diff --git a/DESCRIPTION b/DESCRIPTION index 59ca6a083..f3ea2aa47 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9205 +Version: 2.1.1.9206 Date: 2025-03-15 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index c8fe47baf..823ef7351 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9205 +# AMR 2.1.1.9206 *(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/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index b456ef6c2..c9ae708e2 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -626,25 +626,28 @@ suppressMessages(reset_AMR_locale()) devtools::load_all(quiet = TRUE) suppressMessages(set_AMR_locale("English")) -# Update URLs ------------------------------------------------------------- -usethis::ui_info("Checking URLs for redirects") -invisible(urlchecker::url_update(".")) - -# Style pkg --------------------------------------------------------------- -usethis::ui_info("Styling package") -styler::style_pkg(include_roxygen_examples = FALSE, - exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")]) - -# Document pkg ------------------------------------------------------------ -files_changed <- function(paths = c("R/", "data/")) { +files_changed <- function(paths = "^(R|data)/") { tryCatch({ changed_files <- system("git diff --name-only", intern = TRUE) - any(changed_files %like% "^(R|data)/") + any(changed_files %like% paths) }, error = function(e) TRUE) } -if (interactive()) { - message("Skipping document in interactive mode") -} else if (files_changed()) { + +# Update URLs ------------------------------------------------------------- +if (files_changed()) { + usethis::ui_info("Checking URLs for redirects") + invisible(urlchecker::url_update(".")) +} + +# Style pkg --------------------------------------------------------------- +if (files_changed(paths = "^(R|tests)/")) { + sethis::ui_info("Styling package") + styler::style_pkg(include_roxygen_examples = FALSE, + exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")]) +} + +# Document pkg ------------------------------------------------------------ +if (files_changed()) { usethis::ui_info("Documenting package") suppressMessages(devtools::document(quiet = TRUE)) } diff --git a/data-raw/gpt_training_text_v2.1.1.9205.txt b/data-raw/gpt_training_text_v2.1.1.9206.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9205.txt rename to data-raw/gpt_training_text_v2.1.1.9206.txt index 870a22d94..f5636d7ed 100644 --- a/data-raw/gpt_training_text_v2.1.1.9205.txt +++ b/data-raw/gpt_training_text_v2.1.1.9206.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 2.1.1.9205. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9206. 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. ----------------------------------------------------------------------------------------------------