From 6cc273bbc798fe6c7452e4ac0f269704a0a12c79 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Fri, 14 Mar 2025 17:12:12 +0100 Subject: [PATCH] (v2.1.1.9201) oops --- DESCRIPTION | 2 +- NEWS.md | 2 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- PythonPackage/AMR/dist/amr-2.1.1.9200.tar.gz | Bin 10104 -> 0 bytes ...ny.whl => amr-2.1.1.9201-py3-none-any.whl} | Bin 10280 -> 10281 bytes PythonPackage/AMR/dist/amr-2.1.1.9201.tar.gz | Bin 0 -> 10104 bytes PythonPackage/AMR/setup.py | 2 +- R/sir.R | 2 +- ....txt => gpt_training_text_v2.1.1.9201.txt} | 2 +- 9 files changed, 6 insertions(+), 6 deletions(-) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9200.tar.gz rename PythonPackage/AMR/dist/{amr-2.1.1.9200-py3-none-any.whl => amr-2.1.1.9201-py3-none-any.whl} (86%) create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9201.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9200.txt => gpt_training_text_v2.1.1.9201.txt} (99%) diff --git a/DESCRIPTION b/DESCRIPTION index 1c16a0e99..abc0d3183 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9200 +Version: 2.1.1.9201 Date: 2025-03-14 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index ec2cae4e4..ecf2538d8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9200 +# AMR 2.1.1.9201 *(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 73e2fa51e..06759f58a 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: 2.1.1.9200 +Version: 2.1.1.9201 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-2.1.1.9200.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9200.tar.gz deleted file mode 100644 index c9f9c4a58ccea03be7c5b4005ad15f67f478d570..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10104 zcmchcRZtvEw5@@`-Q9x(cPD6Y55e8t-Q8UR!69gZyX)X?e{d(b4KBmX;Z)t{`*iD8 z_paKt`s?2Pvio5*RRS_HmFBVy9MsIoosFBF>thIUb8@nKnz_SV203^fv^ANEo$K5P z223qxvYnsm)T(Vwh^DV)S@e`j$Y7 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z_N52)ZS47hnw|^J3HBgs;^bVtMqbr2{JW<9|CKf0T{a+s84dxU0{fB=!Eey`)8g$N z==LL?g|z?x_&5{rI`9mI&3RPsNlK31B~KrT6x~C*iPGC7l5%XFj>ut_dm;NKXU&<+ zn)^M^P{mMKS*^SE>w{i#7ffXs2K8tPgYG-P9sKvuiFH?3dLy`U2=xRsPxyAj?{!En zLT8;IivruJU#s39z3ePsj!=V? zE?X4O8m79w4N=0OV literal 0 HcmV?d00001 diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 95a66acb0..49a58a71a 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='2.1.1.9200', + version='2.1.1.9201', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/sir.R b/R/sir.R index 2c21d253f..85a2ce907 100755 --- a/R/sir.R +++ b/R/sir.R @@ -626,7 +626,7 @@ as.sir.disk <- function(x, ab = ab, guideline = guideline, uti = uti, - capped_mic_handling = FALSE, # there are no MICs here + capped_mic_handling = "standard", # will be ignored for non-MIC anyway add_intrinsic_resistance = add_intrinsic_resistance, reference_data = reference_data, substitute_missing_r_breakpoint = substitute_missing_r_breakpoint, diff --git a/data-raw/gpt_training_text_v2.1.1.9200.txt b/data-raw/gpt_training_text_v2.1.1.9201.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9200.txt rename to data-raw/gpt_training_text_v2.1.1.9201.txt index bacbf05da..204f10be1 100644 --- a/data-raw/gpt_training_text_v2.1.1.9200.txt +++ b/data-raw/gpt_training_text_v2.1.1.9201.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 2.1.1.9200. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9201. 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. ----------------------------------------------------------------------------------------------------