diff --git a/DESCRIPTION b/DESCRIPTION index 436912be3..46f0fda36 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9155 +Version: 2.1.1.9156 Date: 2025-02-23 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 434953dbb..ab955619a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9155 +# AMR 2.1.1.9156 *(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 7e2f2d1fd..8ae386eaf 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: 2.1.1.9155 +Version: 2.1.1.9156 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-2.1.1.9155-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9156-py3-none-any.whl similarity index 85% rename from PythonPackage/AMR/dist/AMR-2.1.1.9155-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9156-py3-none-any.whl index 42baddfc3..b5ad7360c 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9155-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9156-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9155.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9155.tar.gz deleted file mode 100644 index 5655fa851..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9155.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9156.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9156.tar.gz new file mode 100644 index 000000000..1c47897e5 Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9156.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 7caaa3f0a..0e25bbdcf 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='2.1.1.9155', + version='2.1.1.9156', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/antibiogram.R b/R/antibiogram.R index b9087166c..0afd42cee 100755 --- a/R/antibiogram.R +++ b/R/antibiogram.R @@ -1245,7 +1245,7 @@ knit_print.antibiogram <- function(x, italicise = TRUE, na = getOption("knitr.ka meet_criteria(italicise, allow_class = "logical", has_length = 1) meet_criteria(na, allow_class = "character", has_length = 1, allow_NA = TRUE) - if (isTRUE(italicise) && "mo" %in% colnames(attributes(x)$long_numeric)) { + if (!isTRUE(attributes(x)$wisca) && isTRUE(italicise) && "mo" %in% colnames(attributes(x)$long_numeric)) { # make all microorganism names italic, according to nomenclature names_col <- ifelse(isTRUE(attributes(x)$has_syndromic_group), 2, 1) x[[names_col]] <- italicise_taxonomy(x[[names_col]], type = "markdown") diff --git a/data-raw/gpt_training_text_v2.1.1.9155.txt b/data-raw/gpt_training_text_v2.1.1.9156.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9155.txt rename to data-raw/gpt_training_text_v2.1.1.9156.txt index ccdfd9f03..6f42d5e7b 100644 --- a/data-raw/gpt_training_text_v2.1.1.9155.txt +++ b/data-raw/gpt_training_text_v2.1.1.9156.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 2.1.1.9155. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9156. 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. ----------------------------------------------------------------------------------------------------