test-coverage.yaml

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: test-coverage

permissions:
  contents: read
  actions: write

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: 'true'
      R_COMPILE_AND_INSTALL_PACKAGES: 'never'
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      RETICULATE_AUTOCONFIGURE: 'FALSE'

    steps:
      - uses: actions/checkout@v4

      - name: Install Homebrew and qpdf (macOS only)
        if: runner.os == 'macOS'
        uses: Homebrew/actions/setup-homebrew@master

      - name: Install qpdf (macOS only)
        if: runner.os == 'macOS'
        shell: bash
        run: brew install qpdf

      - name: Install system dependencies
        if: runner.os == 'Linux'
        shell: bash
        run: |
          . /etc/os-release
          while read -r cmd
          do
            echo "$cmd"
            sudo $cmd
          done < <(Rscript -e "writeLines(remotes::system_requirements('$ID-$VERSION_ID'))")

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

      - name: Cache R packages
        uses: actions/cache@v3
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-coverage-{{ hashFiles('**/DESCRIPTION') }}
          restore-keys: |
            ${{ runner.os }}-r-coverage-

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::covr
            any::xml2
            any::remotes
            any::reticulate
            any::rcmdcheck
            any::sessioninfo
            any::devtools

      - name: Cache Python environment
        if: runner.os == 'Linux' || runner.os == 'macOS'
        uses: actions/cache@v3
        with:
          path: ~/.virtualenvs
          key: ${{ runner.os }}-python-env-coverage-${{ hashFiles('**/DESCRIPTION') }}
          restore-keys: |
            ${{ runner.os }}-python-env-coverage-

      - name: Cache Python environment (Windows)
        if: runner.os == 'Windows'
        uses: actions/cache@v3
        with:
          path: '%LOCALAPPDATA%/r-reticulate'
          key: ${{ runner.os }}-python-env-${{ hashFiles('**/DESCRIPTION') }}
          restore-keys: |
            ${{ runner.os }}-python-env-            

      - name: Install greta and dependencies
        shell: Rscript {0}
        run: |
          install.packages("greta", repos = c("https://greta-dev.r-universe.dev", "https://cloud.r-project.org"))
          library(greta)
          install_greta_deps(timeout = 120)

      - name: Generate coverage report
        shell: Rscript {0}
        run: |
          library(covr)
          cov <- covr::package_coverage(quiet = FALSE, clean = FALSE)
          covr::to_cobertura(cov, output_file = "coverage.xml")

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v5
        with:
          fail_ci_if_error: true
          files: coverage.xml
          disable_search: true
          verbose: true