ steps.github-token.outputs.token }} | |
| publish_dir: ./coverage-report | |
| destination_dir: ${{ inputs.release-candidate-alt-name }}/coverage-report | |
| - name: Upload coverage report to GitHub pages (non-multiversion) 🗞️ | |
| if: needs.coverage.outputs.multiversion-docs == 'false' | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ steps.github-token.outputs.token }} | |
| publish_dir: ./coverage-report | |
| destination_dir: coverage-report |