chore: migrate test data files from qs to qs2 format (GDR-3351)

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: gDRtestData
 Title: gDRtestData - R data package with testing dose response data
-Version: 1.9.1
-Date: 2025-10-30
+Version: 1.9.2
+Date: 2026-04-13
 Description: R package with internal dose-response test data. Package provides functions to generate
-  input testing data that can be used as the input for gDR pipeline. It also contains qs files
+  input testing data that can be used as the input for gDR pipeline. It also contains qs2 files
   with MAE data processed by gDR.
 Authors@R: c(person("Aleksander", "Chlebowski", role=c("aut")),
              person("Bartosz", "Czech", role=c("aut"),
@@ -27,7 +27,7 @@ Suggests:
     BiocStyle,
     gDRstyle (>= 1.7.1),
     knitr,
-    qs,
+    qs2,
     reshape2,
     rmarkdown,
     SummarizedExperiment,

NEWS.md

@@ -1,3 +1,6 @@
+## gDRtestData 1.9.2 - 2026-04-13
+* migrate test data files from `.qs` to `.qs2` format
+
 ## gDRtestData 1.9.1 - 2025-10-30
 * synchronize Bioconductor and GitHub versioning
 

R/get_test_datasets.R

@@ -4,7 +4,7 @@
 #'
 #' @param datasets_dir path to directory with datasets (default \code{NULL}).
 #' If \code{NULL}, then \code{inst/testdata} directory from \code{gDRtestData} will be used.
-#' @param pattern used to: (1) filter to qs files from the dataset_dir path
+#' @param pattern used to: (1) filter to qs2 files from the dataset_dir path
 #'        and (2) prettify the labels of the files
 #' @keywords generate_test_data
 #'
@@ -33,8 +33,8 @@ get_test_dataset_paths <-
 
    checkmate::assert_string(pattern, min.chars = 1)
 
-   epaths <- list.files(datasets_dir, pattern = pattern, full.names = TRUE)
-   enames <- gsub(pattern, "", gsub(".qs", "", basename(epaths)))
+   epaths <- list.files(datasets_dir, pattern = paste0(pattern, ".*\\.qs2$"), full.names = TRUE)
+   enames <- gsub(pattern, "", gsub("\\.qs2$", "", basename(epaths)))
    structure(epaths, names = enames)
  }
 

README.md

@@ -5,7 +5,7 @@ gDRtestData - R data package with testing dose response data to be used by all g
 
 # Available data
 
-- `inst/testdata/` directory with R datasets provided in the package in qs format
+- `inst/testdata/` directory with R datasets provided in the package in qs2 format
 
 - `inst/annotation_data/`	annotation data provided in the package
 

inst/testdata/synthetic_list.yml

@@ -1,72 +1,72 @@
 combo_2dose_nonoise:
   name: finalMAE_combo_2dose_nonoise
-  file: finalMAE_combo_2dose_nonoise.qs
+  file: finalMAE_combo_2dose_nonoise.qs2
   script: generateComboNoNoiseData
   imported_as_example: TRUE
   description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 cell lines; co-treatment drug occurs also as a primary drug"
 combo_2dose_nonoise2:
   name: finalMAE_combo_2dose_nonoise2
-  file: finalMAE_combo_2dose_nonoise2.qs
+  file: finalMAE_combo_2dose_nonoise2.qs2
   script: generateComboNoNoiseData2
   imported_as_example: FALSE
   description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 cell lines; co-treatment drug occurs also as a primary drug"
 combo_2dose_nonoise3:
   name: finalMAE_combo_2dose_nonoise3
-  file: finalMAE_combo_2dose_nonoise3.qs
+  file: finalMAE_combo_2dose_nonoise3.qs2
   script: generateComboNoNoiseData3
   imported_as_example: FALSE
   description: "3 drugs x 2 co-treatment (1 drug at 2 doses) by 3 lines; co-treatment drug does NOT have single agent response"
 combo_codilution_small:
   name: finalMAE_combo_codilution_small
-  file: finalMAE_combo_codilution_small.qs
+  file: finalMAE_combo_codilution_small.qs2
   script: generateCodilutionSmall
   imported_as_example: FALSE
   description: "4 x 1 drugs (co-dilution) for 2 cell lines; no noise"
 combo_codilution:
   name: finalMAE_combo_codilution
-  file: finalMAE_combo_codilution.qs
+  file: finalMAE_combo_codilution.qs2
   script: generateCodilution
   imported_as_example: FALSE
   description: "12 x 1 drugs (co-dilution) for 8 cell lines; no noise"
 combo_matrix_small:
   name: finalMAE_combo_matrix_small
-  file: finalMAE_combo_matrix_small.qs
+  file: finalMAE_combo_matrix_small.qs2
   script: generateComboMatrixSmall
   imported_as_example: FALSE
   description: "3 x 2 drugs (matrix) for 2 cell lines; no noise"
 combo_matrix:
   name: finalMAE_combo_matrix
-  file: finalMAE_combo_matrix.qs
+  file: finalMAE_combo_matrix.qs2
   script: generateComboMatrix
   imported_as_example: TRUE
   description: "6 x 3 drugs (matrix) for 8 cell lines"
 combo_triple:
   name: finalMAE_combo_triple
-  file: finalMAE_combo_triple.qs
+  file: finalMAE_combo_triple.qs2
   script: generateTripleComboMatrix
   imported_as_example: TRUE
   description: "2 x 3 x 2 drugs (triple matrix) for 4 cell lines"
 medium:
   name: finalMAE_medium
-  file: finalMAE_medium.qs
+  file: finalMAE_medium.qs2
   script: generateMediumData
   imported_as_example: TRUE
   description: "40 drugs (6 different drug_moa) by 15 lines (3 tissues); single agent"
 small_no_noise:
   name: finalMAE_small_no_noise
-  file: finalMAE_small_no_noise.qs
+  file: finalMAE_small_no_noise.qs2
   script: generateNoNoiseRawData
   imported_as_example: FALSE
   description: "10 drugs (3 different drug_moa) by 10 lines (3 tissues); single agent - no noise in the data"
 small:
   name: finalMAE_small
-  file: finalMAE_small.qs
+  file: finalMAE_small.qs2
   script: generateNoiseRawData
   imported_as_example: TRUE
   description: "10 drugs (3 different drug_moa) by 10 lines (3 tissues); single agent"
 wLigand:
   name: finalMAE_wLigand
-  file: finalMAE_wLigand.qs
+  file: finalMAE_wLigand.qs2
   script: generateLigandData
   imported_as_example: TRUE
   description: "3 drugs by 4 lines (3 tissues); `Ligand = 0.1` as reference; single agent"

vignettes/gDRtestData.Rmd

@@ -109,7 +109,7 @@ head(response_data)
 
 The gDR data model is built on the MultiAssayExperiments (MAE) structure. A detailed description of the gDR data model can be found in `gDRcore` package vignette.  
 
-In `inst/testdata` the user may find a set of `qs` files that are examples of gDR data model for different data types. In the file `synthetic_list.yml` one can find a list of these datasets. Currently available are: 
+In `inst/testdata` the user may find a set of `qs2` files that are examples of gDR data model for different data types. In the file `synthetic_list.yml` one can find a list of these datasets. Currently available are: 
 ```{r echo=FALSE}
 yml_path <- system.file(package = "gDRtestData", "testdata", "synthetic_list.yml")
 cat(paste0("* ", names(yaml::read_yaml(yml_path)), collapse = ", \n"), ".")