From c588902f4c38eb392638215a22ad3303ac0382b5 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Sun, 6 Oct 2024 16:25:31 +0200
Subject: [PATCH] (v2.1.1.9092) Fix website

---
 DESCRIPTION       | 4 ++--
 NEWS.md           | 2 +-
 _pkgdown.yml      | 5 +----
 pkgdown/extra.css | 4 ++++
 pkgdown/extra.js  | 7 ++++++-
 5 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f32292ca..368e022a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9090
-Date: 2024-10-04
+Version: 2.1.1.9092
+Date: 2024-10-06
 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 a0c9916e..da408f98 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9090
+# AMR 2.1.1.9092
 
 *(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! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index ef56c538..47ef7619 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -57,10 +57,7 @@ footer:
 
 home:
   sidebar:
-    structure: [gpthelp, toc, links, authors]
-    components:
-      gpthelp: 
-        text: '<a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg" style="width: 80%;"></a>'
+    structure: [toc, links, authors]
 
 navbar:
   title: "AMR (for R)"
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index 957e9ce1..2ea66684 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -119,6 +119,10 @@ body.amr-for-python * {
   width: 150px;
 }
 
+.amr-gpt-assistant * {
+  width: 90%;
+}
+
 .template-reference-index .section-desc {
   font-style: italic;
   text-align: justify;
diff --git a/pkgdown/extra.js b/pkgdown/extra.js
index 752c9a38..c102ef83 100644
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@@ -30,8 +30,10 @@
 */
 
 $(document).ready(function() {
+  // add GPT assistant info
+  $('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"></a></div>');
 
-  // Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
+  // replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
   $(".developers h2").text("Maintainers");
   $(".citation h2:nth(0)").text("All contributors");
   $(".citation h2:nth(1)").text("How to Cite");
@@ -42,6 +44,9 @@ $(document).ready(function() {
     $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
     $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
   }
+  
+  // rename 'Package index' to 'Manual' (weird design choice to pick 'Package index')
+  
 
   // remove leading newline in code examples on changelog
   if ($("body .template-news").length > 0) {