code-coverage.yml

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/branch-names@v5.4

      - 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@v2

      - 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/CodeCoverageSummary@v1.2.0
        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 "action@github.com"
          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