mirror of
https://github.com/msberends/AMR.git
synced 2026-03-25 19:32:22 +01:00
(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
@@ -263,8 +263,7 @@ first_isolate <- function(x = NULL,
|
||||
),
|
||||
""
|
||||
)
|
||||
),
|
||||
add_fn = font_red
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
@@ -272,7 +271,7 @@ first_isolate <- function(x = NULL,
|
||||
# -- mo
|
||||
if (is.null(col_mo)) {
|
||||
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
|
||||
stop_if(is.null(col_mo), "`col_mo` must be set")
|
||||
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
|
||||
}
|
||||
|
||||
# methods ----
|
||||
@@ -309,7 +308,7 @@ first_isolate <- function(x = NULL,
|
||||
# -- date
|
||||
if (is.null(col_date)) {
|
||||
col_date <- search_type_in_df(x = x, type = "date", info = info)
|
||||
stop_if(is.null(col_date), "`col_date` must be set")
|
||||
stop_if(is.null(col_date), "{.arg col_date} must be set")
|
||||
}
|
||||
|
||||
# -- patient id
|
||||
@@ -318,11 +317,11 @@ first_isolate <- function(x = NULL,
|
||||
# WHONET support
|
||||
x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
|
||||
col_patient_id <- "patient_id"
|
||||
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
|
||||
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for {.arg col_patient_id}")
|
||||
} else {
|
||||
col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
|
||||
}
|
||||
stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
|
||||
stop_if(is.null(col_patient_id), "{.arg col_patient_id} must be set")
|
||||
}
|
||||
|
||||
# -- specimen
|
||||
@@ -334,7 +333,7 @@ first_isolate <- function(x = NULL,
|
||||
check_columns_existance <- function(column, tblname = x) {
|
||||
if (!is.null(column)) {
|
||||
stop_ifnot(column %in% colnames(tblname),
|
||||
"Column '", column, "' not found.",
|
||||
"Column '{column}' not found.",
|
||||
call = FALSE
|
||||
)
|
||||
}
|
||||
@@ -363,9 +362,7 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
# remove testcodes
|
||||
if (!is.null(testcodes_exclude) && isTRUE(info) && message_not_thrown_before("first_isolate", "excludingtestcodes")) {
|
||||
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
|
||||
add_fn = font_red
|
||||
)
|
||||
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE))
|
||||
}
|
||||
|
||||
if (is.null(col_specimen)) {
|
||||
@@ -376,9 +373,7 @@ first_isolate <- function(x = NULL,
|
||||
if (!is.null(specimen_group)) {
|
||||
check_columns_existance(col_specimen, x)
|
||||
if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
|
||||
message_("Excluding other than specimen group '", specimen_group, "'",
|
||||
add_fn = font_red
|
||||
)
|
||||
message_("Excluding other than specimen group '", specimen_group, "'")
|
||||
}
|
||||
}
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
@@ -420,7 +415,6 @@ first_isolate <- function(x = NULL,
|
||||
if (abs(row.start) == Inf || abs(row.end) == Inf) {
|
||||
if (isTRUE(info)) {
|
||||
message_("=> Found ", font_bold("no isolates"),
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
@@ -429,7 +423,6 @@ first_isolate <- function(x = NULL,
|
||||
if (row.start == row.end) {
|
||||
if (isTRUE(info)) {
|
||||
message_("=> Found ", font_bold("1 first isolate"), ", as the data only contained 1 row",
|
||||
add_fn = font_black,
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
@@ -437,9 +430,8 @@ first_isolate <- function(x = NULL,
|
||||
}
|
||||
if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
|
||||
if (isTRUE(info)) {
|
||||
message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
|
||||
", as all isolates were different microbial species",
|
||||
add_fn = font_black,
|
||||
n_rows <- length(c(row.start:row.end))
|
||||
message_("=> Found {.strong ", n_rows, " first isolates}, as all isolates were different microbial species",
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
@@ -456,16 +448,16 @@ first_isolate <- function(x = NULL,
|
||||
if (!is.null(col_keyantimicrobials)) {
|
||||
if (isTRUE(info) && message_not_thrown_before("first_isolate", "type")) {
|
||||
if (type == "keyantimicrobials") {
|
||||
message_("Basing inclusion on key antimicrobials, ",
|
||||
message_(
|
||||
"Basing inclusion on key antimicrobials, ",
|
||||
ifelse(ignore_I == FALSE, "not ", ""),
|
||||
"ignoring I",
|
||||
add_fn = font_red
|
||||
"ignoring I"
|
||||
)
|
||||
}
|
||||
if (type == "points") {
|
||||
message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
|
||||
points_threshold,
|
||||
add_fn = font_red
|
||||
message_(
|
||||
"Basing inclusion on all antimicrobial results, using a points threshold of ",
|
||||
points_threshold
|
||||
)
|
||||
}
|
||||
}
|
||||
@@ -524,9 +516,7 @@ first_isolate <- function(x = NULL,
|
||||
if (any(!is.na(x$newvar_is_icu)) && any(x$newvar_is_icu == TRUE, na.rm = TRUE)) {
|
||||
if (icu_exclude == TRUE) {
|
||||
if (isTRUE(info)) {
|
||||
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
|
||||
add_fn = font_red
|
||||
)
|
||||
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.")
|
||||
}
|
||||
x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
|
||||
} else if (isTRUE(info)) {
|
||||
@@ -550,9 +540,8 @@ first_isolate <- function(x = NULL,
|
||||
paste0('"', x, '"')
|
||||
}
|
||||
})
|
||||
message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
|
||||
as_note = FALSE,
|
||||
add_fn = font_red
|
||||
message_("\nGroup: ", toString(paste0(names(group), " = ", group)), "\n",
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
}
|
||||
@@ -565,8 +554,7 @@ first_isolate <- function(x = NULL,
|
||||
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
|
||||
decimal.mark = decimal.mark, big.mark = big.mark
|
||||
),
|
||||
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')",
|
||||
add_fn = font_red
|
||||
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
|
||||
)
|
||||
}
|
||||
x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
|
||||
@@ -577,8 +565,7 @@ first_isolate <- function(x = NULL,
|
||||
"Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
|
||||
decimal.mark = decimal.mark, big.mark = big.mark
|
||||
),
|
||||
" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')",
|
||||
add_fn = font_red
|
||||
" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')"
|
||||
)
|
||||
}
|
||||
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
|
||||
@@ -624,7 +611,7 @@ first_isolate <- function(x = NULL,
|
||||
),
|
||||
p_found_total, " of total where a microbial ID was available)"
|
||||
),
|
||||
add_fn = font_black, as_note = FALSE
|
||||
as_note = FALSE
|
||||
)
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user