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AMR/DESCRIPTION
Matthijs Berends 4171d5b778 (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>
2026-03-20 17:01:34 +01:00

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Package: AMR
Version: 3.0.1.9036
Date: 2026-03-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Authors@R: c(
person(given = c("Matthijs", "S."), family = "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
person(given = c("Dennis"), family = "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
person(given = c("Erwin", "E.", "A."), family = "Hassing", role = c("aut", "ctb")),
person(given = c("Aislinn"), family = "Cook", role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
person(given = c("Andrew", "P."), family = "Norgan", role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
person(given = c("Anita"), family = "Williams", role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
person(given = c("Annick"), family = "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
person(given = c("Anthony"), family = "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
person(given = c("Anton"), family = "Mymrikov", role = "ctb"),
person(given = c("Bart", "C."), family = "Meijer", role = "ctb"),
person(given = c("Christian", "F."), family = "Luz", role = "ctb", comment = c(ORCID = "0000-0001-5809-5995")),
person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
person(given = c("Jonas"), family = "Salm", role = "ctb"),
person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
person(given = c("Casper", "J."), family = "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
person(given = c("Corinna"), family = "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")))
Depends: R (>= 3.0.0)
Suggests:
cleaner,
cli,
crayon,
curl,
data.table,
dplyr,
ggplot2,
knitr,
openxlsx,
parallelly,
pillar,
progress,
readxl,
recipes,
rlang,
rmarkdown,
rstudioapi,
rvest,
skimr,
testthat,
tibble,
tidymodels,
tidyselect,
tinytest,
vctrs,
xml2,
usethis
VignetteBuilder: knitr,rmarkdown
URL: https://amr-for-r.org, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE, old_usage = TRUE)
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