mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 22:46:11 +01:00
108 lines
4.8 KiB
Bash
Executable File
108 lines
4.8 KiB
Bash
Executable File
#!/bin/sh
|
|
|
|
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
echo "Running pre-commit hook..."
|
|
|
|
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
if command -v Rscript > /dev/null; then
|
|
if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
|
|
Rscript -e "source('data-raw/_pre_commit_hook.R')"
|
|
currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
|
|
echo "- Adding changed files in ./data-raw and ./man to this commit"
|
|
git add data-raw/*
|
|
git add man/*
|
|
git add R/sysdata.rda
|
|
git add NAMESPACE
|
|
else
|
|
echo "- R package 'pkgload', 'devtools', 'dplyr', or 'styler' not installed!"
|
|
currentpkg="your"
|
|
fi
|
|
else
|
|
echo "- R is not available on your system!"
|
|
currentpkg="your"
|
|
fi
|
|
echo ""
|
|
|
|
|
|
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
echo "Updating semantic versioning and date..."
|
|
|
|
# get tags from remote, and remove tags not on remote:
|
|
git fetch origin --prune --prune-tags --quiet
|
|
currenttagfull=$(git describe --tags --abbrev=0)
|
|
currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
|
|
# assume main branch to be 'main' or 'master', pick the right name:
|
|
defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
|
|
if [ "$currenttag" = "" ]; then
|
|
# there is no tag, so set tag to 0.0.1 and commit index to current count
|
|
currenttag="0.0.1"
|
|
currentcommit=$(git rev-list --count ${defaultbranch})
|
|
echo "- no git tags found, create one in format 'v(x).(y).(z)' - curently ${currentcommit} previous commits in '${defaultbranch}'"
|
|
else
|
|
# there is a tag, so base version number on that
|
|
currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
|
|
if (( "$currentcommit" == 0 )); then
|
|
# tag is new, so this must become the version number
|
|
currentversion="$currenttag"
|
|
fi
|
|
echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
|
|
fi
|
|
if [ "$currentversion" = "" ]; then
|
|
# combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
|
|
currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
|
|
fi
|
|
echo "- ${currentpkg} pkg version set to ${currentversion}"
|
|
|
|
# set version number and date to DESCRIPTION file
|
|
sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
|
|
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
|
|
echo "- updated version number and date in ./DESCRIPTION"
|
|
# remove leftover on macOS
|
|
rm -f DESCRIPTION--
|
|
# add to commit
|
|
git add DESCRIPTION
|
|
|
|
# set version number to NEWS file
|
|
if [ -e "NEWS.md" ]; then
|
|
if [ "$currentpkg" = "your" ]; then
|
|
currentpkg=""
|
|
fi
|
|
sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
|
|
echo "- updated version number in ./NEWS.md"
|
|
# remove leftover on macOS
|
|
rm -f NEWS.md--
|
|
# add to commit
|
|
git add NEWS.md
|
|
else
|
|
echo "- no NEWS.md found!"
|
|
fi
|
|
echo ""
|