From 22e66741ccb4febc3d8585d0e4dacdc7cc18adc0 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 26 Feb 2025 20:28:33 +0100 Subject: [PATCH] (v2.1.1.9160) cleanup --- .github/workflows/lintr.yaml | 5 +- DESCRIPTION | 2 +- NEWS.md | 2 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- PythonPackage/AMR/dist/amr-2.1.1.9159.tar.gz | Bin 10123 -> 0 bytes ...ny.whl => amr-2.1.1.9160-py3-none-any.whl} | Bin 10303 -> 10305 bytes PythonPackage/AMR/dist/amr-2.1.1.9160.tar.gz | Bin 0 -> 10117 bytes PythonPackage/AMR/setup.py | 2 +- R/ab.R | 45 +++++++----------- R/custom_antimicrobials.R | 10 ++-- ....txt => gpt_training_text_v2.1.1.9160.txt} | 10 ++-- man/add_custom_antimicrobials.Rd | 8 ++-- tests/testthat/test-amr_selectors.R | 2 +- 13 files changed, 38 insertions(+), 50 deletions(-) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9159.tar.gz rename PythonPackage/AMR/dist/{amr-2.1.1.9159-py3-none-any.whl => amr-2.1.1.9160-py3-none-any.whl} (85%) create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9160.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9159.txt => gpt_training_text_v2.1.1.9160.txt} (99%) diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index 982e789a7..595c2cdfd 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -53,7 +53,9 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::lintr + extra-packages: | + any::lintr + any::cyclocomp - name: Lint run: | @@ -63,6 +65,7 @@ jobs: linters <- sort(linters[grepl("_linter$", linters)]) # lose deprecated linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)] + linters <- linters[linters != "linter"] # and the ones we find unnnecessary linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)] # put the functions in a list diff --git a/DESCRIPTION b/DESCRIPTION index 4f68d510f..834f6473e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9159 +Version: 2.1.1.9160 Date: 2025-02-26 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 0e8dbb204..ab9fda8ef 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9159 +# AMR 2.1.1.9160 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index f7b2915db..a33a88066 100644 --- a/PythonPackage/AMR/AMR.egg-info/PKG-INFO +++ b/PythonPackage/AMR/AMR.egg-info/PKG-INFO @@ -1,6 +1,6 @@ Metadata-Version: 2.2 Name: AMR -Version: 2.1.1.9159 +Version: 2.1.1.9160 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9159.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9159.tar.gz deleted file mode 100644 index a9af2aaafccd5e4674392f826734d62b5e0ed017..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10123 zcmch6RZtwjwk__1ySoI}0KuK0!QI{6-8B#(5S#>ecXxN0;FjPvI1IzwocHd>`+9%( zR@bUtd-bZ`AKlemyEauK3W}9czbzcp+}VSjhlBgy5aQ++;_x!}fVm9z_uTAga(!Pb z-vezKW@@z6Y%7Tt3TLzNb}}VS7i4>0{V5Z~MpY#CB;#n}SFE}M`k7t_rvU*Gx%3fD zOzz)M1ru3{P~W;1?TRED7Ddk}A%_uL?+WpX5P8!-XQR67yC$xJ6Ia~5yJYu)DJ`4w zSZ=bC3PBa`i|zgZ#vBTs+=8bR`CibeotwyML7uWIQ?2~jD-wqVI5yIS>RsqEMJ=UI z4=PTXa@e2#?CQ$(;qgTZN|hv^F2C_i1Ma6#u2iGoW&R1@w0?2!2z6n zvB9BDv+pVLqWo|{iI339^XX#FCFr#cG&Y!8^AT#;2#uU9gHU|{L#ZD_8(g5{+XYQ; 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zx_^Y_#=^`0KhR#d)60W7!`<6z=1;g7Hu}B(13c}x#RdN0kX2gt2ISSe+NM6#Hnv_~ zF=!Rgb4}3we?;G~+DED%XFtMj{#}wkFL{;OGwL}!0T)s5AZ|1c9zP0jIfsMdD_ET1 z7uF^h$5usqjx;o)bcRRGF^1*7MOQS;GoqX=(u&zg0C?0gi(b@zFdV#E_eOy#mXnBwt)?xW}9Xq;VRk9VwiHsa2_g>*~% z6M+ak8$oPoW6IPJR>GCD;ZCcE_5zeEh~Kty#?ZYdwld)W@MaI|`rTEVYzn=v%IGMG z$*DUvZ6j!Q<>?rW 1)) { - abnames <- ab_name(from_text, tolower = TRUE, loop_time = loop_time + 1) + if (isTRUE(length(from_text) > 1)) { + abnames <- ab_name(from_text, tolower = TRUE) if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|(avi|tazo|mono|vabor)bactam)") { abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam", "tazobactam", "vaborbactam", "monobactam")] } @@ -190,15 +186,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(), x_new[is.na(x)] <- NA already_known[is.na(x)] <- FALSE - if (loop_time == 1 && sum(already_known) < length(x)) { + if (sum(already_known) < length(x)) { progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25 on.exit(close(progress)) } for (i in which(!already_known)) { - if (loop_time == 1) { - progress$tick() - } + progress$tick() if (is.na(x[i]) || is.null(x[i])) { next @@ -218,7 +212,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(), } if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") { - from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 1, translate_ab = FALSE)[[1]]), + from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]), error = function(e) character(0) ) } else { @@ -331,9 +325,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(), next } - # INITIAL SEARCH - More uncertain results ---- - if (loop_time == 1 && fast_mode == FALSE) { - # only run on first and second try + # More uncertain results ---- + if (fast_mode == FALSE) { ab_df <- AMR_env$AB_lookup ab_df$length_name <- nchar(ab_df$generalised_name) @@ -391,23 +384,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(), x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1]) } - if (loop_time == 1 && sum(already_known) < length(x)) { + if (sum(already_known) < length(x)) { close(progress) } # save to package env to save time for next time - if (loop_time == 1) { - AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE] - AMR_env$ab_previously_coerced <- unique(rbind_AMR( - AMR_env$ab_previously_coerced, - data.frame( - x = x, - ab = x_new, - x_bak = x_bak[match(x, x_bak_clean)], - stringsAsFactors = FALSE - ) - )) - } + AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE] + AMR_env$ab_previously_coerced <- unique(rbind_AMR( + AMR_env$ab_previously_coerced, + data.frame( + x = x, + ab = x_new, + x_bak = x_bak[match(x, x_bak_clean)], + stringsAsFactors = FALSE + ) + )) # take failed ATC codes apart from rest if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) { diff --git a/R/custom_antimicrobials.R b/R/custom_antimicrobials.R index 661d792e1..c8b611cd0 100755 --- a/R/custom_antimicrobials.R +++ b/R/custom_antimicrobials.R @@ -69,11 +69,8 @@ #' @export #' @examples #' \donttest{ -#' -#' # returns NA and throws a warning (which is suppressed here): -#' suppressWarnings( -#' as.ab("testab") -#' ) +#' # returns a wildly guessed result: +#' as.ab("testab") #' #' # now add a custom entry - it will be considered by as.ab() and #' # all ab_*() functions @@ -109,6 +106,7 @@ #' ab_name("J01CR50") #' #' # even antimicrobial selectors work +#' # see ?amr_selector #' x <- data.frame( #' random_column = "some value", #' coflu = as.sir("S"), @@ -155,7 +153,7 @@ add_custom_antimicrobials <- function(x) { } AMR_env$AB_lookup <- unique(rbind_AMR(AMR_env$AB_lookup, new_df)) - AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% x$ab), , drop = FALSE] + AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE] class(AMR_env$AB_lookup$ab) <- c("ab", "character") message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.") } diff --git a/data-raw/gpt_training_text_v2.1.1.9159.txt b/data-raw/gpt_training_text_v2.1.1.9160.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9159.txt rename to data-raw/gpt_training_text_v2.1.1.9160.txt index deffcfe6d..7a14eb64c 100644 --- a/data-raw/gpt_training_text_v2.1.1.9159.txt +++ b/data-raw/gpt_training_text_v2.1.1.9160.txt @@ -1,6 +1,6 @@ This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse. -First and foremost, you are trained on version 2.1.1.9159. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9160. Remember this whenever someone asks which AMR package version you’re at. Below are the contents of the file, the file, and all the files (documentation) in the package. Every file content is split using 100 hypens. ---------------------------------------------------------------------------------------------------- @@ -1324,11 +1324,8 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to } \examples{ \donttest{ - -# returns NA and throws a warning (which is suppressed here): -suppressWarnings( - as.ab("testab") -) +# returns a wildly guessed result: +as.ab("testab") # now add a custom entry - it will be considered by as.ab() and # all ab_*() functions @@ -1364,6 +1361,7 @@ ab_atc("Co-fluampicil") ab_name("J01CR50") # even antimicrobial selectors work +# see ?amr_selector x <- data.frame( random_column = "some value", coflu = as.sir("S"), diff --git a/man/add_custom_antimicrobials.Rd b/man/add_custom_antimicrobials.Rd index 839b953b2..85c0625b1 100644 --- a/man/add_custom_antimicrobials.Rd +++ b/man/add_custom_antimicrobials.Rd @@ -50,11 +50,8 @@ Use \code{\link[=clear_custom_antimicrobials]{clear_custom_antimicrobials()}} to } \examples{ \donttest{ - -# returns NA and throws a warning (which is suppressed here): -suppressWarnings( - as.ab("testab") -) +# returns a wildly guessed result: +as.ab("testab") # now add a custom entry - it will be considered by as.ab() and # all ab_*() functions @@ -90,6 +87,7 @@ ab_atc("Co-fluampicil") ab_name("J01CR50") # even antimicrobial selectors work +# see ?amr_selector x <- data.frame( random_column = "some value", coflu = as.sir("S"), diff --git a/tests/testthat/test-amr_selectors.R b/tests/testthat/test-amr_selectors.R index f452d0d19..5d2071807 100644 --- a/tests/testthat/test-amr_selectors.R +++ b/tests/testthat/test-amr_selectors.R @@ -59,7 +59,7 @@ expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, toleran expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5) expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5) -expect_message(carbapenems()) +expect_message(expect_stdout(print(carbapenems()))) expect_error(administrable_per_os()) # Examples: