diff --git a/DESCRIPTION b/DESCRIPTION index 4c2b3fc3c..65d02f4d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9137 +Version: 2.1.1.9138 Date: 2025-01-31 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ce22e36da..ac220914e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9137 +# AMR 2.1.1.9138 *(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 36cb78a22..ebb640a7b 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: 2.1.1.9137 +Version: 2.1.1.9138 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-2.1.1.9137-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl similarity index 52% rename from PythonPackage/AMR/dist/AMR-2.1.1.9137-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl index dd2332a73..01c8f42f5 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9137-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9138-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9137.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9137.tar.gz deleted file mode 100644 index a01684bf8..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9137.tar.gz and /dev/null 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 new file mode 100644 index 000000000..0caf2c52e Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9138.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index e8bf942bc..a88e40267 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='2.1.1.9137', + version='2.1.1.9138', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/data-raw/gpt_training_text_v2.1.1.9137.txt b/data-raw/gpt_training_text_v2.1.1.9138.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9137.txt rename to data-raw/gpt_training_text_v2.1.1.9138.txt index c148bacba..d379e4344 100644 --- a/data-raw/gpt_training_text_v2.1.1.9137.txt +++ b/data-raw/gpt_training_text_v2.1.1.9138.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 2.1.1.9137. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9138. 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 ba7fa255f..bdcb59210 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -115,7 +115,6 @@ call_functions <- c( "kable" = "knitr", "knit_print" = "knitr", "opts_chunk" = "knitr", - "rmarkdown" = "knitr", # pillar "pillar_shaft" = "pillar", "tbl_format_footer" = "pillar", @@ -141,8 +140,13 @@ call_functions <- c( ) import_functions <- c(import_functions, call_functions) -suggests <- desc::desc(".")$get_deps() -suggests <- suggests[which(suggests$type == "Suggests"), ]$package + +if (AMR:::pkg_is_available("desc")) { + suggests <- desc::desc(".")$get_deps() + suggests <- suggests[which(suggests$type == "Suggests"), ]$package +} else { + suggests <- import_functions +} for (i in seq_len(length(import_functions))) { fn <- names(import_functions)[i] pkg <- unname(import_functions[i])