AMR/.github/workflows/lintr.yaml

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# ==================================================================== #
# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
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# 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 #
# #
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# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
# 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 #
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# the Free Software Foundation.
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# 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. #
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# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
on:
push:
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branches: '**'
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pull_request:
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branches: '**'
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name: lintr
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jobs:
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lintr:
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runs-on: ubuntu-latest
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env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
# use RStudio Package Manager to quickly install packages
use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::lintr
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- name: Lint
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run: |
# old: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
# now get ALL linters, not just default ones
linters <- ls(envir = asNamespace("lintr"), pattern = "_linter$")
# 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"))
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shell: Rscript {0}