Update transform-notebooks.yml

.github/workflows/transform-notebooks.yml

@@ -40,6 +40,7 @@ jobs:
 
     - name: Strip outputs from .ipynb files
       run: |
+        git pull
         dirs=(PM1 PM2 PM3 PM4 PM5 CM1 CM2 CM3 AC1 AC2 T)
         for dir in "${dirs[@]}"; do
         # Check if directory exists
@@ -67,13 +68,14 @@ jobs:
             # first we delete all Rmd files and regenerate. This will make sure
             # that if a .irnb file is deleted then the corresponding .Rmd file
             # will also be removed by this script.
-            rm "$dir"/*.Rmd
+            git rm "$dir"/*.Rmd
             R -e "
               files <- list.files(path = '$dir', pattern = '\\\\.irnb$', full.names = TRUE, recursive = FALSE)
               lapply(files, function(input) {
                 rmarkdown::convert_ipynb(input)
               })
             "
+            git add "$dir"/*.Rmd
         else
             echo "Directory $dir does not exist."
         fi