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
c0a394008e
(v3.0.1.9027) Fixes #252 and add documentation update regarding #253
2026-03-06 13:10:33 +01:00
60e8f2bae6
(v3.0.1.9026) fix ab_group(NA)
2026-03-06 12:41:27 +01:00
adee419f1c
v3.0.1
2025-09-20 17:14:07 +01:00
4d7c4ca52c
(v3.0.0.9027) skimr update and as.ab warning - fixes #234 , fixes #232
2025-09-10 13:32:52 +02:00
d94bdd2c6a
(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD
2025-07-17 17:05:41 +02:00
80f08f91da
(v2.1.1.9285) mdro fix
2025-05-21 16:51:40 +02:00
38cebc1541
(v2.1.1.9279) fix documentation, add foreign S3 exports to functions
2025-05-16 16:55:29 +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
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
49da312506
(v2.1.1.9228) repo cleaning
2025-03-28 11:17:49 +01:00
58d7aa8790
(v2.1.1.9199) fix eucast
2025-03-14 13:43:22 +01:00
07efc292bc
(v2.1.1.9163) cleanup
2025-02-27 14:04:29 +01:00
22afd918e6
(v2.1.1.9136) console colours, updated Suggests, added as.ab() improvement
2025-01-31 16:01:52 +01:00
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
1ca40e8d67
(v2.1.1.9079) fix for uti in as.sir()
2024-09-24 15:34:12 +02:00
ddb23b6e73
(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi
2024-09-19 11:44:56 +02:00
573c0346ed
(v2.1.1.9070) fix for mo_current mo (no-verify)
2024-07-19 18:05:49 +02:00
7258a491b9
(v2.1.1.9068) fix for mo_url() and as.mo() for synonyms
2024-07-17 14:29:55 +02:00
7f344836ea
(v2.1.1.9064) unit tests
2024-07-16 15:55:58 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +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
0d8a91db49
rename pre-commit hook to pre-commit checks (no-check)
2024-04-23 10:55:48 +02:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
ea2a4652e9
mouse-hover fixes
2023-07-12 15:27:43 +01:00
0c46f61260
MO group fixes
2023-07-12 15:04:48 +01:00
66eeeb4b88
cleanup
2023-07-11 14:29:40 +02:00
a4e2e25e3f
reftbl in plots, speedup for as.sir() and mo_validate
2023-07-10 16:43:46 +02:00
70c601ca11
breakpoints UTI interpretation fix
2023-07-10 13:41:52 +02:00
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
2d97cca6d9
fix reference_df endless loop
2023-06-26 13:52:02 +02:00
1d9ee39cc7
fix for mo codes
2023-06-22 15:24:18 +02:00
Dr. Matthijs Berends
f065945d7b
Update clinical breakpoints and fix some as.mo() bugs ( #117 )
...
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102 , fixes #112 , fixes #113 , fixes #114 , fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
9591688811
documentation update
2023-05-27 10:39:22 +02:00
766db4e21f
as.mo fix
2023-05-26 19:20:21 +02:00
c6135d2082
updated microorganism codes
2023-05-26 16:10:01 +02:00
0bcf55d3b6
improve as.mo()
2023-05-24 15:55:53 +02:00
91fa73dedf
add oxygen tolerance
2023-05-11 21:56:27 +02:00
bf08d136a0
fix coercing NA to custom codes, fixes #107
2023-05-08 13:04:18 +02:00
cabffb22fd
anaerobic codes
2023-04-17 11:26:19 +02:00
1a02d302d4
Fix translatable strings
2023-04-15 09:32:13 +02:00
147f9112e9
Fix some WHONET codes
2023-04-14 11:12:26 +02:00
80cfc503c2
check for 2.0
2023-03-12 13:02:37 +01:00
262598b8d7
support for old rsi arguments
2023-03-11 14:24:34 +01:00
4416394e10
website update
2023-02-26 21:26:58 +01:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
45a9697c84
unit tests
2023-02-12 17:10:48 +01:00
