mirror of https://github.com/msberends/AMR.git
72 lines
3.6 KiB
YAML
72 lines
3.6 KiB
YAML
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# CITE 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. #
|
|
# doi:10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# 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}
|