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
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
63099cd81e
(v2.1.1.9232) is.mic() iteration, documentation cleanup
2025-03-31 10:51:31 +02:00
92c4fc0f94
(v2.1.1.9125) replace 'antibiotic selectors' with 'antimicrobial selectors'
2025-01-17 12:09:39 +01:00
1ca40e8d67
(v2.1.1.9079) fix for uti in as.sir()
2024-09-24 15:34:12 +02:00
640888f408
(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update
2024-07-16 14:53:17 +02:00
7be4dabbc0
support veterinary MIC/disk translation
2024-02-24 15:16:52 +01:00
acb534102b
new species groups, updated clinical breakpoints
2023-07-08 17:30:05 +02:00
9591688811
documentation update
2023-05-27 10:39:22 +02:00
80cfc503c2
check for 2.0
2023-03-12 13:02:37 +01:00
dad25302f2
make rsi work in more cases, documentation update
2023-02-22 14:38:57 +01:00
eef00069fd
add all options to documentation
2023-01-23 20:07:57 +01:00
19fd0ef121
sort sir history
2023-01-23 15:01:21 +01:00
Dr. Matthijs Berends
98e62c9af2
Replace RSI with SIR
2023-01-21 23:47:20 +01:00
593d740b84
documentation, file permissions
2023-01-19 12:54:53 +01:00
84ed8c32bb
documentation
2023-01-06 19:21:04 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
85e2fbe4a3
remove warnings from unit tests
2022-10-19 11:47:57 +02:00
Dr. Matthijs Berends
cd2acc4a29
New mo algorithm, prepare for 2.0
2022-10-05 09:12:22 +02:00
4d050aef7c
styled, unit test fix
2022-08-28 10:31:50 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
1c891cc90c
(v1.8.1.9003) set_mo_source() fix
2022-05-09 20:36:44 +02:00
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
f406319503
(v1.7.0.9000) package size
2021-05-30 22:14:38 +02:00
8fda473e49
(v1.5.0.9015) unit test fix, grouped first isolates
2021-02-04 16:48:16 +01:00
2eca8c3f01
(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement
2021-02-02 23:57:35 +01:00
286eaa9699
(v1.5.0.9010) MDRO vignette update, get_episode for < day
2021-01-24 14:48:56 +01:00
4eab095306
(v1.5.0.9006) major documentation update
2021-01-18 16:57:56 +01:00
afc325c314
(v1.4.0.9050) ab selectors base R
2020-12-27 20:32:40 +01:00
8b52f9b1be
(v1.4.0.9047) unit tests
2020-12-27 00:30:28 +01:00
acbd0cf7ca
(v1.4.0.9046) get_episode
2020-12-27 00:07:00 +01:00
df37584189
(v1.4.0.9044) mo tibble printing, mo_shortname() fix
2020-12-24 23:29:10 +01:00
128ebcfd62
(v1.4.0.9043) documentation update
2020-12-22 00:51:17 +01:00
ee70883246
(v1.4.0.9042) auto dark theme website
2020-12-21 22:46:29 +01:00
81af41da3a
(v1.4.0.9041) updates based on review
2020-12-17 16:22:25 +01:00
15c732703d
(v1.4.0.9015) bugfix
2020-11-10 16:35:56 +01:00
5a607abb36
(v1.4.0.9011) message formatting
2020-10-27 15:56:51 +01:00
4e9ccb4435
(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening
2020-10-19 17:09:19 +02:00
28e77680c5
(v1.4.0) matching score update
2020-10-08 11:16:03 +02:00
baf510183c
(v1.3.0.9038) prefinal 1.4.0
2020-10-04 19:26:43 +02:00
c19095a3d5
(v1.3.0.9026) eucast expert rules 3.2
2020-09-24 00:30:11 +02:00
4e40e42011
(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix
2020-09-18 16:05:53 +02:00
c4b87fe241
(v1.3.0.9014) as.mo() speed improvement
2020-09-03 12:31:48 +02:00
6ab468362d
(v1.2.0.9034) code cleaning
2020-07-13 09:17:24 +02:00
76fc8e1b14
(v1.2.0.9026) move to github
2020-07-08 14:48:06 +02:00
93a158aebd
(v1.2.0.9011) mo_domain(), improved error handling
2020-06-22 11:18:40 +02:00
ac12392da3
(v1.2.0.9008) ab_class improvement
2020-06-17 15:14:37 +02:00
ae1969b941
(v1.1.0.9019) mo_source fix
2020-05-25 01:01:14 +02:00
f68d71a5e0
(v1.1.0.9007) lose dependencies
2020-05-16 21:40:50 +02:00
