(v2.1.1.9133) (v2.1.1.9132) unit test, final fixes

.github/workflows/check-current-testthat.yaml

@@ -53,22 +53,20 @@ jobs:
       matrix:
         config:
           # current development version, check all major OSes:
-          - {os: macOS-latest,   r: 'devel', allowfail: false}
+          - {os: macOS-latest,   r: 'devel', allowfail: true}
           - {os: windows-latest, r: 'devel', allowfail: false}
           - {os: ubuntu-latest,  r: 'devel', allowfail: false, http-user-agent: 'release'}
 
           # current 'release' version, check all major OSes:
-          - {os: macOS-latest,   r: 'release', allowfail: false}
+          - {os: macOS-latest,   r: 'release', allowfail: true}
           - {os: windows-latest, r: 'release', allowfail: false}
           - {os: ubuntu-latest,  r: 'release', allowfail: false}
 
           # older versions (see also check-old-tinytest.yaml for even older versions):
-          - {os: ubuntu-latest, r: '4.3', allowfail: false}
+          - {os: ubuntu-latest, r: 'oldrel', allowfail: false}
-          - {os: ubuntu-latest, r: '4.2', allowfail: false}
+          - {os: ubuntu-latest, r: 'oldrel-1', allowfail: false}
-          - {os: ubuntu-latest, r: '4.1', allowfail: false}
+          - {os: ubuntu-latest, r: 'oldrel-2', allowfail: false}
-          - {os: ubuntu-latest, r: '4.0', allowfail: false}
+          - {os: ubuntu-latest, r: 'oldrel-3', allowfail: false}
-          - {os: ubuntu-latest, r: '3.6', allowfail: false}
-          # when testthat loses support for a version, move it to check-old-tinytest.yaml
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

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

@@ -122,5 +122,6 @@ jobs:
         if: always()
         run: |
           cd ../AMR.Rcheck
+          ls
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9131
+Version: 2.1.1.9133
 Date: 2025-01-27
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9131
+# AMR 2.1.1.9133
 
 *(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).)*
 

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9131
+Version: 2.1.1.9133
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/AMR/datasets.py

@@ -18,6 +18,8 @@ os.makedirs(r_lib_path, exist_ok=True)
 base = importr('base')
 utils = importr('utils')
 
+base.options(warn = -1)
+
 # Override R library paths globally for the session
 robjects.r(f'.Library <- "{r_lib_path}"')  # Replace default library
 robjects.r(f'.Library.site <- "{r_lib_path}"')  # Replace site-specific library
@@ -73,4 +75,6 @@ microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR:
 antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
 clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
 
+base.options(warn = 0)
+
 print(f"AMR: Done.", flush=True)

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9131',
+    version='2.1.1.9133',
     packages=find_packages(),
     install_requires=[
         'rpy2',

_pkgdown.yml

@@ -173,9 +173,10 @@ reference:
     desc: >
       Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
       With `antibiogram()`, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination
-      antibiogram(WISCA). This function also comes with support for R Markdown and Quarto.
+      antibiogram (WISCA). This function also comes with support for R Markdown and Quarto.
       Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`.
-      You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
+      You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`),
+      or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
     contents:
     - "`antibiogram`"
     - "`proportion`"
@@ -184,9 +185,9 @@ reference:
     - "`first_isolate`"
     - "`key_antimicrobials`"
     - "`mdro`"
-    - "`count`"
     - "`bug_drug_combinations`"
     - "`antimicrobial_class_selectors`"
+    - "`top_n_microorganisms`"
     - "`mean_amr_distance`"
     - "`resistance_predict`"
     - "`guess_ab_col`"

cran-comments.md

@@ -1,9 +1,5 @@
-**On the 15th of October, 2023, we received an email from Prof Ripley about an issue in UTF-8 strings in our documentation. This version contains a fix to this issue.**
-
-Previous comments:
-
 As with all previous >20 releases, some CHECKs might return a NOTE for *just* hitting the installation size limit, though its size has been brought down to a minimum in collaboration with CRAN maintainers previously.
 
-We consider this a high-impact package: it was published in the Journal of Statistical Software (2022), is included in a CRAN Task View (Epidemiology), and is according to download stats used in almost all countries in the world. If there is anything to note, please let us know up-front without directly archiving the current version. That said, we continually unit test our package extensively and have no reason to assume that anything is wrong.
+We consider this a high-impact package: it was published in the Journal of Statistical Software (2022), is included in a CRAN Task View (Epidemiology), and is according to download stats (cranlogs) used in almost all countries in the world. If there is anything to note, please let us know up-front without directly archiving the current version. That said, we continually unit test our package extensively and have no reason to assume that anything is wrong.
 
 Thanks for maintaining and hosting CRAN! It's empowering R and its use enormously!

data-raw/_generate_python_wrapper.sh

@@ -62,6 +62,8 @@ os.makedirs(r_lib_path, exist_ok=True)
 base = importr('base')
 utils = importr('utils')
 
+base.options(warn = -1)
+
 # Override R library paths globally for the session
 robjects.r(f'.Library <- "{r_lib_path}"')  # Replace default library
 robjects.r(f'.Library.site <- "{r_lib_path}"')  # Replace site-specific library
@@ -117,6 +119,8 @@ microorganisms = pandas2ri.rpy2py(robjects.r('AMR::microorganisms[, !sapply(AMR:
 antibiotics = pandas2ri.rpy2py(robjects.r('AMR::antibiotics[, !sapply(AMR::antibiotics, is.list)]'))
 clinical_breakpoints = pandas2ri.rpy2py(robjects.r('AMR::clinical_breakpoints[, !sapply(AMR::clinical_breakpoints, is.list)]'))
 
+base.options(warn = 0)
+
 print(f"AMR: Done.", flush=True)
 EOL
 

data-raw/gpt_training_text_v2.1.1.9133.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 2.1.1.9131. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9133. 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.
 ----------------------------------------------------------------------------------------------------