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
7df28bce28
(v3.0.1.9015) fix translations
2026-01-08 10:21:48 +01:00
7b9c151241
(v3.0.1.9014) try-again fix
2026-01-07 15:10:21 +01:00
85e8e814e8
(v3.0.1.9013) fix translations
2026-01-07 13:30:54 +01:00
fa827f27f4
(v3.0.1.9012) fix translations
2026-01-07 11:00:58 +01:00
cfbbfb4fa5
(v3.0.1.9007) fix #246
2026-01-06 23:08:50 +01:00
753f0e1ef9
(v3.0.0.9001) the first fixes
2025-06-04 13:10:20 +02:00
b8f0f64287
(v2.1.1.9269) Support 7 new languages
2025-05-02 19:25:19 +02:00
2461631bce
(v2.1.1.9268) WISCA vignette, antibiogram sorting, fix translations
2025-05-01 14:45:21 +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
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
a3071cf58b
(v2.1.1.9042) update translations and example isolates
2024-06-09 11:31:04 +02:00
af74e1d4f2
(v2.1.1.9041) antibiotics update
2024-06-08 17:35:25 +02:00
7cda9e575b
prepare for CRAN
2023-10-20 14:51:48 +02:00
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
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
bc434db835
bring back antibiogram(), without deps
2023-02-10 16:18:00 +01:00
1a0dc4bf46
revert back to pre-antibiogram
2023-02-09 13:07:39 +01:00
9e99e66f01
use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi
2023-02-06 11:57:22 +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
e4ea96cbf9
fix for R < 3.4
2022-12-30 12:57:27 +01:00
f619fb683b
support new mo codes
2022-12-27 15:16:15 +01:00
eed1c14b96
website update
2022-12-11 11:44:29 +01:00
b1ead9c0fe
doc update
2022-12-10 10:09:57 +01:00
e7d7b94b3e
no obligatory note on startup
2022-12-09 15:10:49 +01:00
56dad34e68
update prevalence with new phyla
2022-12-09 13:37:08 +01:00
7ca44fb756
cleanup and new intro logo
2022-11-13 13:44:25 +01:00
d40e0ef20b
completely updated antibiotics
2022-10-30 14:31:45 +01:00
4fe90092c7
fix for NA in as.ab()
2022-10-10 15:44:59 +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
303d61b473
new tibble export
2022-08-27 20:49:37 +02:00
952d16de33
new, automated website
2022-08-21 16:37:20 +02:00
7226b70c3d
update languages
2022-08-20 20:17:14 +02:00
3f2f60ab77
language updates
2022-08-19 12:33:14 +02:00
3b2b2be5f8
(v1.8.0.9002) as.rsi() cleanup, more informative warnings
2022-03-02 15:38:55 +01:00
25cef46c59
(v1.8.0) prerelease 1.8.0
2021-12-23 18:56:28 +01:00
1e66a3daf3
(v1.7.1.9068) new logo, unit tests
2021-12-12 11:07:02 +01:00
56f1ce328a
(v1.7.1.9067) Support for Swedish and Russian
2021-12-12 09:42:03 +01:00
37e6e35ec4
(v1.7.1.9051) updated taxonomy, updated git branch name
2021-10-06 13:23:57 +02:00
93a4734b44
(v1.7.1.9040) Support for Danish
2021-09-29 12:12:35 +02:00
1908e7cc7a
(v1.7.1.9000) ab_class update, unit tests
2021-06-04 21:07:55 +02:00
