⚠️ SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026).
Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
Package:
- stop_() called cli::ansi_has_hyperlink_support() before checking that cli is available, so without cli every error became "there is no package called 'cli'"
- interpretive_rules() failed on R 3.0 for guidelines without AmpC rules (assignment to zero rows)
- Guard the ggplot2 example of wisca_plot()
CI:
- check-old: R 3.0 could not install tinytest over HTTPS, so no unit tests ran; install it with curl, and fail when tinytest is missing or any test fails
- tinytest shim: record expectations in the test file environment, support skips and errors per test_that() block, add missing testthat equivalents, source helper files
- Add R 4.0 (oldrel-6) to check-old, and oldrel-5 to check-recent
* Update taxonomy of microorganisms (2026-10)
Rebuild of the microorganisms data set from COL 2026-04-18 XR, LPSN and BacDive of October 2026
and MycoBank of January 2026, with v3.0.1 as the previous data set: 111,103 records (v3.0.1:
78,679), 0 changed MO codes of existing names, 522 released codes retired (275 to be reviewed).
Script fixes (data-raw/_reproduction_scripts/reproduction_of_microorganisms.R):
- previous data set from the last release; COL read as COL Data Package (NameUsage.tsv)
- keep COL records without authors (a filter on NA dropped them, e.g. Balamuthia mandrillaris)
- genus homonyms: unclassified MycoBank entries are not authoritative; the released domain of a
genus wins if a source supports it (e.g. Moorella, Serpula, Pirella stay Bacteria)
- protect current names of relevant species instead of whole current genera (data set tripled)
- current names and synonyms only within the same domain and for known names (Brugia -> Lycoperdon)
- MycoBank names in Latin script only; old records outside their source's scope become manually added
- Graphium butterflies of v3.0.1 are not carried over, re-added or restored
- restore released taxa by name and rank; retire older cross-domain homonyms for review
- fill empty families from COL and a commented override list (Ascaris, Balamuthia)
- add Brugia malayi and B. timori; remove Salmonella species synonyms that are serovars
- BacDive: a minority of facultative strain records no longer decides (C. difficile)
- translate codes of other data sets with the development version; review unmatched codes
- scope decisions: COL XR names only if relevant or released; Protozoa follow the Fungi rules
Also: all checkpoints (data-raw/taxonomy*.rds), updated data sets, Bartlett et al. list, accessed
dates in TAXONOMY_VERSION, NEWS, two staphylococci added to CoNS, tests updated for real taxonomic
changes, known defects file removed (all solved), and the findings report with all review files in
data-raw/taxonomy_review/2026-10/.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: note on the .dta export and the single commit
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Fix as.mo() for Salmonella serovars written with the species; add S. xeri to CoNS
- "Salmonella enterica (subsp. enterica) serovar Typhi" returned S. bongori, and
"S. enterica Typhimurium" S. enterica diarizonae; "Paratyphi A/B/C" became serogroups
- Staphylococcus xeri and S. parequorum confirmed as coagulase-negative
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy build: remove lichens (decision of 5 October 2026)
Fungi in the lichen-forming classes and the order Verrucariales are removed unless their genus is
clinically relevant, with the synonyms that point to them (4,155 records); released lichens are
restored. microorganisms now has 107,126 records (Fungi 45,739); all tests pass.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review decisions: microsporidia in Fungi, accepted names, missing protozoa
- all microsporidia in the Fungi (1,394 names of v3.0.1 from P_ to F_, old codes translated by name)
- Enterocytozoon bieneusi and Encephalitozoon cuniculi as accepted names (accepted_name_override)
- Balantidium and Isospora added to MO_RELEVANT_GENERA; Cystoisospora belli as synonym of Isospora belli
- synonym cycles decided: Capillidium and Scolecobasidium are the current genera
- removed the stale data-raw/taxonomy_lpsn0.rds
- microorganisms now has 107,253 records; all tests pass
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: all items reviewed
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Rule matching by accepted taxon; Erysipelatoclostridium as synonym of Thomasclavelia
- interpretive_rules(): species named in a rule (literal names, genus_species/fullname) now also match all other
names of the same accepted taxon, e.g. 'Clostridium ramosum' for Thomasclavelia ramosa; not for genera or regex rules
- Erysipelatoclostridium and its species are synonyms of Thomasclavelia (accepted_name_override); E. merdavium is
retired by decision of 6 October 2026, and the build removes taxa retired by a human decision
- microorganisms patched with the same logic as the build script (no full rebuild): 107,252 records
- intrinsic_resistant regenerated with the new taxonomy and rule matching: 308,646 rows
- clinical_breakpoints: EUCAST workbook rows merged again, 24 EUCAST 2026 rows moved from C. ramosum to T. ramosa
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy: correct records for names listed twice, no synonyms without a current name, strict data tests
- one record per name keeps the accepted record (e.g. Eggerthella lenta, Gordonia amarae, Anisakis simplex and
Enterobius vermicularis were synonyms without a current name), links to dropped records are moved
- LPSN lookup reads the taxonomic status and correct name; validly published synonyms are no longer 'accepted'
- synonyms without a current name: linked via LPSN or removed, released codes retired (3,668); records with kept
children become 'unknown'; the M. tuberculosis complex is protected (decisions of 7 October 2026)
- subspecies codes reserved, current names of synonyms kept when pruning, missing parent records added or moved,
higher taxonomy harmonised, shared identifiers resolved per domain and rank, pointers and parent links cleaned
- data sets refer only to current names (except intrinsic_resistant); group members only from current names;
internal CoNS/CoPS/streptococcal lists keep a synonym only with its current name
- intrinsic_resistant, clinical_breakpoints (EUCAST workbooks) and microorganisms.groups regenerated
- 28 new tests in test-data.R; devtools::test(): 1,581 expectations, 0 failures
- open decisions listed in data-raw/taxonomy_review/2026-10/REPORT.md, section 6
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy: protect WHO priority genera, follow LPSN for the M. tuberculosis complex, place protist groups in one domain
- all taxa of the genera in MO_WHO_PRIORITY_GENERA are protected, also names that are not validly published
(replaces the hard-coded M. tuberculosis complex; keeps e.g. Klebsiella quasivariicola, M. canettii, M. orygis)
- LPSN is followed for the M. tuberculosis complex: M. bovis, M. africanum, M. caprae, M. microti and M. pinnipedii
are heterotypic synonyms of M. tuberculosis (Riojas et al. 2018); a test enforces this
- labyrinthulids in the Chromista (Aplanochytrium), Dictydiaethalium in the Protozoa (genus_domain_move), and the
rank suffix also between domains ('Acantharia {class}' next to the fungal genus Acantharia)
- devtools::test(): 1,582 expectations, 0 failures
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy build no longer depends on the previous build
- intrinsic_resistant is no input of the microorganisms build anymore (it is computed from it); the genera named in
the interpretive rules are read from the rules instead
- the previous data set no longer makes genera relevant; Debaryomyces added to MO_RELEVANT_GENERA
- new run_after_microorganisms_build.R recreates microorganisms.groups, the EUCAST breakpoints and
intrinsic_resistant in the right order, and the build runs it at its end
- reproduction_of_intrinsic_resistant.R uses devtools::load_all() instead of the installed package
- effect: 24 never released, not relevant COL records less; devtools::test(): 1,582 expectations, 0 failures
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* Taxonomy review report: summary updated to the second round
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
* MO code retirements: mark the 265 reviewed retirements as reviewed
The Graphium and v2.x Protozoa retirements were reviewed and accepted on 6 October 2026 (see the taxonomy review
report, section 5); 'NEEDS REVIEW' is replaced by 'reviewed by Matthijs S. Berends on 2026-10-06'.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
* Generalise interpretive rules for multi-guideline support (#268)
- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider
column (value: "EUCAST") to distinguish future CLSI rows
- Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R;
filter by rule.provider == guideline when applying rules in interpretive_rules()
- Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class
"custom_interpretive_rules"; old function becomes a deprecated wrapper in
zz_deprecated.R; backward-compat S3 dispatch shims added for old class
- Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors
- Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF
for transitional compatibility until sysdata.rda is regenerated
https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
* Fix namespace load failure: remove assignInNamespace from .onLoad (#268)
assignInNamespace cannot add NEW bindings to a locked package namespace
(R locks namespace bindings before .onLoad runs). Replace the .onLoad
shim with a runtime fallback inside interpretive_rules(): if
INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive
it from EUCAST_RULES_DF by adding the rule.provider column. This also
fixes the screening_abx line to reuse the already-resolved
interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF
reference.
https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
* fixes
* fixes
---------
Co-authored-by: Claude <noreply@anthropic.com>
* 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
* Replace {.fun} with {.help} for all exported functions in messaging
All function names referenced via {.fun …} in cli-style messages are
exported in NAMESPACE, so {.help …} is the appropriate markup — it
renders as a clickable help link rather than plain function styling.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Qualify all {.help} tags with AMR:: and convert backtick ?func references
- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Require cli >= 3.0.0 for cli_inform/cli_warn/cli_abort availability checks
cli_inform, cli_warn, and cli_abort were introduced in cli 3.0.0.
Add min_version = "3.0.0" (as character) to all four pkg_is_available("cli")
checks so older cli versions fall back to base R messaging.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Implement cli::code_highlight() for R code examples in messages (issue #191)
Add highlight_code() helper that wraps cli::code_highlight() when cli >= 3.0.0
is available, falling back to plain code otherwise. Apply it to all inline
R code examples embedded in message/warning/stop strings across the package.
Also convert remaining backtick-quoted function and argument references in
messaging calls to proper cli markup: {.help AMR::fn}(), {.arg arg},
{.code expr}, and {.pkg pkg} throughout ab.R, ab_from_text.R, av_from_text.R,
amr_selectors.R, count.R, custom_antimicrobials.R, custom_microorganisms.R,
interpretive_rules.R, mo.R, mo_property.R, sir.R, sir_calc.R.
Fixes#191https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix {.help} markup to use correct cli link format [{.fun fn}](AMR::fn)
Replace all instances of {.help AMR::fn}() (incorrect format with manual
parentheses outside the link) with {.help [{.fun fn}](AMR::fn)} which is
the correct cli hyperlink syntax: the display text [{.fun fn}] renders the
function name with parentheses automatically, and (AMR::fn) is the link target.
Also update the plain-text fallback handler in aa_helper_functions.R to
extract the display text from the [text](topic) markdown link format,
so that non-cli environments show just the function name (e.g. `fn()`),
not the raw link markup.
Dynamic cases in amr_selectors.R and mo_property.R also updated.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Add {.topic} markup for non-function help page references
Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.
Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).
Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.
Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix {.topic} to use required pkg::topic format with display text
{.topic} in cli requires a package-qualified topic reference to generate
a valid x-r-help:pkg::topic URI. Bare {.topic AMR-options} produced a
malformed x-r-help:AMR-options URI (no package prefix).
Use the [display_text](pkg::topic) form throughout:
{.topic [AMR-options](AMR::AMR-options)}
{.topic [AMR-deprecated](AMR::AMR-deprecated)}
The hyphen in the topic name is fine as a URI string even though
AMR::AMR-options is not a valid R symbol expression.
The fallback handler in format_message() already handles the [text](uri)
form by extracting the display text, so plain-text output is unchanged.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Fix regexec() calls: remove perl=TRUE unsupported in older R
regexec() only gained the perl argument in R 4.1.0. The CI matrix
covers oldrel-1 through oldrel-4 (R 3.x/4.0.x), so perl=TRUE caused
an 'unused argument' error on every message_() call in those
environments.
All four affected regexec() calls use POSIX-extended compatible
patterns, so dropping perl=TRUE is safe.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Slim CI matrix for PRs to ubuntu-latest / r-release only
For pull requests, check-recent now runs a single job (ubuntu-latest,
r-release) via a setup job that emits the matrix as JSON. On push and
schedule the full matrix is unchanged (devel + release on all OSes,
oldrel-1 through oldrel-4).
Also removed the pull_request trigger from check-recent-dev-pkgs; the
dev-packages check only needs to run on push/schedule.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Restrict dev-versions and old-tinytest CI to main branch only
Both workflows were triggering on every push to every branch.
Narrowed push trigger to [main] so they only run after merging,
not on every feature/PR branch push.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Update NEWS.md to continuous log + add concise style rules to CLAUDE.md
NEWS.md is now a single continuous log under one heading per dev series,
not a new section per version bump. CLAUDE.md documents: only replace
line 1 (heading), append new entries, keep them extremely concise with
no trailing full stop.
Merged 9035 and 9036 entries into one section; condensed verbose 9036
bullets; added CI workflow change entry.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace single-quoted literals in messaging calls with cli markup
Converted bare 'value' strings inside stop_(), warning_(), message_()
to appropriate cli markup:
- {.val}: option values ('drug', 'dose', 'administration', 'SDD', 'logbook')
- {.cls}: class names ('sir', 'mo')
- {.field}: column names ('mo' in mo_source)
- {.code}: object/dataset names ('clinical_breakpoints')
Files changed: ab_from_text.R, av_from_text.R, sir.R, sir_calc.R, mo_source.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging
- 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)}
- "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax
- Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}}
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace glue-style dynamic markup with paste0() construction
{.field {variable}} and {.cls {variable}} patterns rely on glue
evaluation which is not safe in a zero-dependency package. Replace
all four occurrences with paste0("{.field ", var, "}") so the value
is baked into the markup string before reaching message_()/stop_().
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in check-recent workflow
push: branches: '**' caused both the push event (9-worker matrix) and
the pull_request event (1-worker matrix) to fire simultaneously on every
PR commit. Restricting push to [main] means PR pushes only trigger the
pull_request path (1 worker), while direct pushes to main still get the
full 9-worker matrix.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Limit push trigger to main in code-coverage workflow
Same fix as check-recent: push: branches: '**' caused the workflow to
run twice per PR commit (once for push, once for pull_request). Restricting
push to [main] ensures coverage runs only once per PR update.
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Replace bare backticks with cli inline markup across all messaging calls
- {.arg} for argument names in stop_/warning_/message_ calls
- {.cls} after "of class" text in format_class() and elsewhere
- {.fun} for function names (replaces `fn()` pattern)
- {.pkg} for tidyverse package names (dplyr, ggplot2)
- {.code} for code literals (TRUE, FALSE, expressions)
- Rewrite print.ab: use cli named-vector with * bullets and code
highlighting when cli >= 3.0.0; keep plain-text fallback otherwise
- Fix typo in as.sir(): "of must be" -> "or must be"
- switch sir.R verbose notes from message() to message_()
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* Pre-evaluate inline expressions, add format_inline_(), fix print.ab
- All bare {variable}/{expression} in message_()/warning_()/stop_() calls
are now pre-evaluated via paste0(), so users without cli/glue never see
raw template syntax (mo_source.R, first_isolate.R, join_microorganisms.R,
antibiogram.R, atc_online.R)
- Add format_inline_() helper: formats a cli-markup string and returns it
(not emits it), using cli::format_inline() when available and cli_to_plain()
otherwise
- Rewrite .onAttach to use format_inline_() for all packageStartupMessage
calls; also adds {.topic} link and {.code} markup for option names
- print.ab: pre-evaluate function_name via paste0 (no .envir needed),
apply highlight_code() to each example bullet for R syntax highlighting
- join_microorganisms: pre-evaluate {type} and {nrow(...)} expressions
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* Replace all "in \`funcname()\`:" with {.help [{.fun funcname}](AMR::funcname)}
Converts all "in `funcname()`:" prefixes in warning_()/message_()/stop_()
calls to the full {.help} link format for clickable help in supported
terminals. Also fixes adjacent backtick argument names to {.arg}.
Files changed: ab.R, ab_property.R, av.R, av_property.R, antibiogram.R,
key_antimicrobials.R, mdro.R, mic.R, mo.R, plotting.R
https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
* fixes
* definitive
* version fix
---------
Co-authored-by: Claude <noreply@anthropic.com>
