From cc2bb151ab833a70ea9bafefbf3ed4eac7e34d63 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Fri, 7 Feb 2025 19:03:02 +0100 Subject: [PATCH] (v2.1.1.9142) unit test fix --- .github/workflows/check-current-testthat.yaml | 2 +- DESCRIPTION | 2 +- NEWS.md | 2 +- PythonPackage/AMR/AMR.egg-info/PKG-INFO | 2 +- ...ny.whl => AMR-2.1.1.9142-py3-none-any.whl} | Bin 10253 -> 10252 bytes PythonPackage/AMR/dist/amr-2.1.1.9141.tar.gz | Bin 10073 -> 0 bytes PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz | Bin 0 -> 10082 bytes PythonPackage/AMR/setup.py | 2 +- R/eucast_rules.R | 29 +++++++++--------- ....txt => gpt_training_text_v2.1.1.9142.txt} | 2 +- tests/testthat/test-zzz.R | 3 +- 11 files changed, 21 insertions(+), 23 deletions(-) rename PythonPackage/AMR/dist/{AMR-2.1.1.9141-py3-none-any.whl => AMR-2.1.1.9142-py3-none-any.whl} (85%) delete mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9141.tar.gz create mode 100644 PythonPackage/AMR/dist/amr-2.1.1.9142.tar.gz rename data-raw/{gpt_training_text_v2.1.1.9141.txt => gpt_training_text_v2.1.1.9142.txt} (99%) diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml index be69d5abb..a33ddb311 100644 --- a/.github/workflows/check-current-testthat.yaml +++ b/.github/workflows/check-current-testthat.yaml @@ -86,7 +86,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck, any::pkgload + extra-packages: any::rcmdcheck needs: check upgrade: 'TRUE' diff --git a/DESCRIPTION b/DESCRIPTION index 04cff6d1c..01f679750 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9141 +Version: 2.1.1.9142 Date: 2025-02-07 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 1d47cfa65..ab670e3d7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9141 +# AMR 2.1.1.9142 *(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 9cf5ed913..07d00dadb 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: 2.1.1.9141 +Version: 2.1.1.9142 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-2.1.1.9141-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl similarity index 85% rename from PythonPackage/AMR/dist/AMR-2.1.1.9141-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9142-py3-none-any.whl index 4fe0a786c61d1d5e3071cbb6d575ecf9020024d2..e8d2f2843db427fd48f4ad7040608fea85e53b0f 100644 GIT binary patch delta 621 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z2{+S^drt62c={G^B#AZILtECNHTQsDZ#x_J0Mo9wr@v>nznp!@g8JTey0+_gOwXaI zT$u#?l{bjTIE_G)E7DGysD-GDx9Ik9ETUK8On$v}Ns>gA4ND=WqZm z^xmZUbpxegUt0SA=f7@Dx ztVPHU@*32?fe&(9DM4B3{Cs%{jmL)Nx4w;xg~p9YRD+>Zm?I<_%xvQz>W%R zNRxHG5T#%4ReM9lFfBX{GEvcosu7AUHVk?@TfR;w*f;-43K@!`AopCeKf;%&5N{4ib z1w?2L-up(sUkuel9}9XM=vBVGv;yhS_IjS&ke4T%8SVeGct>Cg#l}9A8iLt{ Gh50Wvy%pU6 literal 0 HcmV?d00001 diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index 828e19a18..03d90f6e9 100644 --- a/PythonPackage/AMR/setup.py +++ b/PythonPackage/AMR/setup.py @@ -2,7 +2,7 @@ from setuptools import setup, find_packages setup( name='AMR', - version='2.1.1.9141', + version='2.1.1.9142', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 2a83872b8..0b7319ac7 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -460,16 +460,14 @@ eucast_rules <- function(x, # >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------ if (any(c("all", "other") %in% rules)) { if (isTRUE(info)) { - cat("\n") + cat(paste0("\n", font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n")) cat(word_wrap( - font_bold(paste0( - "Rules by this AMR package (", - font_red(paste0( - "v", utils::packageDescription("AMR")$Version, ", ", - format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y") - )), "), see `?eucast_rules`\n" - )) + paste0("Rules by the ", + font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)), + " (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"), + "), see `?eucast_rules`\n") )) + cat("\n\n") } ab_enzyme <- subset(AMR::antibiotics, name %like% "/")[, c("ab", "name"), drop = FALSE] colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name") @@ -495,8 +493,8 @@ eucast_rules <- function(x, ## Set base to R where base + enzyme inhibitor is R ---- rule_current <- paste0( - ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ", - tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R" + ab_enzyme$base_name[i], " (`", col_base, "`) = R if ", + tolower(ab_enzyme$enzyme_name[i]), " (`", col_enzyme, "`) = R" ) if (isTRUE(info)) { cat(word_wrap(rule_current, @@ -536,8 +534,8 @@ eucast_rules <- function(x, ## Set base + enzyme inhibitor to S where base is S ---- rule_current <- paste0( - ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ", - tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S" + ab_enzyme$enzyme_name[i], " (`", col_enzyme, "`) = S if ", + tolower(ab_enzyme$base_name[i]), " (`", col_base, "`) = S" ) if (isTRUE(info)) { @@ -559,7 +557,8 @@ eucast_rules <- function(x, original_data = x.bak, warned = warned, info = info, - verbose = verbose + verbose = verbose, + overwrite = overwrite ) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed @@ -1037,9 +1036,9 @@ eucast_rules <- function(x, cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n")) if (isFALSE(verbose) && total_n_added + total_n_changed > 0) { - cat("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "") + cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "") } else if (isTRUE(verbose)) { - cat("\n", word_wrap("Used 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data."), "\n\n", sep = "") + cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "") } } diff --git a/data-raw/gpt_training_text_v2.1.1.9141.txt b/data-raw/gpt_training_text_v2.1.1.9142.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9141.txt rename to data-raw/gpt_training_text_v2.1.1.9142.txt index e20604b69..f09d09aab 100644 --- a/data-raw/gpt_training_text_v2.1.1.9141.txt +++ b/data-raw/gpt_training_text_v2.1.1.9142.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 2.1.1.9141. Remember this whenever someone asks which AMR package version you’re at. +First and foremost, you are trained on version 2.1.1.9142. 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. ---------------------------------------------------------------------------------------------------- diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R index 70bc10801..3a704b403 100644 --- a/tests/testthat/test-zzz.R +++ b/tests/testthat/test-zzz.R @@ -141,8 +141,7 @@ call_functions <- c( import_functions <- c(import_functions, call_functions) -suggests <- tryCatch(strsplit(pkgload::pkg_desc()$get_field("Suggests"), "[,\n ]+")[[1]], - error = function(e) unname(import_functions)) +suggests <- strsplit(utils::packageDescription("AMR")$Suggests, "[,\n ]+")[[1]] for (i in seq_len(length(import_functions))) { fn <- names(import_functions)[i] pkg <- unname(import_functions[i])