diff --git a/DESCRIPTION b/DESCRIPTION index 65d02f4d8..839ad37c9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9138 -Date: 2025-01-31 +Version: 2.1.1.9139 +Date: 2025-02-01 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 ac220914e..7847a9919 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9138 +# AMR 2.1.1.9139 *(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/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index ebb640a7b..6048f01fd 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9138 +Version: 2.1.1.9139 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9139-py3-none-any.whl similarity index 52% rename from PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9139-py3-none-any.whl index 01c8f42f5..5e476bb59 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9139-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9138.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9138.tar.gz deleted file mode 100644 index 0caf2c52e..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9138.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9139.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9139.tar.gz new file mode 100644 index 000000000..8703644fa Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9139.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index a88e40267..64c5d109a 100644 --- a/PythonPackage/AMR/setup.py +++ b/PythonPackage/AMR/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages setup( name='AMR', - version='2.1.1.9138', + version='2.1.1.9139', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/data-raw/gpt_training_text_v2.1.1.9138.txt b/data-raw/gpt_training_text_v2.1.1.9139.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9138.txt rename to data-raw/gpt_training_text_v2.1.1.9139.txt index d379e4344..ac6b904b5 100644 --- a/data-raw/gpt_training_text_v2.1.1.9138.txt +++ b/data-raw/gpt_training_text_v2.1.1.9139.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 2.1.1.9138. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9139. 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. ---------------------------------------------------------------------------------------------------- diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R index bdcb59210..57c7b0a2b 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -141,12 +141,7 @@ call_functions <- c( import_functions <- c(import_functions, call_functions) -if (AMR:::pkg_is_available("desc")) { - suggests <- desc::desc(".")$get_deps() - suggests <- suggests[which(suggests$type == "Suggests"), ]$package -} else { - suggests <- import_functions -} +suggests <- strsplit(utils::packageDescription(pkg = ".", lib.loc = ".", fields = "Suggests"), "[,\n ]+")[[1]] for (i in seq_len(length(import_functions))) { fn <- names(import_functions)[i] pkg <- unname(import_functions[i])