Update R/dbetabinom.R #29
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| --- | ||
| name: Coverage 📔 | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| 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 | ||
| secrets: | ||
| 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_4.2.1_bioc_3.15:latest | ||
| steps: | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Install R package 🚧 | ||
| run: | | ||
| setwd("${{ github.event.repository.name }}") | ||
| if (file.exists("renv.lock")) renv::restore() | ||
| install.packages(".", repos=NULL, type="source") | ||
| shell: Rscript {0} | ||
| - name: Install covr 🎪 | ||
| run: if (!require("covr")) install.packages("covr") | ||
| shell: Rscript {0} | ||
| - name: Run coverage 👟 | ||
| run: | | ||
| oldwd <- getwd() | ||
| setwd("${{ github.event.repository.name }}") | ||
| if (file.exists("renv.lock")) { | ||
| renv::restore() | ||
| } | ||
| setwd(oldwd) | ||
| tryCatch( | ||
| expr = { | ||
| x <- covr::package_coverage( | ||
| path="${{ github.event.repository.name }}", | ||
| clean = FALSE, | ||
| quiet = FALSE | ||
| ) | ||
| print(x) | ||
| covr::to_cobertura(x, filename = "coverage.xml") | ||
| p <- 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 <- stringr::str_match(e, "\`(.*?)\`")[, 2] | ||
| if (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: Post coverage report 🗞 | ||
| if: steps.check_coverage_reports.outputs.files_exists == 'true' | ||
| uses: insightsengineering/coverage-action@v1 | ||
| with: | ||
| path: coverage.xml | ||
| threshold: 80 | ||
| fail: false | ||
| publish: ${{ inputs.publish-coverage-report }} | ||
| - name: Upload report 🔼 | ||
| if: steps.check_coverage_reports.outputs.files_exists == 'true' | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| name: coverage-report | ||
| path: "coverage-report.html" | ||
| 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_4.2.1_bioc_3.15:latest | ||
| steps: | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v2 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Run Covtracer 🐄 | ||
| uses: insightsengineering/covtracer-action@v1 | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| with: | ||
| path: ${{ github.event.repository.name }} | ||
| allow-failure: ${{ inputs.allow-failure }} | ||
