fix git hooks

.github/prehooks/pre-commit

@@ -33,8 +33,15 @@
 # This script runs before every commit #
 ########################################
 
-# check the commit message
-COMMIT_MSG=$(cat "$1")
+# try to fetch the commit message from the standard location
+COMMIT_MSG_PATH=".git/COMMIT_EDITMSG"
+if [ -f "$COMMIT_MSG_PATH" ]; then
+    COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
+else
+    echo "Commit message file not found."
+    echo 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)."
@@ -42,7 +49,6 @@ if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
   exit 0
 fi
 
-
 echo "Running pre-commit checks..."
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9025
+Version: 2.1.1.9028
 Date: 2024-04-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9025
+# AMR 2.1.1.9028
 
 *(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!)*
 

R/ab.R

@@ -645,14 +645,14 @@ generalise_antibiotic_name <- function(x) {
   x <- gsub("_(MIC|RSI|SIR|DIS[CK])$", "", x, perl = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
   x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
-  # correct for 'high level' antibiotics
-  x <- gsub("([^A-Z0-9]+)?(HIGH(.?LEVEL)?|H[^A-Z0-9]?L)([^A-Z0-9]+)?", "-HIGH", x, perl = TRUE)
-  # remove part between brackets if that's followed by another string
-  x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # keep only max 1 space
   x <- trimws2(gsub(" +", " ", x, perl = TRUE))
   # non-character, space or number should be a slash
-  x <- gsub("[^A-Z0-9 -]", "/", x, perl = TRUE)
+  x <- gsub("[^A-Z0-9 -)(]", "/", x, perl = TRUE)
+  # correct for 'high level' antibiotics
+  x <- gsub("([^A-Z0-9/ -]+)?(HIGH(.?LE?VE?L)?|[^A-Z0-9/]H[^A-Z0-9]?L)([^A-Z0-9 -]+)?", "-HIGH", x, perl = TRUE)
+  # remove part between brackets if that's followed by another string
+  x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # spaces around non-characters must be removed: amox + clav -> amox/clav
   x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
   x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x, perl = TRUE)