AMR/.github/prehooks/pre-commit

#!/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/   #
# ==================================================================== #

########################################
# This script runs before every commit #
########################################

# try to fetch the commit message from the standard location
COMMIT_MSG_PATH=".git/COMMIT_EDITMSG"
if [ -f "$COMMIT_MSG_PATH" ]; then
  COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
else
  echo "Commit message file not found."
  COMMIT_MSG=""
fi
# check the commit message, cancel commit if needed
if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
  echo "Not running pre-commit checks:"
  echo "Commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
  echo ""
  exit 0
fi

echo "Running pre-commit checks..."

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if command -v Rscript > /dev/null; then
  if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
    Rscript -e "source('data-raw/_pre_commit_checks.R')"
    currentpkg=$(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})
  echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
fi
# 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
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

# Prepend the version number to the commit message
if [ -f "$COMMIT_MSG_PATH" ]; then
  # Prepend the version number
  echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_PATH"
  echo "- prepended version number to commit message"
else
  echo ""
  echo "Commit message file not found. Unable to prepend version number."
fi

echo ""