(v2.1.1.9049) new 2024 breakpoints, add AMO
, set NI instead of N
#846
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# ==================================================================== # | |
# 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} |