From c1c49fa46346628e8e462662fcd699ffe5570107 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Thu, 4 Sep 2025 14:40:24 +0200
Subject: [PATCH] (v3.0.0.9025) fix todo tracker

---
 .github/workflows/todo-tracker.yml | 7 ++++---
 DESCRIPTION                        | 2 +-
 NEWS.md                            | 2 +-
 README.Rmd                         | 5 ++++-
 README.md                          | 6 +++++-
 5 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/todo-tracker.yml b/.github/workflows/todo-tracker.yml
index d36242dd8..43ed5664f 100644
--- a/.github/workflows/todo-tracker.yml
+++ b/.github/workflows/todo-tracker.yml
@@ -47,19 +47,20 @@ jobs:
           echo "" >> todo.md
           echo "_This overview is automatically updated on each push to \`main\`. It provides an automated overview of all mentions of the text \`TODO\`._" >> todo.md
           echo "" >> todo.md
-          todos=$(grep -rn --include=\*.{R,Rmd,yaml,yml,md,css,js} --exclude=todo-tracker.yml "TODO" . || true)
+          todos=$(grep -rn --include=\*.{R,Rmd,yaml,yml,md,css,js}  --exclude={todo-tracker.yml,todo.md} "TODO" . || true)
           if [ -z "$todos" ]; then
             echo "✅ No TODOs found." >> todo.md
           else
-            echo "$todos" | awk -F: '
+            echo "$todos" | awk -F: -v repo="https://github.com/msberends/AMR/blob/main/" '
               {
                 file = $1
+                gsub("^\\./", "", file)  # remove leading ./ if present
                 line = $2
                 text = substr($0, index($0,$3))
                 if (file != last_file) {
                   if (last_file != "") print "```"
                   print ""
-                  print "### " file
+                  print "### [`" file "`](" repo file ")"
                   print "```r"
                   last_file = file
                 }
diff --git a/DESCRIPTION b/DESCRIPTION
index e05ce4944..3b01982a3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.0.9024
+Version: 3.0.0.9025
 Date: 2025-09-04
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 931f9001b..dbdcf0981 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.0.9024
+# AMR 3.0.0.9025
 
 This is a bugfix release following the release of v3.0.0 in June 2025.
 
diff --git a/README.Rmd b/README.Rmd
index 329cabdd4..79bcbd685 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -49,8 +49,11 @@ To install the latest 'beta' version:
 
 ```{r, eval = FALSE}
 install.packages("AMR", repos = "beta.amr-for-r.org")
+```
 
-# if this does not work, try to install directly from GitHub using the 'remotes' package:
+If this does not work, try to install directly from GitHub using the `remotes` package:
+
+```{r, eval = FALSE}
 remotes::install_github("msberends/AMR")
 ```
 
diff --git a/README.md b/README.md
index 88edbd8e5..681722c7b 100755
--- a/README.md
+++ b/README.md
@@ -58,8 +58,12 @@ To install the latest ‘beta’ version:
 
 ``` r
 install.packages("AMR", repos = "beta.amr-for-r.org")
+```
 
-# if this does not work, try to install directly from GitHub using the 'remotes' package:
+If this does not work, try to install directly from GitHub using the
+`remotes` package:
+
+``` r
 remotes::install_github("msberends/AMR")
 ```