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Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)

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Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.

Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.

Dynamic cases in amr_selectors.R and mo_property.R also updated.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 22:37:46 +00:00
parent 10c00ff606
commit 3928a3de55
18 changed files with 55 additions and 51 deletions
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8
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warning_("{.help AMR::as.mo}() returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) 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)
warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) 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 ----
@@ -907,14 +907,14 @@ 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 {.help AMR::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 [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
return(invisible(NULL))
} else if (NROW(x) > 50) {
more_than_50 <- TRUE
x <- x[1:50, , drop = FALSE]
}
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help AMR::mo_matching_score}().\n\n")))
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))
add_MO_lookup_to_AMR_env()
@@ -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 {.help AMR::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 [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
return(invisible(NULL))
}