(v3.0.1.9130) Add workflow to check reverse dependencies against the development version on every push to main, list WT/NWT for ECOFFs as breaking change, and update cran-comments.md for v3.1.0

.github/scripts/check_revdeps.R

@@ -0,0 +1,87 @@
+# ==================================================================== #
+# 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              #
+# ==================================================================== #
+
+# Run R CMD check on all CRAN packages that depend on AMR, against the INSTALLED development version of AMR.
+# Used by .github/workflows/check-revdeps.yaml; run from the root of the repository, after installing AMR from it:
+#   Rscript .github/scripts/check_revdeps.R
+# Fails if any reverse dependency returns an ERROR or WARNING.
+
+# only CRAN, also when other repositories are set, since this is about CRAN releases
+repos <- c(CRAN = "https://cloud.r-project.org")
+db <- utils::available.packages(repos = repos)
+revdeps <- sort(tools::package_dependencies("AMR", db = db, reverse = TRUE, which = "all")[["AMR"]])
+if (length(revdeps) == 0) {
+  message("No reverse dependencies on CRAN")
+  quit(status = 0)
+}
+message("Reverse dependencies: ", paste(revdeps, collapse = ", "))
+
+# all dependencies of the reverse dependencies, but never AMR itself, which is the development version installed from this repository
+deps <- unique(unlist(tools::package_dependencies(revdeps, db = db, which = "all"), use.names = FALSE))
+base_pkgs <- rownames(utils::installed.packages(priority = "base"))
+deps <- setdiff(deps, c("AMR", base_pkgs, rownames(utils::installed.packages())))
+if (length(deps) > 0) {
+  # pak also installs the system requirements of these packages
+  tryCatch(pak::pkg_install(deps, upgrade = FALSE), error = function(e) {
+    message("pak failed (", conditionMessage(e), "), falling back to install.packages()")
+    utils::install.packages(deps)
+  })
+}
+amr_version <- read.dcf("DESCRIPTION", fields = "Version")[1, 1]
+if (as.character(utils::packageVersion("AMR")) != amr_version) {
+  stop("installed AMR is v", utils::packageVersion("AMR"), ", expected the development version v", amr_version)
+}
+message("Checking against AMR v", amr_version)
+
+check_dir <- file.path(tempdir(), "revdeps")
+dir.create(check_dir, showWarnings = FALSE)
+tarballs <- utils::download.packages(revdeps, destdir = check_dir, repos = repos, type = "source")[, 2]
+
+results <- vapply(tarballs, FUN.VALUE = character(1), function(tarball) {
+  pkg <- sub("_.*", "", basename(tarball))
+  message("\n=== Checking ", pkg, " ===")
+  out <- suppressWarnings(system2(
+    file.path(R.home("bin"), "R"),
+    c("CMD", "check", "--no-manual", "--as-cran", "-o", shQuote(check_dir), shQuote(tarball)),
+    stdout = TRUE,
+    stderr = TRUE,
+    # skip the incoming checks for CRAN submission, which concern the maintainers of the reverse dependencies
+    env = c("_R_CHECK_FORCE_SUGGESTS_=false", "_R_CHECK_CRAN_INCOMING_=false")
+  ))
+  cat(out, sep = "\n")
+  status <- grep("^Status:", out, value = TRUE)
+  if (length(status) == 0) "ERROR (check did not finish)" else trimws(sub("^Status:", "", status[length(status)]))
+}, USE.NAMES = FALSE)
+names(results) <- revdeps
+
+message("\n=== Summary against AMR v", amr_version, " ===")
+message(paste0(format(names(results)), "  ", results, collapse = "\n"))
+if (any(grepl("ERROR|WARNING", results))) {
+  quit(status = 1)
+}

.github/workflows/check-revdeps.yaml

@@ -0,0 +1,74 @@
+# ==================================================================== #
+# 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              #
+# ==================================================================== #
+
+# Run R CMD check on all CRAN packages that depend on AMR, against the development version of AMR installed from this repository.
+# This is informative only: it is not a required check, so a failure does not block anything, but it shows which reverse dependencies break before a CRAN release.
+
+on:
+  push:
+    # only on main
+    branches: [main]
+  # allow manual runs from the Actions tab
+  workflow_dispatch:
+
+name: check-revdeps
+
+jobs:
+  check-revdeps:
+    runs-on: ubuntu-latest
+
+    name: Reverse dependencies (R-release)
+
+    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:
+          # AMR has no hard dependencies; pak is used to install the dependencies of the reverse dependencies
+          dependencies: '"hard"'
+          extra-packages: any::pak
+
+      - name: Install AMR from this repository
+        shell: bash
+        run: R CMD INSTALL .
+
+      - name: Check reverse dependencies against the installed AMR
+        shell: bash
+        run: Rscript .github/scripts/check_revdeps.R

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9129
+Version: 3.0.1.9130
 Date: 2026-10-13
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9129
+# AMR 3.0.1.9130
 
 Planned as v3.1.0, mid October 2026.
 
@@ -24,6 +24,7 @@ Planned as v3.1.0, mid October 2026.
   Previously, `mo_domain()` was an alias of `mo_kingdom()`; it is now a distinct function. Its output is therefore unchanged, while `mo_kingdom()` now returns the new formal kingdom. A one-time note per session explains this change when bacterial or archaeal records are queried.
 * Parallel computing in `as.sir()`, `antibiogram()`, and `wisca()` now uses the `future` and `future.apply` packages, which is faster. A non-sequential plan (e.g., `future::plan(future::multisession)`) must be active before using `parallel = TRUE` (#281).
 * The options of `capped_mic_handling` in `as.sir()` have been redefined as `"none"`, `"conservative"`, `"standard"` (default), and `"lenient"`. The option `"inverse"` is no longer available (#243).
+* `as.sir()` now returns WT/NWT (Wildtype/Non-wildtype) instead of S/R when using ECOFF-based interpretation with `breakpoint_type = "ECOFF"`. WT/NWT results are fully supported in all resistance and susceptibility functions and in all plots (#254).
 
 ### New
 * **Updated clinical breakpoints**
@@ -32,8 +33,6 @@ Planned as v3.1.0, mid October 2026.
     * `clinical_breakpoints` now contains blocking rows (`NA` breakpoints, with the reason in `note`) where EUCAST gives no breakpoint for an organism, so that `as.sir()` no longer falls back to the breakpoint of a broader taxon
     * Restrictions in EUCAST notes are applied, e.g., zone diameter breakpoints for *E. coli* only
     * EUCAST PK-PD (non-species related) breakpoints of 2019-2023 and *H. parainfluenzae* MIC breakpoints are now included
-* **Wildtype/Non-wildtype interpretation**
-  * `as.sir()` now returns WT/NWT (Wildtype/Non-wildtype) when using ECOFF-based interpretation with `breakpoint_type = "ECOFF"`. WT/NWT results are fully supported in all resistance and susceptibility functions and in all plots (#254).
 * **Unified interpretive rules**
   * New function `interpretive_rules()` applies the interpretive rules of both EUCAST and CLSI. `eucast_rules()` is now a wrapper around this function (#235, #259).
   * Species named in a rule now also match all other names of the same accepted taxon (e.g., 'Clostridium ramosum' for *Thomasclavelia ramosa*). This also updated the `intrinsic_resistant` data set.

cran-comments.md

@@ -1,4 +1,13 @@
-This version is a bugfix release (v3.0.1) following the release of v3.0.0 in June 2025.
+This version is a minor release (v3.1.0) following the bugfix release v3.0.1 in September 2025. It adds the EUCAST 2026 and CLSI 2026 clinical breakpoints (EUCAST 2026 is now the default), a taxonomic update of all microorganisms, unified EUCAST and CLSI interpretive rules, support for `tidymodels` pipelines, and many improvements and bug fixes, as listed in `NEWS.md`.
+
+This release contains four breaking changes, each documented in `NEWS.md`:
+
+* Following the reclassification of Bacteria and Archaea into new kingdoms (Göker and Oren, 2024), `mo_kingdom()` now returns the formal kingdom, while the new function `mo_domain()` returns the former output
+* Parallel computing in `as.sir()`, `antibiogram()`, and `wisca()` now uses the suggested packages `future` and `future.apply`
+* The options of the `capped_mic_handling` argument of `as.sir()` have been redefined
+* `as.sir()` now returns WT/NWT (wildtype/non-wildtype) instead of S/R for interpretation based on epidemiological cut-off values (ECOFFs)
+
+This package has two reverse dependencies, `MIC` and `MIMER`, both checked against this version. `MIMER` passes. `MIC` is affected by the WT/NWT change, which makes some of its unit tests fail; its maintainer has been informed in advance through an issue in its GitHub repository.
 
 As with all previous >20 releases, some CHECKs on `oldrel` may return a `NOTE` for narrowly exceeding the installation size limit. This has been reduced to a minimum in prior coordination with CRAN maintainers and currently returns only an `INFO` on `release` and `devel`.