fix website nav header (no-check)

.github/prehooks/commit-msg

@@ -29,7 +29,17 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-echo "Running pre-commit hook..."
+#!/bin/bash
+
+echo "Running commit-msg hook..."
+
+# check if the commit message contains '(no-check)' or '(no-verify)'
+COMMIT_MSG=$(cat "$1")
+if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-verify\) ]]; then
+  echo "Commit check bypassed by commit message."
+  exit 0
+fi
+
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 if command -v Rscript > /dev/null; then

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9021
-Date: 2024-04-19
+Version: 2.1.1.9022
+Date: 2024-04-23
 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 2.1.1.9021
+# AMR 2.1.1.9022
 
 *(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/antibiogram.R

@@ -294,7 +294,7 @@ antibiogram <- function(x,
   } else if (mo_transform == "name") {
     x$`.mo` <- mo_name(x$`.mo`, language = language)
   } else {
-    x$`.mo` <- mo_property(x$`.mo`, language = language)
+    x$`.mo` <- mo_property(x$`.mo`, property = mo_transform, language = language)
   }
   x$`.mo`[is.na(x$`.mo`)] <- "(??)"
 

pkgdown/extra.css

@@ -36,11 +36,10 @@
   --amr-green-dark-rgb: 18, 143, 118;
   --amr-green-middle: #60a799;
   --amr-green-middle-rgb: 96, 167, 153;
-  --amr-blue-light: #a8d5ef
+  --amr-blue-light: #a8d5ef;
   --amr-blue-light-rgb: 168, 213, 239;
 
-  --bs-success: var(--amr-green-dark) !important);
-  --bs-link-color: var(--amr-green-dark) !important;
+  --bs-success: var(--amr-green-dark) !important;
   --bs-light: var(--amr-green-light) !important;
   /* --bs-light was this: #128f76a6; that's success with 60% alpha */
   --bs-info: var(--amr-green-middle) !important;
@@ -58,14 +57,34 @@
   --bs-navbar-brand-color: white !important;
   --bs-navbar-brand-color-hover: white !important;
   --bs-nav-link-color: white !important;
+  --bs-navbar-active-color: var(--amr-green-light) !important;
   --bs-bg-opacity: 1 !important;
+  
+  --bs-dropdown-bg: var(--amr-green-dark) !important;
+  --bs-dropdown-link-color: white !important;
+  --bs-dropdown-link-color: white !important;
+  --bs-dropdown-link-hover-color: var(--amr-green-light) !important;
+  --bs-dropdown-link-hover-bg: var(--amr-green-dark) !important;
+  --bs-dropdown-link-active-color: white !important;
+  
 }
-.nav-text.text-muted {
-  color: var(--amr-green-dark) !important;
+.nav-text.text-muted,
+.bg-primary .navbar-nav .show>.nav-link,
+.bg-primary .navbar-nav .nav-link.active,
+.bg-primary .navbar-nav .nav-link:hover,
+.bg-primary .navbar-nav .nav-link:focus {
+  color: var(--amr-green-light) !important;
+}
+.navbar-dark .navbar-nav .nav-item > .nav-link:hover,
+.navbar-light .navbar-nav .nav-item>.nav-link:hover {
+  background: none !important;
 }
 .navbar-dark input[type="search"] {
   background-color: var(--amr-green-light) !important;
 }
+.navbar-nav .nav-item > .nav-link {
+  border-radius: 0 !important;
+}
 .form-control:focus {
   box-shadow: none !important;
 }