test-coverage.yaml

---
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@509_macos
        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