mirror of https://github.com/msberends/AMR.git
check for windows unit test (no-check)
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#!/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, 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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# 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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#######################################
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# This script runs on commit-msg hook #
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#######################################
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# Path to the commit message file
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COMMIT_MSG_FILE=$1
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# Read the current commit message
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COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
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# check the commit message, cancel commit if needed
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if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
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exit 0
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fi
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# Path to the DESCRIPTION file
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DESCRIPTION_FILE="DESCRIPTION"
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# Read the version number from the DESCRIPTION file
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if [ -f "$DESCRIPTION_FILE" ]; then
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currentversion=$(grep "^Version:" "$DESCRIPTION_FILE" | awk '{print $2}')
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else
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echo "Error: DESCRIPTION file not found. Unable to prepend version number."
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exit 1
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fi
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# Prepend the version number to the commit message
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echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"
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@ -33,23 +33,25 @@
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# This script runs before every commit #
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########################################
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# try to fetch the commit message from the standard location
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COMMIT_MSG_PATH=".git/COMMIT_EDITMSG"
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if [ -f "$COMMIT_MSG_PATH" ]; then
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COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
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COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
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# Read the commit message
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if [ -f "$COMMIT_MSG_FILE" ]; then
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COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
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else
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echo "Commit message file not found."
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exit 1
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fi
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# check the commit message, cancel commit if needed
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if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
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echo "Not running pre-commit checks:"
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echo "Commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
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# Check the commit message and skip checks if needed
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if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
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echo "Not running prehook:"
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echo "Commit message contains 'no-check' or 'no-verify'."
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echo ""
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exit 0
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fi
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echo "Running pre-commit checks..."
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echo "Running prehook..."
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# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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if command -v Rscript > /dev/null; then
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@ -119,3 +121,6 @@ else
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echo "- no NEWS.md found!"
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fi
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echo ""
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# Prepend the version number to the commit message
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echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"
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@ -326,6 +326,7 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11))
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expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
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sir_history <- sir_interpretation_history()
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print(sir_history$host)
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expect_identical(sir_history$host,
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c("poultry", "cattle", "poultry", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "horse", "dogs", "horse", "horse", "horse", "cattle", "horse", "cattle", "cattle", "cattle",
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"cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "cattle", "dogs", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cats", "cats",
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