mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 16:02:02 +02:00
New mo algorithm, prepare for 2.0
This commit is contained in:
Dr. Matthijs Berends
committed by
GitHub
GitHub
parent
63fe160322
commit
cd2acc4a29
51
.github/prehooks/pre-commit
vendored
51
.github/prehooks/pre-commit
vendored
@ -1,5 +1,34 @@
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#!/bin/sh
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# ==================================================================== #
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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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echo "Running pre-commit hook..."
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -7,11 +36,11 @@ if command -v Rscript > /dev/null; then
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if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"', '"'styler'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
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Rscript -e "source('data-raw/_pre_commit_hook.R')"
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currentpkg=`Rscript -e "cat(pkgload::pkg_name())"`
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echo "-> Adding all files in folders 'data-raw', 'inst', 'man', and 'R' to this git commit"
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echo "-> Adding all files in 'data-raw' to this commit"
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git add data-raw/*
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git add inst/*
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git add man/*
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git add R/*
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git add R/sysdata.rda
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git add NAMESPACE
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else
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echo "- R package 'pkgload', 'devtools', 'dplyr', or 'styler' not installed!"
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currentpkg="your"
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@ -24,7 +53,7 @@ echo ""
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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echo ">> Updating semantic versioning and date..."
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echo "Updating semantic versioning and date..."
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# get tags from remote, and remove tags not on remote:
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git fetch origin --prune --prune-tags --quiet
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@ -32,7 +61,7 @@ currenttagfull=`git describe --tags --abbrev=0`
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currenttag=`git describe --tags --abbrev=0 | sed 's/v//'`
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if [ "$currenttag" = "" ]; then
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# there is no tag, so set tag to 0.0.1 and commit index to current count
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echo ">> - no git tags found, create one in this format: 'v(x).(y).(z)'!"
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echo "- no git tags found, create one in this format: 'v(x).(y).(z)'!"
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currenttag="0.0.1"
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currentcommit=`git rev-list --count HEAD`
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else
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@ -42,18 +71,18 @@ else
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# tag is new, so this must become the version number
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currentversion="$currenttag"
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fi
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echo ">> - latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
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echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
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fi
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if [ "$currentversion" = "" ]; then
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# combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
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currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
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fi
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echo ">> - ${currentpkg} pkg version set to ${currentversion}"
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echo "- ${currentpkg} pkg version set to ${currentversion}"
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# set version number and date to DESCRIPTION file
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sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
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sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
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echo ">> - updated DESCRIPTION"
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echo "- updated DESCRIPTION"
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# remove leftover on macOS
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rm -f DESCRIPTION--
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# add to commit
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@ -65,12 +94,12 @@ if [ -e "NEWS.md" ]; then
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currentpkg=""
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fi
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sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
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echo ">> - updated NEWS.md"
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echo "- updated NEWS.md"
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# remove leftover on macOS
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rm -f NEWS.md--
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# add to commit
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git add NEWS.md
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else
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echo ">> - no NEWS.md found!"
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echo "- no NEWS.md found!"
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fi
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echo ">> "
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echo ""
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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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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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@ -27,14 +31,13 @@ on:
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pull_request:
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# run in each PR in this repo
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branches: '**'
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push:
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branches: '**'
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name: R-code-check-PR
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name: check-devel
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jobs:
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R-code-check-PR:
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# do not run if we are the authors - the other checks will already run
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if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
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R-code-check:
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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@ -46,16 +49,13 @@ jobs:
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matrix:
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config:
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- {os: macOS-latest, r: 'devel', allowfail: true}
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: ubuntu-latest, r: 'devel', allowfail: true}
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- {os: ubuntu-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: 'release', allowfail: false}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v3
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@ -65,7 +65,7 @@ jobs:
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with:
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r-version: ${{ matrix.config.r }}
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# use RStudio Package Manager to quickly install packages
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use-public-rspm: true
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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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@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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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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@ -32,12 +36,12 @@ on:
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# this is to check that all dependencies are still available (see R/zzz.R)
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- cron: '0 1 * * *'
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name: R-code-check
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name: check-release
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jobs:
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R-code-check:
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
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@ -46,13 +50,11 @@ jobs:
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fail-fast: false
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matrix:
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config:
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# test all systems against all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: 'devel', allowfail: true}
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# test all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: '4.2', allowfail: false}
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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@ -63,7 +65,6 @@ jobs:
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- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: '4.2', allowfail: false}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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@ -72,14 +73,14 @@ jobs:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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R_REPOSITORIES: "https://cran.rstudio.com"
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Install Linux dependencies
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@ -89,7 +90,7 @@ jobs:
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# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
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run: |
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sudo apt install -y libssl-dev libxml2-dev libcurl4-openssl-dev
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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@ -102,7 +103,7 @@ jobs:
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run: |
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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- name: Show session info
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if: always()
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run: |
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@ -110,7 +111,7 @@ jobs:
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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- name: Remove vignettes on R without knitr support
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if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3'
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# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite
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@ -156,4 +157,4 @@ jobs:
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uses: actions/upload-artifact@v2
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with:
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name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
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path: /home/runner/work/AMR.Rcheck
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path: ${GITHUB_WORKSPACE}.Rcheck
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10
.github/workflows/codecovr.yaml
vendored
10
.github/workflows/codecovr.yaml
vendored
@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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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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23
.github/workflows/lintr.yaml
vendored
23
.github/workflows/lintr.yaml
vendored
@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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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||||
# LICENCE #
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||||
# (c) 2018-2022 Berends MS, Luz CF et al. #
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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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||||
@ -52,5 +56,16 @@ jobs:
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extra-packages: any::lintr
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- name: Lint
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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"))
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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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||||
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||||
10
.github/workflows/website.yaml
vendored
10
.github/workflows/website.yaml
vendored
@ -1,12 +1,16 @@
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||||
# ==================================================================== #
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||||
# 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 #
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||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
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||||
# 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. #
|
||||
|
||||
Reference in New Issue
Block a user