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
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
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +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
8dab0a3730
(v3.0.0.9007) allow any tidyselect language in as.sir()
2025-07-17 14:29:35 +02:00
753f0e1ef9
(v3.0.0.9001) the first fixes
2025-06-04 13:10:20 +02:00
1710e220dd
AMR v3.0\!
2025-06-02 12:11:00 +02:00
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +02:00
2461631bce
(v2.1.1.9268) WISCA vignette, antibiogram sorting, fix translations
2025-05-01 14:45:21 +02:00
5e6bbdf3d1
(v2.1.1.9267) update ATCs
2025-05-01 11:48:49 +02:00
c70ac149ff
new WISCA vignette
2025-04-30 17:33:03 +02:00
6013a7edc5
(v2.1.1.9261) fix knit printing antibiograms
2025-04-29 16:29:12 +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
579025f678
(v2.1.1.9241) fix sir
2025-04-18 13:25:59 +02:00
cf91e677c6
(v2.1.1.9240) fix sir interpretation
2025-04-16 15:22:12 +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
bb110646db
(v2.1.1.9223) allow + ab
2025-03-20 22:56:32 +01:00
79f56ad8a4
(v2.1.1.9220) unit test
2025-03-19 16:13:43 +01:00
287e361a54
(v2.1.1.9218) Fix unit tests
2025-03-19 16:05:24 +01:00
4dc4398ad1
(v2.1.1.9217) allow + in amr selectors
2025-03-18 16:35:22 +01:00
32024e597a
(v2.1.1.9191) unit tests
2025-03-10 12:16:45 +01:00
a2c2be23c1
(v2.1.1.9190) antibiotics deprecation in antibiogram()
2025-03-09 10:41:11 +01:00
245483e41c
(v2.1.1.9188) fix antibiogram plot
2025-03-07 23:01:25 +01:00
b67613ce08
(v2.1.1.9187) WISCA fix
2025-03-07 22:27:21 +01:00
f7938289eb
(v2.1.1.9186) replace antibiotics with antimicrobials!
2025-03-07 20:43:26 +01:00
07efc292bc
(v2.1.1.9163) cleanup
2025-02-27 14:04:29 +01:00
195dfb4b91
(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram
2025-02-26 13:27:20 +01:00
b10989f431
(v2.1.1.9156) fix for knitr in WISCA
2025-02-23 19:18:42 +01:00
aa8f6af185
(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro
2025-02-23 11:18:08 +01:00
ef02f4a7f2
(v2.1.1.9151) update readme
2025-02-15 20:53:12 +01:00
9650545d6e
(v2.1.1.9150) unit tests
2025-02-15 13:40:51 +01:00
9d636983ac
(v2.1.1.9148) scale fix, antibiogram fix
2025-02-15 12:38:29 +01:00
d94efb0f5e
(v2.1.1.9147) scale fixes and WISCA update, fix conserved capped values
2025-02-14 14:16:46 +01:00
2171f05951
(v2.1.1.9143) unit tests
2025-02-07 19:18:55 +01:00
8ba2e4ed94
(v2.1.1.9141) new AMR selectors, eucast overwrite arg
2025-02-07 18:01:22 +01:00
baea4323c7
(v2.1.1.9140) WISCA fix
2025-02-05 20:48:35 +01:00
700522b466
(v2.1.1.9135) documentation fix
2025-01-28 15:16:55 +01:00
e740aa691b
(v2.1.1.9134) add Gamma to WISCA documentation
2025-01-27 23:11:10 +01:00
2561494e06
(v2.1.1.9133) update math formulae
2025-01-27 22:43:35 +01:00
1149360b27
(v2.1.1.9129) unit test fix
2025-01-27 16:17:03 +01:00
7accf6ff13
(v2.1.1.9127) unit tests
2025-01-27 10:46:43 +01:00
66833b4f5a
(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper
2025-01-26 23:01:17 +01:00
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
5c4d8fcd2a
(v2.1.1.9095) Python support
2024-10-15 17:12:55 +02:00
