diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml index 57668dab6..a33ddb311 100644 --- a/.github/workflows/check-current-testthat.yaml +++ b/.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 diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index fc5ed3cde..de3f52fdf 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 4bec57659..33eb2f717 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9215 -Date: 2025-03-16 +Version: 2.1.1.9216 +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 diff --git a/NEWS.md b/NEWS.md index 5dc62d16c..180d96ce2 100644 --- a/NEWS.md +++ b/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).)* diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh index ae38033c4..ed3963e1f 100644 --- a/data-raw/_generate_python_wrapper.sh +++ b/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: diff --git a/data-raw/gpt_training_text_v2.1.1.9215.txt b/data-raw/gpt_training_text_v2.1.1.9216.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9215.txt rename to data-raw/gpt_training_text_v2.1.1.9216.txt index 9973c3347..bde3bea84 100644 --- a/data-raw/gpt_training_text_v2.1.1.9215.txt +++ b/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: diff --git a/vignettes/AMR_for_Python.Rmd b/vignettes/AMR_for_Python.Rmd index ccb62fe0a..9db3f5cab 100755 --- a/vignettes/AMR_for_Python.Rmd +++ b/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: