R-CMD-check.yaml

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  push:
    branches-ignore: [gh-pages]
  pull_request:
    branches-ignore:  [gh-pages]

name: R-CMD-check

env:
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
  _R_CHECK_FORCE_SUGGESTS_: false
  _R_CHECK_CRAN_INCOMING_REMOTE_: false

jobs:
  R-CMD-check:
    if: "! contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ${{ matrix.config.os }}
    name: Check ${{ matrix.config.os }} (${{ matrix.config.r }})
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: windows-latest, r: 'release'}
          - {os: macOS-latest,   r: 'release'}
          - {os: ubuntu-22.04,   r: 'release'}
          - {os: ubuntu-20.04,   r: '3.6'}
          # 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
        run: git config --global core.autocrlf false
        
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-pandoc@v2

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::remotes, any::rcmdcheck
          needs: check
          cache-version: 1
 
      - name: Install latex
        uses: r-lib/actions/setup-tinytex@v2
        env:
          # https://github.com/rstudio/tinytex-releases#releases
          TINYTEX_INSTALLER: TinyTeX-0

      - name: Install latex packages
        run: |
          remotes::install_cran("tinytex")
          tinytex::tlmgr_install("pdfcrop")
        shell: Rscript {0}

      - name: Install macos dependencies
        if: runner.os == 'macOS'
        run: brew install gsl gawk automake
                             
      - name: Check (CRAN)
        env:
          NOT_CRAN: false
        run: |
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - 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")
        shell: Rscript {0}

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

      - name: Install package
        run: |
          remotes::install_local(".", force = TRUE, upgrade = "never", build_manual = TRUE, build_vignettes = TRUE)
        shell: Rscript {0}
        
      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

  rchk:
    needs: R-CMD-check
    name: rchk ${{ matrix.config.os }} (${{ matrix.config.r }})
    runs-on: ${{ matrix.config.os }}
    strategy:
      matrix:
        config:
          - {os: ubuntu-latest,   r: 'release'}
    container:
      image: rhub/ubuntu-rchk
      options: --user=root
      
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    steps:
      - uses: actions/checkout@v3
      - uses: r-lib/actions/run-rchk@v2
        with:
          setup-only: true

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, local::.
          needs: check
          
      - uses: r-lib/actions/run-rchk@v2
        with:
          run-only: true
          
  coverage:
    needs: rchk
    name: Coverage ${{ matrix.config.os }} (${{ matrix.config.r }})
    runs-on: ${{ matrix.config.os }}
    strategy:
      matrix:
        config:
          - {os: ubuntu-latest,   r: 'release'}
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
 
    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
          r-version: ${{ matrix.config.r }}
          
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::covr
          needs: coverage

      - name: Test coverage
        env:
          NOT_CRAN: false
        run: |
          covr::codecov(type="all", quiet=FALSE, commentDonttest = FALSE, commentDontrun = FALSE)
        shell: Rscript {0}

  pkgdown:
    needs: R-CMD-check
    if: contains('
        refs/heads/master
        refs/heads/main
      ', github.ref) && github.event_name == 'push'
    name: pkgdown ${{ matrix.config.os }} (${{ matrix.config.r }})
    runs-on: ${{ matrix.config.os }}
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-latest,   r: 'release'}
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v3

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

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website

      - name: Deploy package
        if: success() && runner.os == 'Linux' && matrix.config.r == 'release' && github.event_name == 'push'
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = TRUE)'
        shell: bash {0}