AMR/.github/workflows/lintr.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, Sinha BNM, Albers CJ, Glasner C    #
# (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://msberends.github.io/AMR/   #
# ==================================================================== #

on:
  push:
    branches: '**'
  pull_request:
    branches: '**'

name: lintr

jobs:
  lintr:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v3

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

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: release
          # use RStudio Package Manager to quickly install packages
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::lintr

      - name: Lint
        run: |
          # old: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
          # now get ALL linters, not just default ones
          linters <- ls(envir = asNamespace("lintr"), pattern = "_linter$")
          # lose deprecated
          linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)]
          # and the ones we find unnnecessary
          linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)]
          # put the functions in a list
          linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
          # run them all!
          lintr::lint_package(linters = linters, exclusions = list("R/aa_helper_pm_functions.R"))
        shell: Rscript {0}