diff --git a/DESCRIPTION b/DESCRIPTION index 786d353e3..f37cea002 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9080 +Version: 3.0.1.9081 Date: 2026-06-27 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 0d470520a..1b3fa465e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9080 +# AMR 3.0.1.9081 Planned as v3.1.0, end of June 2026. diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index 49a90e5e8..106fc433b 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -337,18 +337,16 @@ test_that("test-mo.R", { c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species") ) } -}) -test_that("as.mo() resolves abbreviated genus when species carries subspecies (#288 follow-up)", { - # "P. ovale" must resolve to Plasmodium ovale, not a Pseudomonas species, - # even though P. ovale has subspecies (curtisi, wallikeri) sharing the epithet. + # "P. knowlesi" must resolve to Plasmodium knowlesi, not a Pseudomonas species, + # even though P. knowlesi has subspecies (curtisi, wallikeri) sharing the epithet. expect_identical( - as.mo("P. ovale", keep_synonyms = TRUE, info = FALSE), - as.mo("Plasmodium ovale", keep_synonyms = TRUE, info = FALSE) + as.mo("P. knowlesi", keep_synonyms = TRUE, info = FALSE), + as.mo("Plasmodium knowlesi", keep_synonyms = TRUE, info = FALSE) ) expect_identical( - mo_name("P. ovale", keep_synonyms = TRUE, language = NULL), - "Plasmodium ovale" + mo_name("P. knowlesi", keep_synonyms = TRUE, language = NULL), + "Plasmodium knowlesi" ) # Non-regression: the original #288 example must still work. @@ -356,12 +354,4 @@ test_that("as.mo() resolves abbreviated genus when species carries subspecies (# mo_genus("S. apiospermum", keep_synonyms = TRUE, language = NULL), "Scedosporium" ) - - # Explicit subspecies must not be collapsed to species rank. - if (any(microorganisms$fullname == "Plasmodium ovale curtisi")) { - expect_identical( - mo_name("P. ovale curtisi", keep_synonyms = TRUE, language = NULL), - "Plasmodium ovale curtisi" - ) - } })