mirror of
https://github.com/msberends/AMR.git
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116 lines
4.8 KiB
Bash
Executable File
116 lines
4.8 KiB
Bash
Executable File
#!/bin/bash
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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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# Check if commit should skip checks
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COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
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if [ -f "$COMMIT_MSG_FILE" ]; then
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COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
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if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
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echo "Not running prehook 'pre-commit':"
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echo "Commit message contains 'no-check' or 'no-verify'."
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echo ""
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exit 0
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fi
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fi
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echo "Running prehook..."
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# Run the R script and stage the modified files
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if command -v Rscript > /dev/null; then
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if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
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Rscript -e "source('data-raw/_pre_commit_checks.R')"
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currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
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bash data-raw/AMRforRGPT.sh
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echo "- Adding changed files in ./data-raw and ./man to this commit"
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git add data-raw/*
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git add man/*
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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', or 'dplyr' not installed!"
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currentpkg="your"
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fi
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else
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echo "- R is not available on your system!"
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currentpkg="your"
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fi
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echo ""
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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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currenttagfull=$(git describe --tags --abbrev=0)
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currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
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# Assume main branch to be 'main' or 'master'
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defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
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if [ "$currenttag" = "" ]; then
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currenttag="0.0.1"
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currentcommit=$(git rev-list --count ${defaultbranch})
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echo "- No git tags found, creating one in format 'v(x).(y).(z)' - currently ${currentcommit} previous commits in '${defaultbranch}'"
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else
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currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
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echo "- Latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
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fi
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# Combine tag and commit number
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currentversion="$currenttag.$((currentcommit + 9001))"
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echo "- ${currentpkg} pkg version set to ${currentversion}"
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# Update version number and date in DESCRIPTION
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sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
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sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
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echo "- Updated version number and date in ./DESCRIPTION"
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rm -f DESCRIPTION--
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git add DESCRIPTION
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# Update version number in NEWS.md
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if [ -e "NEWS.md" ]; then
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if [ "$currentpkg" = "your" ]; then
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currentpkg=""
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fi
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sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
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echo "- Updated version number in ./NEWS.md"
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rm -f NEWS.md--
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git add NEWS.md
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else
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echo "- No NEWS.md found!"
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fi
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echo ""
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# Save the version number for use in the commit-msg hook
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echo "${currentversion}" > .git/commit_version.tmp
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exit 0
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