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(v3.0.0.9036) Modernise messaging infrastructure to use cli markup (#265)
* Modernise messaging infrastructure with cli support
Rewrites message_(), warning_(), stop_() to use cli::cli_inform(),
cli::cli_warn(), and cli::cli_abort() when the cli package is available,
with a fully functional plain-text fallback for environments without cli.
Key changes:
- New cli_to_plain() helper converts cli inline markup ({.fun}, {.arg},
{.val}, {.field}, {.cls}, {.pkg}, {.href}, {.url}, etc.) to readable
plain-text equivalents for the non-cli fallback path
- word_wrap() simplified: drops add_fn, ANSI re-index algorithm, RStudio
link injection, and operator spacing hack; returns pasted input unchanged
when cli is available
- stop_() no longer references AMR_env$cli_abort; uses pkg_is_available()
directly; passes sys.call() objects to cli::cli_abort() call= argument
- Removed add_fn parameter from message_(), warning_(), and word_wrap()
- All call sites across R/ updated: add_fn arguments removed, some paste0-
based string construction converted to cli glue syntax ({.fun as.mo},
{.arg col_mo}, {n} results, etc.)
- cli already listed in Suggests; no DESCRIPTION dependency changes needed
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace {.fun} with {.help} for all exported functions in messaging
All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Qualify all {.help} tags with AMR:: and convert backtick ?func references
- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Require cli >= 3.0.0 for cli_inform/cli_warn/cli_abort availability checks
cli_inform, cli_warn, and cli_abort were introduced in cli 3.0.0.
Add min_version = "3.0.0" (as character) to all four pkg_is_available("cli")
checks so older cli versions fall back to base R messaging.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Implement cli::code_highlight() for R code examples in messages (issue #191)
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
* Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
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
* Add {.topic} markup for non-function help page references
Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.
Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).
Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.
Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix {.topic} to use required pkg::topic format with display text
{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).
Use the [display_text](pkg::topic) form throughout:
{.topic [AMR-options](AMR::AMR-options)}
{.topic [AMR-deprecated](AMR::AMR-deprecated)}
The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.
The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix regexec() calls: remove perl=TRUE unsupported in older R
regexec() only gained the perl argument in R 4.1.0. The CI matrix
covers oldrel-1 through oldrel-4 (R 3.x/4.0.x), so perl=TRUE caused
an 'unused argument' error on every message_() call in those
environments.
All four affected regexec() calls use POSIX-extended compatible
patterns, so dropping perl=TRUE is safe.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Slim CI matrix for PRs to ubuntu-latest / r-release only
For pull requests, check-recent now runs a single job (ubuntu-latest,
r-release) via a setup job that emits the matrix as JSON. On push and
schedule the full matrix is unchanged (devel + release on all OSes,
oldrel-1 through oldrel-4).
Also removed the pull_request trigger from check-recent-dev-pkgs; the
dev-packages check only needs to run on push/schedule.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Restrict dev-versions and old-tinytest CI to main branch only
Both workflows were triggering on every push to every branch.
Narrowed push trigger to [main] so they only run after merging,
not on every feature/PR branch push.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Update NEWS.md to continuous log + add concise style rules to CLAUDE.md
NEWS.md is now a single continuous log under one heading per dev series,
not a new section per version bump. CLAUDE.md documents: only replace
line 1 (heading), append new entries, keep them extremely concise with
no trailing full stop.
Merged 9035 and 9036 entries into one section; condensed verbose 9036
bullets; added CI workflow change entry.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace single-quoted literals in messaging calls with cli markup
Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')
Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging
- 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)}
- "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax
- Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}}
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace glue-style dynamic markup with paste0() construction
{.field {variable}} and {.cls {variable}} patterns rely on glue
evaluation which is not safe in a zero-dependency package. Replace
all four occurrences with paste0("{.field ", var, "}") so the value
is baked into the markup string before reaching message_()/stop_().
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in check-recent workflow
push: branches: '**' caused both the push event (9-worker matrix) and
the pull_request event (1-worker matrix) to fire simultaneously on every
PR commit. Restricting push to [main] means PR pushes only trigger the
pull_request path (1 worker), while direct pushes to main still get the
full 9-worker matrix.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in code-coverage workflow
Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace bare backticks with cli inline markup across all messaging calls
- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Pre-evaluate inline expressions, add format_inline_(), fix print.ab
- All bare {variable}/{expression} in message_()/warning_()/stop_() calls
are now pre-evaluated via paste0(), so users without cli/glue never see
raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R,
antibiogram.R, atc_online.R)
- Add format_inline_() helper: formats a cli-markup string and returns it
(not emits it), using cli::format_inline() when available and cli_to_plain()
otherwise
- Rewrite .onAttach to use format_inline_() for all packageStartupMessage
calls; also adds {.topic} link and {.code} markup for option names
- print.ab: pre-evaluate function_name via paste0 (no .envir needed),
apply highlight_code() to each example bullet for R syntax highlighting
- join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* Replace all "in \`funcname()\`:" with {.help [{.fun funcname}](AMR::funcname)}
Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.
Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* definitive
* version fix
---------
Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
GitHub
50
R/ab.R
50
R/ab.R
@@ -191,12 +191,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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x_new[known_codes_cid] <- AMR_env$AB_lookup$ab[match(x[known_codes_cid], AMR_env$AB_lookup$cid)]
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previously_coerced <- x %in% AMR_env$ab_previously_coerced$x
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x_new[previously_coerced & is.na(x_new)] <- AMR_env$ab_previously_coerced$ab[match(x[is.na(x_new) & x %in% AMR_env$ab_previously_coerced$x], AMR_env$ab_previously_coerced$x)]
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previously_coerced_mention <- x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
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previously_coerced_mention <- !is.na(x) & x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
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if (any(previously_coerced_mention) && isTRUE(info) && message_not_thrown_before("as.ab", entire_session = TRUE)) {
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only_one <- length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) == 1
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message_(
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"Returning previously coerced ",
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ifelse(length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) > 1, "value for an antimicrobial", "values for various antimicrobials"),
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". Run `ab_reset_session()` to reset this. This note will be shown once per session."
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"Returning ", ifelse(only_one, "a ", ""), "previously coerced ",
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ifelse(only_one, "value for an antimicrobial", "values for various antimicrobials"),
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". Run {.help [{.fun ab_reset_session}](AMR::ab_reset_session)} to reset this. This note will be shown once per session."
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)
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}
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@@ -210,7 +211,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
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on.exit(close(progress))
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if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
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warning_("in `as.ab()`: some input seems to resemble antiviral drugs - use `as.av()` or e.g. `av_name()` for these, not `as.ab()` or e.g. `ab_name()`.")
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warning_("in {.help [{.fun as.ab}](AMR::as.ab)}: some input seems to resemble antiviral drugs - use {.help [{.fun as.av}](AMR::as.av)} or e.g. {.help [{.fun av_name}](AMR::av_name)} for these, not {.help [{.fun as.ab}](AMR::as.ab)} or e.g. {.help [{.fun ab_name}](AMR::ab_name)}.")
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}
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}
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@@ -444,7 +445,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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# take failed ATC codes apart from rest
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if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
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warning_(
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"in `as.ab()`: these ATC codes are not (yet) in the antimicrobials data set: ",
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"in {.help [{.fun as.ab}](AMR::as.ab)}: these ATC codes are not (yet) in the antimicrobials data set: ",
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vector_and(x_unknown_ATCs), "."
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)
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}
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@@ -458,12 +459,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
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if (length(x_unknown) > 0 && fast_mode == FALSE) {
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warning_(
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"in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
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"in {.help [{.fun as.ab}](AMR::as.ab)}: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
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vector_and(x_unknown), "."
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)
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}
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# Throw note about uncertainties
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x_uncertain <- x_uncertain[!is.na(x_uncertain)]
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AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[!is.na(AMR_env$ab_previously_coerced$x), ]
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if (isTRUE(info) && length(x_uncertain) > 0 && fast_mode == FALSE) {
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x_uncertain <- unique(x_uncertain)
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if (message_not_thrown_before("as.ab", "uncertainties", x_bak)) {
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@@ -481,7 +484,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
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}
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message_(
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"Antimicrobial translation was uncertain for ", examples,
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". If required, use `add_custom_antimicrobials()` to add custom entries."
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". If required, use {.help [{.fun add_custom_antimicrobials}](AMR::add_custom_antimicrobials)} to add custom entries."
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)
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}
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}
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@@ -551,14 +554,25 @@ type_sum.ab <- function(x, ...) {
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print.ab <- function(x, ...) {
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if (!is.null(attributes(x)$amr_selector)) {
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function_name <- attributes(x)$amr_selector
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message_(
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"This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
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" ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
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" ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
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" ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
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" ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
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" ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
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)
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if (pkg_is_available("cli", min_version = "3.0.0")) {
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cli::cli_inform(c(
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"i" = paste0("This {.cls ab} vector was retrieved using {.fun ", function_name, "}, which should normally be used inside a {.pkg dplyr} verb or {.cls data.frame} call, e.g.:"),
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paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(", function_name, "())"))),
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paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% select(column_a, column_b, ", function_name, "())"))),
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paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data %>% filter(any(", function_name, "() == \"R\"))"))),
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paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data[, ", function_name, "()]"))),
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paste0("\u00a0\u00a0", AMR_env$bullet_icon, " ", highlight_code(paste0("your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]")))
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))
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} else {
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message(word_wrap(paste0(
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"This 'ab' vector was retrieved using `", function_name, "()`, which should normally be used inside a dplyr verb or data.frame call, e.g.:\n",
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"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
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"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
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"\u00a0\u00a0", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
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"\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
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"\u00a0\u00a0", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
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), as_note = TRUE))
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}
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}
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cat("Class 'ab'\n")
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print(as.character(x), quote = FALSE)
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@@ -704,8 +718,8 @@ get_translate_ab <- function(translate_ab) {
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} else {
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translate_ab <- tolower(translate_ab)
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stop_ifnot(translate_ab %in% colnames(AMR::antimicrobials),
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"invalid value for 'translate_ab', this must be a column name of the `antimicrobials` data set\n",
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"or `TRUE` (equals 'name') or `FALSE` to not translate at all.",
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"invalid value for {.arg translate_ab}, this must be a column name of the {.topic [antimicrobials](AMR::antimicrobials)} data set\n",
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"or {.code TRUE} (equals {.val name}) or {.code FALSE} to not translate at all.",
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call = FALSE
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)
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translate_ab
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