(v3.0.0.9025) fix todo tracker

.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=$(find R/ -type f ! -name "sysdata.rda" -exec grep -nH "TODO" {} + || true)
+          todos=$(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
                 }
@@ -74,6 +75,6 @@ jobs:
         with:
           token: ${{ secrets.GH_REPO_SCOPE }}
           issue-number: 231
-          comment-id: 3379846566
+          comment-id: 3253439219
           body-file: todo.md
           edit-mode: replace

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.0.9023
+Version: 3.0.0.9025
 Date: 2025-09-04
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.0.9023
+# AMR 3.0.0.9025
 
 This is a bugfix release following the release of v3.0.0 in June 2025.
 

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")
 ```
 

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")
 ```
 

_pkgdown.yml

@@ -234,7 +234,7 @@ reference:
     - "`antimicrobials`"
     - "`clinical_breakpoints`"
     - "`example_isolates`"
-    - "`esbl_isolates`"
+    # TODO - "`esbl_isolates`"
     - "`microorganisms.codes`"
     - "`microorganisms.groups`"
     - "`intrinsic_resistant`"