.github/prehooks/pre-commit

@@ -49,6 +49,7 @@ if command -v Rscript > /dev/null; then
   if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
     Rscript -e "source('data-raw/_pre_commit_checks.R')"
     currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
+    bash data-raw/AMRforRGPT.sh
     echo "- Adding changed files in ./data-raw and ./man to this commit"
     git add data-raw/*
     git add man/*
@@ -111,8 +112,4 @@ echo ""
 # Save the version number for use in the commit-msg hook
 echo "${currentversion}" > .git/commit_version.tmp
 
-# Generate GPT knowledge info for our Assistant (https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant)
-bash data-raw/_generate_GPT_knowledge_input.sh "${currentversion}"
-git add data-raw/*
-
 exit 0

.github/workflows/publish-to-pypi.yml

@@ -59,9 +59,9 @@ jobs:
           bash _generate_python_wrapper.sh
       
       - name: Publish to PyPI
-        env:
+        # env:
-          TWINE_USERNAME: "__token__"
+        #   TWINE_USERNAME: "__token__"
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        #   TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
           cd data-raw/python_wrapper/AMR
           python -m twine upload dist/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9103
+Version: 2.1.1.9100
-Date: 2024-10-18
+Date: 2024-10-17
 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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9103
+# AMR 2.1.1.9100
 
 *(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).)*
 

R/sir.R

@@ -1739,12 +1739,12 @@ summary.sir <- function(object, ...) {
 c.sir <- function(...) {
   lst <- list(...)
   
-  guideline <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$guideline %or% NA_character_)
+  guideline <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$guideline %||% NA_character_)
-  mo <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$mo %or% NA_character_)
+  mo <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$mo %||% NA_character_)
-  ab <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ab %or% NA_character_)
+  ab <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ab %||% NA_character_)
-  method <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$method %or% NA_character_)
+  method <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$method %||% NA_character_)
-  ref_tbl <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_tbl %or% NA_character_)
+  ref_tbl <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_tbl %||% NA_character_)
-  ref_breakpoints <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_breakpoints %or% NA_character_)
+  ref_breakpoints <- vapply(FUN.VALUE = character(1), lst, function(x) attributes(x)$ref_breakpoints %||% NA_character_)
   
   out <- as.sir(unlist(lapply(list(...), as.character)))
   

data-raw/AMRforRGPT.sh

@@ -7,11 +7,10 @@ if [ "$(basename "$PWD")" != "AMR" ]; then
 fi
 
 # Define the output file, located in ./data-raw
-version="$1"
+output_file="data-raw/gpt_training_text.txt"
-output_file="data-raw/gpt_training_text_v${version}.txt"
 
 # Clear the output file if it exists
-echo "This files contains all context you must know about the AMR package for R." > "$output_file"
+echo "This files contains all context you must know about the AMR package for R."> "$output_file"
 echo -e "\n\n\n\n" >> "$output_file"
 
 # Function to remove header block (delimited by # ======)
@@ -21,7 +20,7 @@ remove_header() {
 
 # Process all .R files in the 'R' folder
 for file in R/*.R; do
-  echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  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"
@@ -29,7 +28,7 @@ done
 
 # Process all .Rmd files in the 'vignettes' folder
 for file in vignettes/*.Rmd; do
-  echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  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"
@@ -38,7 +37,7 @@ done
 # Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
 for file in DESCRIPTION NAMESPACE index.md; do
   if [[ -f $file ]]; then
-    echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+    echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
     echo -e "\n\n" >> "$output_file"
     cat "$file" >> "$output_file"
     echo -e "\n\n" >> "$output_file"
@@ -47,7 +46,7 @@ done
 
 # Process test files (if available) in the 'tests' folder
 for file in tests/*.R; do
-  echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  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"
@@ -55,7 +54,7 @@ done
 
 # Process all .Rd files from the 'man' folder
 for file in man/*.Rd; do
-  echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  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"