diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml index c00d160b2..9b02589e2 100644 --- a/.github/workflows/check-current-testthat.yaml +++ b/.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: '4.2', allowfail: false} - - {os: ubuntu-latest, r: '4.1', allowfail: false} - - {os: ubuntu-latest, r: '4.0', allowfail: false} - - {os: ubuntu-latest, r: '3.6', allowfail: false} - # when testthat loses support for a version, move it to check-old-tinytest.yaml + - {os: ubuntu-latest, r: 'oldrel', allowfail: false} + - {os: ubuntu-latest, r: 'oldrel-1', allowfail: false} + - {os: ubuntu-latest, r: 'oldrel-2', allowfail: false} + - {os: ubuntu-latest, r: 'oldrel-3', allowfail: false} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/check-old-tinytest.yaml b/.github/workflows/check-old-tinytest.yaml index b740a953d..2a9c94379 100644 --- a/.github/workflows/check-old-tinytest.yaml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 011ea1bf1..da893faff 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index 5a8659664..297421965 100644 --- a/NEWS.md +++ b/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).)* diff --git a/PythonPackage/AMR/AMR.egg-info/PKG-INFO b/PythonPackage/AMR/AMR.egg-info/PKG-INFO index 943704a47..0086df7ed 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: 2.1.1.9131 +Version: 2.1.1.9133 Summary: A Python wrapper for the AMR R package Home-page: https://github.com/msberends/AMR Author: Matthijs Berends diff --git a/PythonPackage/AMR/AMR/datasets.py b/PythonPackage/AMR/AMR/datasets.py index 28774b333..546f74d6a 100644 --- a/PythonPackage/AMR/AMR/datasets.py +++ b/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) diff --git a/PythonPackage/AMR/dist/AMR-2.1.1.9131-py3-none-any.whl b/PythonPackage/AMR/dist/AMR-2.1.1.9133-py3-none-any.whl similarity index 73% rename from PythonPackage/AMR/dist/AMR-2.1.1.9131-py3-none-any.whl rename to PythonPackage/AMR/dist/AMR-2.1.1.9133-py3-none-any.whl index 785e61c5a..8fc5e165d 100644 Binary files a/PythonPackage/AMR/dist/AMR-2.1.1.9131-py3-none-any.whl and b/PythonPackage/AMR/dist/AMR-2.1.1.9133-py3-none-any.whl differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9131.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9131.tar.gz deleted file mode 100644 index 2f8774944..000000000 Binary files a/PythonPackage/AMR/dist/amr-2.1.1.9131.tar.gz and /dev/null differ diff --git a/PythonPackage/AMR/dist/amr-2.1.1.9133.tar.gz b/PythonPackage/AMR/dist/amr-2.1.1.9133.tar.gz new file mode 100644 index 000000000..5347ec49e Binary files /dev/null and b/PythonPackage/AMR/dist/amr-2.1.1.9133.tar.gz differ diff --git a/PythonPackage/AMR/setup.py b/PythonPackage/AMR/setup.py index c4cc427cd..c27ecdd1b 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='2.1.1.9131', + version='2.1.1.9133', packages=find_packages(), install_requires=[ 'rpy2', diff --git a/_pkgdown.yml b/_pkgdown.yml index 64a267a82..93b476bda 100644 --- a/_pkgdown.yml +++ b/_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`" diff --git a/cran-comments.md b/cran-comments.md index 13a5d98b6..c131e679d 100644 --- a/cran-comments.md +++ b/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! diff --git a/data-raw/_generate_python_wrapper.sh b/data-raw/_generate_python_wrapper.sh index e5f7519e1..87da6e854 100644 --- a/data-raw/_generate_python_wrapper.sh +++ b/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 diff --git a/data-raw/gpt_training_text_v2.1.1.9131.txt b/data-raw/gpt_training_text_v2.1.1.9133.txt similarity index 99% rename from data-raw/gpt_training_text_v2.1.1.9131.txt rename to data-raw/gpt_training_text_v2.1.1.9133.txt index 478b94be3..0e9ad65b3 100644 --- a/data-raw/gpt_training_text_v2.1.1.9131.txt +++ b/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. ----------------------------------------------------------------------------------------------------