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Pre-evaluate inline expressions, add format_inline_(), fix print.ab

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- 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
This commit is contained in:
Claude
2026-03-19 10:39:26 +00:00
parent 1dabd4df3d
commit 51f689b069
10 changed files with 44 additions and 33 deletions
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DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.1.9037
Version: 3.0.1.9038
Date: 2026-03-19
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)