(v2.1.1.9216) PyPI access token

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

@@ -94,13 +94,3 @@ jobs:
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
-          artifact-name: 'AMR-{matrix.config.os}-r{matrix.config.r}-result'
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: 'AMR-{matrix.config.os}-r{matrix.config.r}-result'
-          path: |
-            /Users/runner/work/AMR/AMR/check/*.(zip|gz)
-            /Users/runner/work/AMR/AMR/check/**/*.(zip|gz)
-            /Users/runner/work/AMR/AMR/check/**/**/*.(zip|gz)
-          if-no-files-found: warn

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

@@ -39,7 +39,7 @@ jobs:
     runs-on: ubuntu-latest
     
     env:
-      PyPI_TOKEN: ${{ secrets.PyPI }}
+      PYPI_PAT: ${{ secrets.PYPI_PAT }}
     
     steps:
       - name: Checkout code
@@ -85,7 +85,7 @@ jobs:
           rm -rf PythonPackage
 
           git init
-          git remote add origin https://$PyPI_TOKEN@github.com/msberends/AMR
+          git remote add origin https://$PYPI_PAT@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"
@@ -94,4 +94,4 @@ jobs:
           git add .
           git commit -m "Python wrapper update"
           # git push origin python-wrapper --force
-          git push https://$PyPI_TOKEN@github.com/msberends/AMR.git python-wrapper --force
+          git push https://$PYPI_PAT@github.com/msberends/AMR.git python-wrapper --force

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9215
+Version: 2.1.1.9216
-Date: 2025-03-16
+Date: 2025-03-17
 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 2.1.1.9215
+# AMR 2.1.1.9216
 
 *(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/_generate_python_wrapper.sh

@@ -83,7 +83,10 @@ except metadata.PackageNotFoundError:
     python_amr_version = ''
 
 # R package version of AMR
-r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_lib_path}"))')[0]
+r_amr_version = robjects.r(f'as.character(packageVersion("AMR", lib.loc = "{r_amr_lib_path}"))')
+
+print(python_amr_version)
+print(r_amr_version)
 
 # Compare R and Python package versions
 if r_amr_version != python_amr_version:

data-raw/gpt_training_text_v2.1.1.9216.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 2.1.1.9215. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9216. 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.
 ----------------------------------------------------------------------------------------------------
@@ -8920,7 +8920,20 @@ The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) an
 
 This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
 
-# Install
+# Prerequisites
+
+This package was only tested with [`venv`](https://docs.python.org/3/library/venv.html). You can set up such a virtual environment by running:
+
+```python
+# for linux and macOS:
+python -m venv /path/to/new/virtual/environment
+# for Windows:
+python -m venv C:\path\to\new\virtual\environment
+```
+
+Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after the which the virtual environment is ready to work with.
+
+# Install AMR
 
 1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run:
 

vignettes/AMR_for_Python.Rmd

@@ -28,7 +28,20 @@ The `AMR` package for R is a powerful tool for antimicrobial resistance (AMR) an
 
 This Python package is a wrapper round the `AMR` R package. It uses the `rpy2` package internally. Despite the need to have R installed, Python users can now easily work with AMR data directly through Python code.
 
-# Install
+# Prerequisites
+
+This package was only tested with [`venv`](https://docs.python.org/3/library/venv.html). You can set up such a virtual environment by running:
+
+```python
+# for linux and macOS:
+python -m venv /path/to/new/virtual/environment
+# for Windows:
+python -m venv C:\path\to\new\virtual\environment
+```
+
+Then you can [activate the environment](https://docs.python.org/3/library/venv.html#how-venvs-work), after the which the virtual environment is ready to work with.
+
+# Install AMR
 
 1. Since the Python package is available on the official [Python Package Index](https://pypi.org/project/AMR/), you can just run: