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(v2.1.1.9234) fix CLSI

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dr. M.S. (Matthijs) Berends
2025-04-07 17:36:01 +01:00
parent 1fdab84103
commit a905303296
18 changed files with 117 additions and 235 deletions
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24
R/aa_helper_functions.R
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@ -1191,12 +1191,16 @@ message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
}
has_colour <- function() {
if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
# disable on emacs, which only supports 8 colours
return(FALSE)
if (is.null(AMR_env$supports_colour)) {
if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
# disable on emacs, which only supports 8 colours
AMR_env$supports_colour <- FALSE
} else {
has_color <- import_fn("has_color", "crayon", error_on_fail = FALSE)
AMR_env$supports_colour <- !is.null(has_color) && isTRUE(has_color())
}
}
has_color <- import_fn("has_color", "crayon", error_on_fail = FALSE)
!is.null(has_color) && isTRUE(has_color())
isTRUE(AMR_env$supports_colour)
}
# set colours if console has_colour()
@ -1216,13 +1220,7 @@ try_colour <- function(..., before, after, collapse = " ") {
}
}
is_dark <- function() {
if (is.null(AMR_env$is_dark_theme) ||
is.null(AMR_env$current_theme) ||
(
!is.null(AMR_env$current_theme) &&
AMR_env$current_theme != tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) "")
)) {
AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
if (is.null(AMR_env$is_dark_theme)) {
AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
}
isTRUE(AMR_env$is_dark_theme)
@ -1545,7 +1543,7 @@ add_MO_lookup_to_AMR_env <- function() {
MO_lookup <- AMR::microorganisms
MO_lookup$kingdom_index <- NA_real_
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Bacteria" | as.character(MO_lookup$mo) == "UNKNOWN"), "kingdom_index"] <- 1
MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 1.25
MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 1.5
MO_lookup[which(MO_lookup$kingdom == "Chromista"), "kingdom_index"] <- 1.75