mirror of
https://github.com/msberends/AMR.git
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203 lines
8.9 KiB
Bash
Executable File
203 lines
8.9 KiB
Bash
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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) 2018-2021 Berends MS, Luz CF et al. #
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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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########################################################################
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# `git_premaster.sh` takes 3 parameters: #
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# 1. Commit message (character) [mandatory] #
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# 2. Lazy website generation (logical), with TRUE only changed #
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# files will be processed [defaults to TRUE] #
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# 3. Version number to be used in DESCRIPTION and NEWS.md #
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# [defaults to current tag and last commit number + 9000] #
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# #
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# To push new commits to the premaster branch, run: #
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# bash git_premaster.sh "commit message" #
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# This creates auto version numbering in DESCRIPTION and NEWS.md. #
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# #
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# After successful test checks, merge it to the master branch with: #
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# bash git_merge.sh #
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# #
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# To prerelease a new version number, run: #
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# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
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# #
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# To only update the website, run: #
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# bash git_siteonly.sh #
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# (which is short for 'bash git_premaster.sh "website update" FALSE') #
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########################################################################
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if [ -z "$1" ]; then
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echo "FATAL - no commit message"
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exit 1
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fi
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if [ -z "$2" ]; then
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lazy="TRUE"
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else
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lazy=$2
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fi
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# be sure to be on premaster branch
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git checkout premaster --quiet
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echo "••••••••••••••••••••••••••••••••••••••••••••"
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echo "• Updating package date and version number •"
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echo "••••••••••••••••••••••••••••••••••••••••••••"
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sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
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if [ -z "$3" ]; then
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# no version number set, so get latest tags to create it
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git pull --tags --quiet
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current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
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if [ -z "current_tag" ]; then
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echo "FATAL - could not determine current tag"
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exit 1
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fi
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current_tag_full=`git describe --tags | sed 's/v//'`
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current_tag_dashes=`echo $current_tag_full | grep -o "[-]" | wc -l`
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if (( "$current_tag_dashes" < 1 )); then
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# so version number is like "1.0.0", commit nr is 0
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current_commit=0
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echo "---------------"
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echo "Mind NEWS.md! Assuming sequence number 9000."
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echo "---------------"
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else
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current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
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fi
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if [ -z "current_commit" ]; then
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echo "FATAL - could not determine last commit index number"
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exit 1
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fi
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# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
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new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
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# add date to 2nd line of NEWS.md when no version number was set
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sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%e %B %Y')\<\/small\>/" NEWS.md
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else
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# version number set in command
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new_version=$3
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# rmove 2nd line of NEWS.md (the last changed date)
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sed -i -- "2s/.*//" NEWS.md
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echo "Run devtools::release() or devtools::submit_cran() after this script. Non-interactive mode will not work."
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fi
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# set version number to DESCRIPTION and NEWS files
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sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
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sed -i -- "1s/.*/# \`AMR\` ${new_version}/" NEWS.md
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rm *-- || true
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echo "• First 3 lines of DESCRIPTION:"
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head -3 DESCRIPTION
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echo
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echo "• First 2 lines of NEWS.md:"
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head -2 NEWS.md
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echo
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echo "R library location:" $(Rscript -e "cat(.libPaths()[1])")
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echo "•••••••••••••••••••••••••••••••••"
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echo "• Reloading/documenting package •"
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echo "•••••••••••••••••••••••••••••••••"
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Rscript -e "devtools::load_all(quiet = TRUE)"
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echo "• Documenting..."
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Rscript -e "suppressMessages(devtools::document())"
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echo
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echo "••••••••••••••••••••••••••"
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echo "• Updating internal data •"
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echo "••••••••••••••••••••••••••"
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Rscript -e "source('data-raw/_internals.R')"
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echo
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echo "••••••••••••••••••••"
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echo "• Building package •"
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echo "••••••••••••••••••••"
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echo "• Building 'data-raw/AMR_latest.tar.gz'..."
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Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
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rm data-raw/AMR_latest.tar.gz
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mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
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# echo "• Installing..."
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# Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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echo
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echo "•••••••••••••••••"
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echo "• Building site •"
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echo "•••••••••••••••••"
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if [ $lazy == "FALSE" ]; then
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Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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Rscript -e "suppressMessages(pkgdown::build_site(lazy = FALSE, examples = FALSE, install = FALSE))"
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else
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if ! git diff --quiet man; then
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# documentation has changed
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Rscript -e "pkgdown::build_reference(lazy = $lazy, examples = FALSE)"
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fi
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if ! git diff --quiet index.md; then
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# home page has changed
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Rscript -e "pkgdown::build_home()"
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fi
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if ! git diff --quiet NEWS.md; then
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# news has changed
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Rscript -e "pkgdown::build_news()"
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fi
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if ! git diff --quiet pkgdown; then
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# something has changed in pkgdown files
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Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE, install = TRUE))"
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fi
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if ! git diff --quiet vignettes; then
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# a vignette has changed
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Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
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Rscript -e "pkgdown::build_articles(lazy = $lazy)"
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fi
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fi
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# always rebuild datasets vignette
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Rscript -e "pkgdown::build_article('datasets', lazy = FALSE, quiet = TRUE)"
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# add the survey page
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Rscript -e "source('data-raw/create_survey_page.R')"
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echo
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echo "•••••••••••••••••••••••••"
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echo "• List of changed files •"
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echo "•••••••••••••••••••••••••"
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git add .
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git status --short
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echo
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read -p "Uploading v${new_version} '$1'. Continue (Y/n)? " choice
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case "$choice" in
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n|N ) exit 1;;
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* ) ;;
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esac
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echo
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echo "•••••••••••••••••••••••••••"
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echo "• Uploading to repository •"
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echo "•••••••••••••••••••••••••••"
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# save latest changes as well
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git add .
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# and commit
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git commit -a -m "(v${new_version}) $1" --quiet
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git push --quiet
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echo "Comparison:"
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echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline"
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echo
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echo "•••••••••"
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echo "• Done •"
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echo "••••••••"
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echo
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