rExpertQuery/.github/workflows/test-coverage.yaml at develop · USEPA/rExpertQuery · GitHub

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name: test-coverage

on:
  push:
    branches: ['**']
  pull_request:
    branches: [develop]
    types: [opened, reopened, synchronize, ready_for_review]
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

permissions:
  contents: write
  checks: write
  statuses: read
  pull-requests: write

jobs:
  test-coverage:
    # Skip draft PRs; run on non-PR triggers and non-draft PR events
    if: ${{ github.event_name != 'pull_request' || github.event.pull_request.draft == false }}
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      EQ_API_KEY: ${{ secrets.EQ_API_KEY }}
    steps:
      - uses: actions/checkout@v6

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::covr
            any::xml2

      - name: Capture Environment Info
        run: |
          Rscript -e '
            env_vars <- Sys.getenv()
            pkg_versions <- installed.packages()[, c("Package", "Version")]
            sys_info <- Sys.info()
            save(env_vars, pkg_versions, sys_info, file = "ci_env_info.RData")
          '

      - name: Upload Environment Info
        uses: actions/upload-artifact@v4
        with:
          name: ci_env_info
          path: ci_env_info.RData

      - name: Test coverage
        shell: Rscript {0}
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          print(cov)
          covr::to_cobertura(cov, file = "cobertura.xml")

      - name: Show testthat output
        if: always()
        run: |
          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload test results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: coverage-test-failures
          path: ${{ runner.temp }}/package
          if-no-files-found: ignore

      - name: Upload coverage report
        uses: actions/upload-artifact@v4
        with:
          name: coverage-report
          path: ./cobertura.xml

      - name: Comment coverage
        uses: 5monkeys/cobertura-action@master
        with:
          report_name: coverage-report
          path: ./cobertura.xml
          minimum_coverage: 10
          only_changed_files: false
          show_missing: true
          link_missing_lines: true
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}