(v2.1.1.9142) unit test fix

.github/workflows/check-current-testthat.yaml

@@ -86,7 +86,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, any::pkgload
+          extra-packages: any::rcmdcheck
           needs: check
           upgrade: 'TRUE'
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9141
+Version: 2.1.1.9142
 Date: 2025-02-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9141
+# AMR 2.1.1.9142
 
 *(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).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9141
+Version: 2.1.1.9142
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9141',
+    version='2.1.1.9142',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/eucast_rules.R

@@ -460,16 +460,14 @@ eucast_rules <- function(x,
   # >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
   if (any(c("all", "other") %in% rules)) {
     if (isTRUE(info)) {
-      cat("\n")
+      cat(paste0("\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
       cat(word_wrap(
-        font_bold(paste0(
-          "Rules by this AMR package (",
-          font_red(paste0(
-            "v", utils::packageDescription("AMR")$Version, ", ",
-            format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y")
-          )), "), see `?eucast_rules`\n"
-        ))
+        paste0("Rules by the ",
+               font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
+               " (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
+               "), see `?eucast_rules`\n")
       ))
+      cat("\n\n")
     }
     ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE]
     colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name")
@@ -495,8 +493,8 @@ eucast_rules <- function(x,
 
         ## Set base to R where base + enzyme inhibitor is R ----
         rule_current <- paste0(
-          ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ",
-          tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R"
+          ab_enzyme$base_name[i], " (`", col_base, "`) = R if ",
+          tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R"
         )
         if (isTRUE(info)) {
           cat(word_wrap(rule_current,
@@ -536,8 +534,8 @@ eucast_rules <- function(x,
 
         ## Set base + enzyme inhibitor to S where base is S ----
         rule_current <- paste0(
-          ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ",
-          tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S"
+          ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ",
+          tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S"
         )
 
         if (isTRUE(info)) {
@@ -559,7 +557,8 @@ eucast_rules <- function(x,
           original_data = x.bak,
           warned = warned,
           info = info,
-          verbose = verbose
+          verbose = verbose,
+          overwrite = overwrite
         )
         n_added <- n_added + run_changes$added
         n_changed <- n_changed + run_changes$changed
@@ -1037,9 +1036,9 @@ eucast_rules <- function(x,
     cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
 
     if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
-      cat("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
+      cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
     } else if (isTRUE(verbose)) {
-      cat("\n", word_wrap("Used 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data."), "\n\n", sep = "")
+      cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
     }
   }
 

data-raw/gpt_training_text_v2.1.1.9142.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 2.1.1.9141. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9142. 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.
 ----------------------------------------------------------------------------------------------------

tests/testthat/test-zzz.R

@@ -141,8 +141,7 @@ call_functions <- c(
 
 import_functions <- c(import_functions, call_functions)
 
-suggests <- tryCatch(strsplit(pkgload::pkg_desc()$get_field("Suggests"), "[,\n ]+")[[1]],
-                     error = function(e) unname(import_functions))
+suggests <- strsplit(utils::packageDescription("AMR")$Suggests, "[,\n ]+")[[1]]
 for (i in seq_len(length(import_functions))) {
   fn <- names(import_functions)[i]
   pkg <- unname(import_functions[i])