(v2.1.1.9040) try to put version number in commit msg

.github/prehooks/commit-msg

@@ -0,0 +1,61 @@
+#!/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, 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/   #
+# ==================================================================== #
+#!/bin/bash
+
+#######################################
+# This script runs on commit-msg hook #
+#######################################
+
+# Path to the commit message file
+COMMIT_MSG_FILE=$1
+
+# Read the current commit message
+COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
+# check the commit message, cancel commit if needed
+if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
+  exit 0
+fi
+
+# Path to the DESCRIPTION file
+DESCRIPTION_FILE="DESCRIPTION"
+# Read the version number from the DESCRIPTION file
+if [ -f "$DESCRIPTION_FILE" ]; then
+  currentversion=$(grep "^Version:" "$DESCRIPTION_FILE" | awk '{print $2}')
+else
+  echo "Error: DESCRIPTION file not found. Unable to prepend version number."
+  exit 1
+fi
+
+# Prepend the version number to the commit message
+echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"
+
+# Print the updated commit message for verification
+echo "Updated commit message: $(cat "$COMMIT_MSG_FILE")"

.github/prehooks/pre-commit

@@ -39,7 +39,7 @@ if [ -f "$COMMIT_MSG_PATH" ]; then
   COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
 else
   echo "Commit message file not found."
-  COMMIT_MSG=""
+  exit 1
 fi
 # check the commit message, cancel commit if needed
 if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
@@ -119,16 +119,8 @@ else
   echo "- no NEWS.md found!"
 fi
 
-# Prepend the version number to the commit message
-if [ -f "$COMMIT_MSG_PATH" ]; then
-    COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
-    echo "Current commit message: $COMMIT_MSG"  # Debug line
-    echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_PATH"
-    echo "- prepended version number to commit message"
-    echo "Updated commit message: $(cat "$COMMIT_MSG_PATH")"  # Debug line
-else
-  echo ""
-  echo "Commit message file not found. Unable to prepend version number."
-fi
+# set the version number as an environment variable for the commit-msg hook
+export COMMIT_VERSION=$currentversion
+echo "- exported COMMIT_VERSION=${currentversion} for the commit-msg hook"
 
 echo ""

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9039
-Date: 2024-06-04
+Version: 2.1.1.9040
+Date: 2024-06-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9039
+# AMR 2.1.1.9040
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*