From 3742e9e9949b6f26ecb9cae2c5bdbc2efdff4d1b Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Fri, 6 Jun 2025 09:37:25 +0200
Subject: [PATCH] (v3.0.0.9002) website version nr

---
 DESCRIPTION       |  4 ++--
 NEWS.md           |  7 +++----
 R/eucast_rules.R  |  7 +++++++
 index.Rmd         |  4 ++--
 pkgdown/extra.css | 13 ++++++++++++-
 pkgdown/extra.js  | 14 +++++++++++++-
 6 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b7b2bab76..4499c0386 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9001
-Date: 2025-06-04
+Version: 3.0.0.9002
+Date: 2025-06-06
 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
diff --git a/NEWS.md b/NEWS.md
index 90b852273..2ee6d61e9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,8 @@
-# AMR 3.0.0.9001
+# AMR 3.0.0.9002
 
-# Changed
+### Changed
 * Fix for `antibiogram()` for when no antimicrobials are set
-* Fixed some specific Dutch translations antimicrobials
-
+* Fixed some specific Dutch translations for antimicrobials
 
 
 # AMR 3.0.0
diff --git a/R/eucast_rules.R b/R/eucast_rules.R
index 90fd82bc0..07f2a6816 100755
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@@ -457,6 +457,13 @@ eucast_rules <- function(x,
   n_added <- 0
   n_changed <- 0
 
+  rule_current <- ""
+  rule_group_current <- ""
+  rule_group_previous <- ""
+  rule_next <- ""
+  rule_previous <- ""
+  rule_text <- ""
+
   # >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
   if (any(c("all", "other") %in% rules)) {
     if (isTRUE(info)) {
diff --git a/index.Rmd b/index.Rmd
index 39faabd1a..776b53666 100644
--- a/index.Rmd
+++ b/index.Rmd
@@ -28,8 +28,8 @@ AMR:::reset_all_thrown_messages()
 > Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more.
 
 <div style="display: flex; font-size: 0.8em;">
-  <p style="text-align:left; width: 50%;"><small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small></p>
-  <p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
+  <p style="text-align:left; width: 50%;"><small><a href="https://amr-for-r.org/">amr-for-r.org</a></small></p>
+  <p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">doi.org/10.18637/jss.v104.i03</a></small></p>
 </div>
 
 <a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" /></a>
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index 7490db2a9..7f943c508 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -41,7 +41,7 @@
 
   --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-light was this: #128f76a6; that's bs-success with 60% alpha */
   --bs-info: var(--amr-green-middle) !important;
   --bs-link-color: var(--amr-green-dark) !important;
   --bs-link-color-rgb: var(--amr-green-dark-rgb) !important;
@@ -104,6 +104,16 @@ body.amr-for-python * {
 .navbar .algolia-autocomplete .aa-dropdown-menu {
   background-color: var(--amr-green-dark) !important;
 }
+
+.version-main {
+  font-weight: bold;
+  color: var(--bs-navbar-brand-color);
+}
+.version-build {
+  font-weight: normal;
+  opacity: 0.75;
+  font-size: 0.85em;
+}
 input[type="search"] {
   color: var(--bs-tertiary-bg) !important;
   background-color: var(--amr-green-light) !important;
@@ -149,6 +159,7 @@ this shows on top of every sidebar to the right
   margin-top: 10px;
   border: 2px dashed var(--amr-green-dark);
   text-align: center;
+  background: var(--bs-body-bg);
 }
 .amr-gpt-assistant * {
   width: 90%;
diff --git a/pkgdown/extra.js b/pkgdown/extra.js
index 8775b3ec7..a827c3a86 100644
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@@ -29,10 +29,22 @@
 # ==================================================================== #
 */
 
-$(document).ready(function() {
+$(function () {
   // add GPT assistant info
   $('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chat.amr-for-r.org"><img src="https://amr-for-r.org/AMRforRGPT.svg"></a></div>');
 
+  // split version number in navbar into main version and build number
+  $('.nav-text').each(function () {
+    const $el = $(this);
+    const text = $.trim($el.text());
+    const lastDotIndex = text.lastIndexOf('.');
+    if (lastDotIndex > -1) {
+      const main = text.substring(0, lastDotIndex);
+      const build = text.substring(lastDotIndex);
+      $el.html(`<span class="version-main">${main}</span><span class="version-build">${build}</span>`);
+    }
+  });
+
   // replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
   $(".developers h2").text("Maintainers");
   $(".template-citation-authors h1:nth(0)").text("Contributors and Citation");