(v2.1.1.9211) fix python wrapper

.github/workflows/check-current-testthat.yaml

@@ -95,7 +95,12 @@ jobs:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
           
-      - name: Show files
+      - name: Debug: List all files in check directory
-        if: matrix.config.os == 'ubuntu-latest'
         run: |
-          ls -lh /home/runner/work/AMR/AMR/check/**/tests*/testthat/_snaps
+          find /Users/runner/work/AMR/AMR/check -type f
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: testthat-snapshots
+          path: /Users/runner/work/AMR/AMR/check/**/*snaps
+          if-no-files-found: warn

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

@@ -76,24 +76,18 @@ jobs:
 
       - name: Git push to python-wrapper branch
         run: |
-          git config user.name "GitHub Actions"
+          find . -mindepth 1 ! -path './PythonPackage*' -exec rm -rf {} +
-          git config user.email "<>"
-          
-          # Create and switch to python-wrapper branch (orphan if it doesn't exist)
-          git fetch origin python-wrapper || true
-          git checkout python-wrapper || git checkout --orphan python-wrapper
-          
-          # Delete all existing files from the working tree (safely)
-          git rm -rf . || true
-          mv .git PythonPackage/AMR/
-          ls -lh PythonPackage/AMR/
-          find . -mindepth 1 ! -name 'PythonPackage' -exec rm -rf {} +
 
           mv PythonPackage/AMR/* .
           rm -rf PythonPackage
-          ls -lh
 
-          # Commit and push if changes exist
+          git init
+          git remote add origin https://github.com/msberends/AMR
+          git checkout --orphan python-wrapper
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+          git rm -rf . || true
           git add .
-          git commit -m "Python wrapper update" || echo "No changes to commit"
+          git commit -m "Python wrapper update"
           git push origin python-wrapper --force

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9210
+Version: 2.1.1.9211
-Date: 2025-03-15
+Date: 2025-03-16
 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 2.1.1.9210
+# AMR 2.1.1.9211
 
 *(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/gpt_training_text_v2.1.1.9211.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 2.1.1.9210. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9211. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the NAMESPACE file, the index.md file, and all the man/*.Rd files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------