AMR/.github/prehooks/pre-commit

#!/bin/bash

# ==================================================================== #
# 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, et al. (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/   #
# ==================================================================== #

# Check if commit should skip checks
COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
if [ -f "$COMMIT_MSG_FILE" ]; then
  COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
  if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
    echo "Not running prehook 'pre-commit':"
    echo "Commit message contains 'no-check' or 'no-verify'."
    echo ""
    exit 0
  fi
fi

echo "Running prehook..."

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Run the R script and stage the modified files
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', or 'dplyr' 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'
defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
if [ "$currenttag" = "" ]; then
  currenttag="0.0.1"
  currentcommit=$(git rev-list --count ${defaultbranch})
  echo "- No git tags found, creating one in format 'v(x).(y).(z)' - currently ${currentcommit} previous commits in '${defaultbranch}'"
else
  currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
  echo "- Latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
fi

# Combine tag and commit number
currentversion="$currenttag.$((currentcommit + 9001))"
echo "- ${currentpkg} pkg version set to ${currentversion}"

# Update version number and date in DESCRIPTION
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"
rm -f DESCRIPTION--
git add DESCRIPTION

# Update version number in NEWS.md
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"
  rm -f NEWS.md--
  git add NEWS.md
else
  echo "- No NEWS.md found!"
fi
echo ""

# Save the version number for use in the commit-msg hook
echo "${currentversion}" > .git/commit_version.tmp

# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
cd data-raw
bash _generate_python_wrapper.sh
cd ..
git add data-raw/*
git add PythonPackage/*
git add -u

exit 0