AMR/.github/workflows/check-current-testthat.yaml

# ==================================================================== #
# TITLE:                                                               #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE CODE:                                                         #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# PLEASE CITE THIS SOFTWARE AS:                                        #
# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
# Journal of Statistical Software, 104(3), 1-31.                       #
# https://doi.org/10.18637/jss.v104.i03                                #
#                                                                      #
# Developed at the University of Groningen and the University Medical  #
# Center Groningen in the Netherlands, in collaboration with many      #
# colleagues from around the world, see our website.                   # 
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://amr-for-r.org              #
# ==================================================================== #

on:
  pull_request:
    # run in each PR in this repo (1 worker, see matrix logic below)
    branches: '**'
  push:
    # only on main; pushing to a PR branch is already covered by pull_request above
    branches: [main]
  schedule:
    # also run a schedule everyday at 1 AM.
    # this is to check that all dependencies are still available (see R/zzz.R)
    - cron:  '0 1 * * *'

name: check-recent

# a new commit cancels the runs of the previous commit on the same PR or branch, a scheduled run is never cancelled by a push
concurrency:
  group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  setup:
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}
    steps:
      - id: set-matrix
        shell: bash
        # entries with "tests": true do not run R CMD check, but run the unit tests from source with .github/scripts/run_tests.sh, optionally:
        # - "interactive": true, in a real interactive R session, so that code behind interactive() is also tested
        # - "scenario", the user environment set up with .github/scripts/setup_test_scenario.R
        # - "lang", the LANG environment variable
        run: |
          if [ "${{ github.event_name }}" = "pull_request" ]; then
            echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false,"tests":true,"label":"interactive","interactive":true}]}' >> "$GITHUB_OUTPUT"
          else
            echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-5","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false,"tests":true,"label":"interactive","interactive":true},{"os":"ubuntu-latest","r":"release","allowfail":false,"tests":true,"label":"interactive, user setup","interactive":true,"scenario":"user"},{"os":"ubuntu-latest","r":"release","allowfail":false,"tests":true,"label":"Dutch locale","lang":"nl_NL.UTF-8"},{"os":"ubuntu-latest","r":"release","allowfail":false,"tests":true,"label":"CLSI as default guideline","scenario":"clsi"}]}' >> "$GITHUB_OUTPUT"
          fi

  R-code-check:
    needs: setup
    runs-on: ${{ matrix.config.os }}

    continue-on-error: ${{ matrix.config.allowfail }}

    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})${{ matrix.config.label && format(' {0}', matrix.config.label) || '' }}

    strategy:
      fail-fast: false
      matrix: ${{ fromJSON(needs.setup.outputs.matrix) }}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      AMR_TEST_INTERACTIVE: ${{ matrix.config.interactive && 'true' || 'false' }}
      AMR_TEST_SCENARIO: ${{ matrix.config.scenario || '' }}

    steps:
      - uses: actions/checkout@v4

      - 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 RStudio Package Manager to quickly install packages
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          # pak solves all suggested packages as one set and fails as a whole if one of them requires a newer R, so such packages are ignored on older R versions (with `pkg=?ignore-before-r=x.y.z`) and the checks run without them
          extra-packages: ${{ matrix.config.tests && 'any::pkgload' || 'any::rcmdcheck' }} readxl=?ignore-before-r=4.2.0
          needs: check
          upgrade: 'TRUE'

      - name: Set LANG
        if: matrix.config.lang
        # the package reads the language from LANG, while R needs a locale that is installed on the runner, so LC_ALL is set to the UTF-8 locale that is always available
        run: |
          echo "LANG=${{ matrix.config.lang }}" >> "$GITHUB_ENV"
          echo "LC_ALL=C.UTF-8" >> "$GITHUB_ENV"

      - name: Set up scenario '${{ matrix.config.scenario }}'
        if: matrix.config.scenario
        run: AMR_TEST_INTERACTIVE=true .github/scripts/run_tests.sh .github/scripts/setup_test_scenario.R

      - name: Run unit tests
        if: matrix.config.tests
        env:
          NOT_CRAN: true
        run: .github/scripts/run_tests.sh .github/scripts/run_tests.R

      - uses: r-lib/actions/check-r-package@v2
        if: ${{ !matrix.config.tests }}
        env:
          # suggested packages ignored on older R versions (see above) must not fail the check
          _R_CHECK_FORCE_SUGGESTS_: false
        with:
          upload-snapshots: true
          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'