R.yml

name: R

on:
  push:
    branches-ignore: [gh-pages]
    paths:
      - ".github/workflows/R.yml"
      - "r/**"
  pull_request:
    branches-ignore:  [gh-pages]
    paths:
      - ".github/workflows/R.yml"
      - "r/**"

env:
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  _R_CHECK_FORCE_SUGGESTS_: false
  _R_CHECK_CRAN_INCOMING_REMOTE_: false

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  R-CMD-check:
    if: "! contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ${{ matrix.os }}
    name: Check ${{ matrix.os }} (${{ matrix.r }})
    strategy:
      # When set to true, GitHub cancels all in-progress jobs if any matrix job fails.
      fail-fast: true
      matrix:
        # macos-15-intel is an intel runner, macos-14 is apple silicon
        os: [ ubuntu-22.04, windows-latest, macos-15-intel, macos-14 ]
        r: [ release ]
        include:
          # Use latest ubuntu to make it easier to install dependencies
          - { os: ubuntu-latest, r: 'devel', http-user-agent: 'release' }
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Disable autocrlf
        if: runner.os == 'Windows'
        run: git config --global core.autocrlf false

      - uses: actions/checkout@v4

      - name: Checkout moocore
        uses: actions/checkout@v4
        with:
          repository: multi-objective/moocore
          path: moocore

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r }}
          http-user-agent: ${{ matrix.http-user-agent }}
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: moocore=local::../moocore/r, any::rcmdcheck, any::spelling, any::remotes
          needs: check
          working-directory: r

      - name: Check (as CRAN)
        env:
          NOT_CRAN: false
        run: |
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check", timeout = 360)
        shell: Rscript {0}
        working-directory: r

      - name: Check (NOT CRAN)
        if: success()
        env:
          NOT_CRAN: true
        run: |
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--run-donttest", "--run-dontrun", "--timings"), error_on = "warning", check_dir = "check", timeout = 360)
        shell: Rscript {0}
        working-directory: r

      - name: Show testthat output
        if: failure()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash
        working-directory: r

      - name: Install package
        run: remotes::install_local(".", force = TRUE, upgrade = "never", build_manual = TRUE, build_vignettes = TRUE)
        shell: Rscript {0}
        working-directory: r

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: results-${{ runner.os }}-r${{ matrix.r }}
          path: r/check

  coverage:
    needs: R-CMD-check
    name: Coverage ${{ matrix.os }} (${{ matrix.r }})
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-22.04]
        r: [release]
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}

    steps:
      - uses: actions/checkout@v4

      - name: Checkout moocore
        uses: actions/checkout@v4
        with:
          repository: multi-objective/moocore
          path: moocore

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
          r-version: ${{ matrix.r }}

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: moocore=local::../moocore/r, any::covr any::xml2
          needs: coverage
          working-directory: r

      - name: Test coverage
        env:
          NOT_CRAN: false
        run: |
          coverage <- covr::package_coverage(type="all", quiet=FALSE, clean = FALSE,
                           commentDonttest = FALSE, commentDontrun = FALSE, flags="R",
                           install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"))
          print(coverage)
          covr::to_cobertura(coverage)
          list.files("../", pattern="*.xml", recursive=TRUE)
        shell: Rscript {0}
        working-directory: r

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v4
        with:
          fail_ci_if_error: true
          file: ./r/cobertura.xml
          verbose: true
          flags: R
          plugin: noop
          disable_search: true
          token: ${{secrets.CODECOV_TOKEN}}

  pkgdown:
    needs: R-CMD-check
    if: contains('
        refs/heads/master
        refs/heads/main
      ', github.ref) && github.event_name == 'push'
    name: pkgdown ${{ matrix.os }} (${{ matrix.r }})
    permissions:
      contents: write # github-pages-deploy-action
    concurrency: web # Recommended if you intend to make multiple deployments in quick succession.
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        r: [release]
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v4

      - name: Checkout moocore
        uses: actions/checkout@v4
        with:
          repository: multi-objective/moocore
          path: moocore

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r }}
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          install-pandoc: true
          extra-packages: moocore=local::../moocore/r, any::pkgdown, local::.
          needs: website
          working-directory: r

      - name: Build website
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, run_dont_run = TRUE)
        shell: Rscript {0}
        working-directory: r

      - name: Deploy 🚀
        if: success() && runner.os == 'Linux' && github.event_name == 'push' && github.ref == 'refs/heads/main'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: r/docs # The folder the action should deploy.
          target-folder: r
          single-commit: true
          clean: true