(v3.0.0.9021) checkouts

.github/workflows/check-old-tinytest.yaml

@@ -49,13 +49,13 @@ jobs:
           # Test all old versions of R >= 3.0, we support them all!
           # For these old versions, dependencies and vignettes will not be checked.
           # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
-          - {os: ubuntu-latest, r: '3.6', allowfail: false}
+          - {os: ubuntu-latest, r: '3.6', allowfail: true}
           # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8
-          - {os: ubuntu-latest, r: '3.4', allowfail: false}
-          - {os: ubuntu-latest, r: '3.3', allowfail: false}
-          - {os: ubuntu-latest, r: '3.2', allowfail: false}
-          - {os: ubuntu-latest, r: '3.1', allowfail: false}
-          - {os: ubuntu-latest, r: '3.0', allowfail: false}
+          - {os: ubuntu-latest, r: '3.4', allowfail: true}
+          - {os: ubuntu-latest, r: '3.3', allowfail: true}
+          - {os: ubuntu-latest, r: '3.2', allowfail: true}
+          - {os: ubuntu-latest, r: '3.1', allowfail: true}
+          - {os: ubuntu-latest, r: '3.0', allowfail: true}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -76,9 +76,14 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install tinytest from CRAN
+      - name: Install suggested pkgs (and tinytest) from CRAN
         run: |
-          install.packages("tinytest", repos = "https://cran.r-project.org")
+          desc_lines <- readLines('DESCRIPTION')
+          suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:|  )", readLines('DESCRIPTION'))]
+          suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
+          suggests <- gsub("[ ,]", "", suggests)
+          pkgs <- unique(c(suggests, "tinytest"))
+          for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
         shell: Rscript {0}
 
       - name: Show session info

.github/workflows/lintr.yaml

@@ -1,85 +0,0 @@
-# ==================================================================== #
-# TITLE:                                                               #
-# AMR: An R Package for Working with Antimicrobial Resistance Data     #
-#                                                                      #
-# SOURCE CODE:                                                         #
-# https://github.com/msberends/AMR                                     #
-#                                                                      #
-# PLEASE CITE THIS SOFTWARE AS:                                        #
-# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
-# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
-# Journal of Statistical Software, 104(3), 1-31.                       #
-# https://doi.org/10.18637/jss.v104.i03                                #
-#                                                                      #
-# Developed at the University of Groningen and the University Medical  #
-# Center Groningen in The Netherlands, in collaboration with many      #
-# colleagues from around the world, see our website.                   # 
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-#                                                                      #
-# Visit our website for the full manual and a complete tutorial about  #
-# how to conduct AMR data analysis: https://amr-for-r.org              #
-# ==================================================================== #
-
-on:
-  push:
-    branches: '**'
-  pull_request:
-    branches: '**'
-
-name: lintr
-
-jobs:
-  lintr:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release
-          # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            any::lintr
-            any::cyclocomp
-            any::roxygen2
-            any::devtools
-            any::usethis
-            
-      - name: Remove unneeded folders
-        run: |
-          # do not check these folders
-          rm -rf data-raw
-          rm -rf tests
-          rm -rf vignettes
-          
-      - name: Lint
-        run: |
-          # get ALL linters, not just default ones
-          linters <- getNamespaceExports(asNamespace("lintr"))
-          linters <- sort(linters[grepl("_linter$", 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$", linters)]
-          linters <- linters[linters != "linter"]
-          # and the ones we find unnnecessary
-          linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)]
-          # put the functions in a list
-          linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
-          names(linters_list) <- linters
-          # run them all!
-          lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R"))
-        shell: Rscript {0}

.github/workflows/website.yaml

@@ -42,16 +42,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: actions/checkout@v4
+      - name: checkout
+        uses: actions/checkout@v4
         with:
           # this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
           # we need this for the download page on our website - dates must be of the files, not of the latest git push
           fetch-depth: 0
 
-      - name: Preserve timestamps
-        run: |
-          sudo apt install git-restore-mtime
-          git restore-mtime
+      - name: restore timestamps
+        uses: chetan/git-restore-mtime-action@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9019
-Date: 2025-09-01
+Version: 3.0.0.9021
+Date: 2025-09-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.0.9019
+# AMR 3.0.0.9021
 
 This is primarily a bugfix release, though we added one nice feature too.