check for windows unit test (no-check)

.github/prehooks/commit-msg

@@ -1,57 +0,0 @@
-#!/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/   #
-# ==================================================================== #
-
-#######################################
-# 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"

.github/prehooks/prepare-commit-msg

@@ -33,23 +33,25 @@
 # 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 "$COMMIT_MSG_PATH")
+COMMIT_MSG_FILE=".git/COMMIT_EDITMSG"
+
+# Read the commit message
+if [ -f "$COMMIT_MSG_FILE" ]; then
+  COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
 else
   echo "Commit message file not found."
   exit 1
 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)."
+
+# Check the commit message and skip checks if needed
+if [[ "$COMMIT_MSG" =~ no-?checks?|no-?verify ]]; then
+  echo "Not running prehook:"
+  echo "Commit message contains 'no-check' or 'no-verify'."
   echo ""
   exit 0
 fi
 
-echo "Running pre-commit checks..."
+echo "Running prehook..."
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 if command -v Rscript > /dev/null; then
@@ -119,3 +121,6 @@ else
   echo "- no NEWS.md found!"
 fi
 echo ""
+
+# Prepend the version number to the commit message
+echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"

inst/tinytest/test-sir.R

@@ -326,6 +326,7 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11))
 expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
 
 sir_history <- sir_interpretation_history()
+print(sir_history$host)
 expect_identical(sir_history$host,
                  c("poultry", "cattle", "poultry", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "horse", "dogs", "horse", "horse", "horse", "cattle", "horse", "cattle", "cattle", "cattle", 
                    "cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "cattle", "dogs", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cats", "cats",