Claude
ad31fba556
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
2026-03-18 12:10:17 +00:00
8439e9c1d2
(v3.0.1.9035) fix loading in Positron
2026-03-18 10:32:11 +01:00
b6f8584994
(v3.0.1.9031) fix MDRO for non-RStudio terminal
2026-03-08 11:30:18 +01:00
499c830ee7
(v3.0.1.9020) unit test fixes
2026-02-09 13:16:36 +01:00
ba4c159154
(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()
...
Fixes #246
Fixes #254
Fixes #255
Fixes #256
2026-02-08 23:15:40 +01:00
2df2911cf4
(v3.0.1.9018) fixes #249
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updates AB groups
2026-01-16 10:57:03 +01:00
151af21f38
(v3.0.1.9005) re-add tidymodels implementation
2025-12-21 12:19:43 +01:00
0b24967b23
(v3.0.1.9001) fix antibiogram
2025-09-30 10:54:07 +02:00
10ba36821e
(v3.0.0.9034) fix MycoBank synonyms
2025-09-18 13:58:34 +01:00
39ea5f6597
(v3.0.0.9011) allow names for age_groups()
2025-07-17 19:32:46 +02:00
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +02:00
8dab0a3730
(v3.0.0.9007) allow any tidyselect language in as.sir()
2025-07-17 14:29:35 +02:00
72db2b2562
(v3.0.0.9003) eucast_rules fix, new tidymodels integration
2025-06-13 14:03:21 +02:00
139f79d372
(v2.1.1.9278) support AMR selectors in custom MDRO guideline
2025-05-16 11:20:19 +02:00
4b171745de
(v2.1.1.9276) mdro() fix
2025-05-15 10:39:48 +02:00
b8f0f64287
(v2.1.1.9269) Support 7 new languages
2025-05-02 19:25:19 +02:00
faa9ae0d85
(v2.1.1.9260) fix antibiogram
2025-04-29 16:15:18 +02:00
4e7fca3b38
(v2.1.1.9253) parallel computing
2025-04-26 15:47:00 +02:00
6135805455
(v2.1.1.9251) fix colour on GitHub docs
2025-04-21 16:04:01 +02:00
40d7a971c3
(v2.1.1.9236) documentation
2025-04-12 11:46:42 +02:00
36fd99e1f4
(v2.1.1.9235) New website!
2025-04-08 15:54:30 +01:00
a905303296
(v2.1.1.9234) fix CLSI
2025-04-07 17:36:01 +01:00
1fdab84103
(v2.1.1.9233) chore: make all argument texts full sentences
2025-03-31 14:53:24 +02:00
63099cd81e
(v2.1.1.9232) is.mic() iteration, documentation cleanup
2025-03-31 10:51:31 +02:00
d77ad6bd6e
(v2.1.1.9227) unit test fixes
2025-03-27 15:36:27 +01:00
bb110646db
(v2.1.1.9223) allow + ab
2025-03-20 22:56:32 +01:00
58d7aa8790
(v2.1.1.9199) fix eucast
2025-03-14 13:43:22 +01:00
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
9a9468fa84
(v2.1.1.9182) fix AMR selectors for tidymodels, add unit tests
2025-03-03 12:59:27 +01:00
07efc292bc
(v2.1.1.9163) cleanup
2025-02-27 14:04:29 +01:00
aa8f6af185
(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro
2025-02-23 11:18:08 +01:00
ecc4e25e75
(v2.1.1.9137) examples fix
2025-01-31 16:28:06 +01:00
22afd918e6
(v2.1.1.9136) console colours, updated Suggests, added as.ab() improvement
2025-01-31 16:01:52 +01:00
15fc72fc66
(v2.1.1.9121) support tidymodels
2024-12-19 20:17:15 +01:00
175a6777f3
(v2.1.1.9116) selectors as separate functions
2024-12-13 09:44:54 +01:00
5c4d8fcd2a
(v2.1.1.9095) Python support
2024-10-15 17:12:55 +02:00
681fe011fe
(v2.1.1.9082) algorithm updates
2024-09-30 18:46:55 +02:00
ac1c40d8bb
(v2.1.1.9081) HUGE microorganisms update for fungi!
2024-09-29 22:17:56 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
2dee1d71dc
(v2.1.1.9053) add verbose to as.sir(), unit test fix
2024-06-17 10:38:45 +02:00
bdbf5198a2
(v2.1.1.9050) vctrs fix for sir, small documentation fixes
2024-06-15 15:33:49 +02:00
9bf7584d58
(v2.1.1.9049) new 2024 breakpoints, add AMO, set NI instead of N
2024-06-14 22:39:01 +02:00
d214f74e25
allow column name for ab in as.sir()
2024-05-20 21:29:13 +02:00
08a27922a8
new SDD and N for as.sir()
2024-05-20 15:27:04 +02:00
0d8a91db49
rename pre-commit hook to pre-commit checks (no-check)
2024-04-23 10:55:48 +02:00
2899b3c840
new mo_group_members()
2024-04-19 10:18:21 +02:00
0039cb05d6
update MIC comparisons
2024-04-05 16:44:43 +02:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
6f417d0ef2
add scale_x_mic()
2023-12-03 01:06:00 +01:00
7cda9e575b
prepare for CRAN
2023-10-20 14:51:48 +02:00
