mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 19:26:12 +01:00
72 lines
3.6 KiB
YAML
72 lines
3.6 KiB
YAML
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# 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 #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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on:
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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:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: release
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# use RStudio Package Manager to quickly install packages
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::lintr
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- name: Lint
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run: |
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# old: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
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# now get ALL linters, not just default ones
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linters <- ls(envir = asNamespace("lintr"), pattern = "_linter$")
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# lose deprecated
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linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)]
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# and the ones we find unnnecessary
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linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)]
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# put the functions in a list
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linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
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# run them all!
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lintr::lint_package(linters = linters, exclusions = list("R/aa_helper_pm_functions.R"))
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shell: Rscript {0}
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