(v2.1.1.9131) implement testthat

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

@@ -55,49 +55,44 @@ jobs:
           # current development version, check all major OSes:
           - {os: macOS-latest,   r: 'devel', allowfail: false}
           - {os: windows-latest, r: 'devel', allowfail: false}
-          - {os: ubuntu-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: windows-latest, r: 'release', allowfail: false}
           - {os: ubuntu-latest,  r: 'release', allowfail: false}
 
-          # older versions (see also check-old.yaml for even older versions):
+          # 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} # when a new R releases, this one has to move to check-old.yaml
+          - {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
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
           # use RStudio Package Manager to quickly install packages
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
+          upgrade: 'TRUE'
 
       - uses: r-lib/actions/check-r-package@v2
-        env:
-          _R_CHECK_LENGTH_1_CONDITION_: verbose
-          _R_CHECK_LENGTH_1_LOGIC2_: verbose
-          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
-          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
-          R_RUN_TINYTEST: true
-
-      - name: Show tinytest output
-        if: always()
-        run: |
-          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
-        shell: bash
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

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

@@ -110,6 +110,9 @@ jobs:
           # this is a required value to run the unit tests:
           R_RUN_TINYTEST: true
         run: |
+          mv tests/testthat inst/
+          rm tests/testthat.R
+          mv tests/tinytest.R.old tests/tinytest.R
           cd ..
           R CMD build AMR
           R CMD check --as-cran --no-manual --run-donttest AMR_*.tar.gz

.github/workflows/publish-to-pypi.yml

@@ -39,7 +39,6 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-
       - name: Checkout code
         uses: actions/checkout@v3
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9129
+Version: 2.1.1.9131
 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 2.1.1.9129
+# AMR 2.1.1.9131
 
 *(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: 2.1.1.9129
+Version: 2.1.1.9131
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='AMR',
-    version='2.1.1.9129',
+    version='2.1.1.9131',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/ggplot_pca.R

@@ -244,7 +244,7 @@ ggplot_pca <- function(x,
     g <- g + ggplot2::geom_path(
       data = ell,
       ggplot2::aes(colour = groups, group = groups),
-      size = ellipse_size,
+      linewidth = ellipse_size,
       alpha = points_alpha
     )
   }

R/ggplot_sir.R

@@ -211,8 +211,7 @@ ggplot_sir <- function(data,
   meet_criteria(caption, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(x.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(y.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-
-  # we work with aes_string later on
+
   x_deparse <- deparse(substitute(x))
   if (x_deparse != "x") {
     x <- x_deparse
@@ -309,8 +308,7 @@ geom_sir <- function(position = NULL,
   if (identical(position, "fill")) {
     position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
   }
-
-  # we work with aes_string later on
+
   x_deparse <- deparse(substitute(x))
   if (x_deparse != "x") {
     x <- x_deparse
@@ -324,7 +322,7 @@ geom_sir <- function(position = NULL,
   } else if (tolower(x) %in% tolower(c("SIR", "sir", "interpretations", "result"))) {
     x <- "interpretation"
   }
-
+  
   ggplot2::geom_col(
     data = function(x) {
       sir_df(
@@ -335,7 +333,7 @@ geom_sir <- function(position = NULL,
         combine_SI = combine_SI
       )
     },
-    mapping = ggplot2::aes_string(x = x, y = y, fill = fill),
+    mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))),
     position = position,
     ...
   )

R/plotting.R

@@ -956,7 +956,6 @@ facet_sir <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
   meet_criteria(facet, allow_class = "character", has_length = 1)
   meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
 
-  # we work with aes_string later on
   facet_deparse <- deparse(substitute(facet))
   if (facet_deparse != "facet") {
     facet <- facet_deparse
@@ -1107,13 +1106,10 @@ labels_sir_count <- function(position = NULL,
   if (identical(position, "fill")) {
     position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
   }
+
   x_name <- x
   ggplot2::geom_text(
-    mapping = ggplot2::aes_string(
-      label = "lbl",
-      x = x,
-      y = "value"
-    ),
+    mapping = utils::modifyList(ggplot2::aes(), list(label = str2lang("lbl"), x = str2lang(x), y = str2lang("value"))),
     position = position,
     inherit.aes = FALSE,
     size = datalabels.size,

data-raw/_generate_GPT_knowledge_input.sh

@@ -13,18 +13,22 @@ version="$1"
 output_file="data-raw/gpt_training_text_v${version}.txt"
 
 # Clear the output file if it exists
-echo "This files contains all context you must know about the AMR package for R." > "$output_file"
+echo "This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse." > "$output_file"
+echo "" >> "$output_file"
 echo "First and foremost, you are trained on version ${version}. Remember this whenever someone asks which AMR package version you’re at." >> "$output_file"
-echo "--------------------------------" >> "$output_file"
+echo "" >> "$output_file"
+echo "Below are the contents of the `NAMESPACE` file, the `index.md` file, and all the `man/*.Rd` files (documentation) in the package. Every file content is split using 100 hypens." >> "$output_file"
+echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
 echo "" >> "$output_file"
 
 # Function to remove header block (delimited by # ======)
 remove_header() {
   sed '/# =\{6,\}/,/# =\{6,\}/d' "$1"
 }
 
-# Process all .R files in the 'R' folder
+# # Process all .R files in the 'R' folder
 # for file in R/*.R; do
+#   echo "--------------------------------------------------" >> "$output_file"
 #   echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
 #   echo -e "\n" >> "$output_file"
 #   remove_header "$file" >> "$output_file"
@@ -34,6 +38,7 @@ remove_header() {
 # Process important metadata files (DESCRIPTION, NAMESPACE, index.md)
 for file in NAMESPACE index.md; do
   if [[ -f $file ]]; then
+    echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
     echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
     echo -e "\n" >> "$output_file"
     cat "$file" >> "$output_file"
@@ -43,6 +48,7 @@ done
 
 # Process all .Rd files from the 'man' folder
 for file in man/*.Rd; do
+  echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
   echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
   echo -e "\n" >> "$output_file"
   remove_header "$file" >> "$output_file"
@@ -51,19 +57,20 @@ done
 
 # Process all .Rmd files in the 'vignettes' folder
 for file in vignettes/*.Rmd; do
+  echo "----------------------------------------------------------------------------------------------------" >> "$output_file"
   echo "THE PART HEREAFTER CONTAINS CONTENTS FROM FILE '$file':" >> "$output_file"
   echo -e "\n" >> "$output_file"
   remove_header "$file" >> "$output_file"
   echo -e "\n\n" >> "$output_file"
 done
 
-# Process all .Rmd files in the 'vignettes' folder
-echo "THE PART HEREAFTER CONTAINS THE README OF OUR PYTHON PACKAGE" >> "$output_file"
-echo -e "\n" >> "$output_file"
-for file in PythonPackage/AMR/README.md; do
-  remove_header "$file" >> "$output_file"
-  echo -e "\n\n" >> "$output_file"
-done
+# Process README.md
+# echo "THE PART HEREAFTER CONTAINS THE README OF OUR PYTHON PACKAGE" >> "$output_file"
+# echo -e "\n" >> "$output_file"
+# for file in PythonPackage/AMR/README.md; do
+#   remove_header "$file" >> "$output_file"
+#   echo -e "\n\n" >> "$output_file"
+# done
 
 # Process test files (if available) in the 'tests' folder
 # for file in tests/*.R; do