(v2.1.1.9099) fix generating GPT training test

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9098
+Version: 2.1.1.9099
 Date: 2024-10-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9098
+# AMR 2.1.1.9099
 
 *(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).)*
 

data-raw/AMRforRGPT.sh

@@ -1,7 +1,13 @@
 #!/bin/bash
 
+# Check if the current directory is named 'AMR'
+if [ "$(basename "$PWD")" != "AMR" ]; then
+  echo "Error: The script must be run from the 'AMR' directory."
+  exit 1
+fi
+
 # Define the output file, located in ./data-raw
-output_file="gpt_training_text.txt"
+output_file="data-raw/gpt_training_text.txt"
 
 # Clear the output file if it exists
 echo "This files contains all context you must know about the AMR package for R."> "$output_file"
@@ -12,16 +18,16 @@ remove_header() {
   sed '/# =\{6,\}/,/# =\{6,\}/d' "$1"
 }
 
-# Process all .R files in the '../R' folder
+# Process all .R files in the 'R' folder
-for file in ../R/*.R; do
+for file in R/*.R; do
   echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
   remove_header "$file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
 done
 
-# Process all .Rmd files in the '../vignettes' folder
+# Process all .Rmd files in the 'vignettes' folder
-for file in ../vignettes/*.Rmd; do
+for file in vignettes/*.Rmd; do
   echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
   remove_header "$file" >> "$output_file"
@@ -29,7 +35,7 @@ for file in ../vignettes/*.Rmd; do
 done
 
 # Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
-for file in ../DESCRIPTION ../NAMESPACE ../index.md; do
+for file in DESCRIPTION NAMESPACE index.md; do
   if [[ -f $file ]]; then
     echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
     echo -e "\n\n" >> "$output_file"
@@ -38,16 +44,16 @@ for file in ../DESCRIPTION ../NAMESPACE ../index.md; do
   fi
 done
 
-# Process test files (if available) in the '../tests' folder
+# Process test files (if available) in the 'tests' folder
-for file in ../tests/*.R; do
+for file in tests/*.R; do
   echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
   remove_header "$file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
 done
 
-# Process all .Rd files from the '../man' folder
+# Process all .Rd files from the 'man' folder
-for file in ../man/*.Rd; do
+for file in man/*.Rd; do
   echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
   remove_header "$file" >> "$output_file"