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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
committed by GitHub
parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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23
.github/workflows/lintr.yaml vendored
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# 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. #
@ -52,5 +56,16 @@ jobs:
extra-packages: any::lintr
- name: Lint
run: 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"))
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}