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(v2.1.1.9150) unit tests

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dr. M.S. (Matthijs) Berends 2025-02-15 13:40:51 +01:00
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commit 9650545d6e
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11 changed files with 14 additions and 10 deletions

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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9149
Version: 2.1.1.9150
Date: 2025-02-15
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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@ -1,4 +1,4 @@
# AMR 2.1.1.9149
# AMR 2.1.1.9150
*(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).)*

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@ -1,6 +1,6 @@
Metadata-Version: 2.2
Name: AMR
Version: 2.1.1.9149
Version: 2.1.1.9150
Summary: A Python wrapper for the AMR R package
Home-page: https://github.com/msberends/AMR
Author: Matthijs Berends

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@ -2,7 +2,7 @@ from setuptools import setup, find_packages
setup(
name='AMR',
version='2.1.1.9149',
version='2.1.1.9150',
packages=find_packages(),
install_requires=[
'rpy2',

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@ -364,7 +364,7 @@
#'
#' ureido <- antibiogram(example_isolates,
#' antibiotics = ureidopenicillins(),
#' syndromic_group = "name",
#' syndromic_group = "ward",
#' wisca = TRUE)
#'
#' # in an Rmd file, you would just need to return `ureido` in a chunk,

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@ -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 2.1.1.9149. Remember this whenever someone asks which AMR package version youre at.
First and foremost, you are trained on version 2.1.1.9150. Remember this whenever someone asks which AMR package version youre 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.
----------------------------------------------------------------------------------------------------
@ -2031,7 +2031,7 @@ antibiogram(example_isolates,
ureido <- antibiogram(example_isolates,
antibiotics = ureidopenicillins(),
syndromic_group = "name",
syndromic_group = "ward",
wisca = TRUE)
# in an Rmd file, you would just need to return `ureido` in a chunk,

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@ -400,7 +400,7 @@ antibiogram(example_isolates,
ureido <- antibiogram(example_isolates,
antibiotics = ureidopenicillins(),
syndromic_group = "name",
syndromic_group = "ward",
wisca = TRUE)
# in an Rmd file, you would just need to return `ureido` in a chunk,

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@ -128,7 +128,9 @@ expect_silent(plot(ab5))
expect_silent(plot(ab6))
expect_silent(plot(ab7))
expect_silent(plot(ab8))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_silent(plot(ab9))
}
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(ab1), "gg")
@ -139,5 +141,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(ab6), "gg")
expect_inherits(ggplot2::autoplot(ab7), "gg")
expect_inherits(ggplot2::autoplot(ab8), "gg")
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_inherits(ggplot2::autoplot(ab9), "gg")
}
}