(v2.1.1.9205) Fix python wrapper

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

@@ -75,24 +75,24 @@ jobs:
           python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
 
       - name: Git push to python-wrapper branch
-          run: |
+        run: |
-            git config user.name "GitHub Actions"
+          git config user.name "GitHub Actions"
-            git config user.email "<>"
+          git config user.email "<>"
           
-            # Create and switch to python-wrapper branch (orphan if it doesn't exist)
+          # Create and switch to python-wrapper branch (orphan if it doesn't exist)
-            git fetch origin python-wrapper || true
+          git fetch origin python-wrapper || true
-            git checkout python-wrapper || git checkout --orphan python-wrapper
+          git checkout python-wrapper || git checkout --orphan python-wrapper
           
-            # Delete all existing files from the working tree (safely)
+          # Delete all existing files from the working tree (safely)
-            git rm -rf . || true
+          git rm -rf . || true
-            rm -rf * || true
+          rm -rf * || true
       
-            # Copy over only PythonPackage/AMR contents from main
+          # Copy over only PythonPackage/AMR contents from main
-            git checkout main -- PythonPackage/AMR
+          git checkout main -- PythonPackage/AMR
-            mv PythonPackage/AMR/* .
+          mv PythonPackage/AMR/* .
-            rm -rf PythonPackage
+          rm -rf PythonPackage
           
-            # Commit and push if changes exist
+          # Commit and push if changes exist
-            git add .
+          git add .
-            git commit -m "Python wrapper update" || echo "No changes to commit"
+          git commit -m "Python wrapper update" || echo "No changes to commit"
-            git push origin python-wrapper --force
+          git push origin python-wrapper --force

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9204
+Version: 2.1.1.9205
 Date: 2025-03-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9204
+# AMR 2.1.1.9205
 
 *(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/_pre_commit_checks.R

@@ -636,9 +636,15 @@ styler::style_pkg(include_roxygen_examples = FALSE,
                   exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")])
 
 # Document pkg ------------------------------------------------------------
+files_changed <- function(paths = c("R/", "data/")) {
+  tryCatch({
+    changed_files <- system("git diff --name-only", intern = TRUE)
+    any(changed_files %like% "^(R|data)/")
+  }, error = function(e) TRUE)
+}
 if (interactive()) {
   message("Skipping document in interactive mode")
-} else {
+} else if (files_changed()) {
   usethis::ui_info("Documenting package")
   suppressMessages(devtools::document(quiet = TRUE))
 }

data-raw/gpt_training_text_v2.1.1.9205.txt

@@ -1,6 +1,6 @@
 This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
 
-First and foremost, you are trained on version 2.1.1.9204. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9205. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the  file, the  file, and all the  files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------