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Implement cli::code_highlight() for R code examples in messages (issue #191)

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Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.

Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.

Fixes #191

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 22:23:39 +00:00
parent b7edf3e548
commit 10c00ff606
13 changed files with 34 additions and 26 deletions
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6
R/mo.R
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@@ -483,7 +483,7 @@ as.mo <- function(x,
}
} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
# keep synonyms is TRUE, so check if any do have synonyms
warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
warning_("{.help AMR::as.mo}() returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
}
# Apply Becker ----
@@ -907,7 +907,7 @@ rep.mo <- function(x, ...) {
print.mo_uncertainties <- function(x, n = 10, ...) {
more_than_50 <- FALSE
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to `as.mo()` or any `mo_*()` function are stored.\n\n")))
cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help AMR::as.mo}() or any mo_*() function are stored.\n\n")))
return(invisible(NULL))
} else if (NROW(x) > 50) {
more_than_50 <- TRUE
@@ -1032,7 +1032,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
#' @noRd
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of `as.mo()` or any `mo_*()` function are stored.\n")))
cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help AMR::as.mo}() or any mo_*() function are stored.\n")))
return(invisible(NULL))
}