chore: migrate from qs to qs2 package (GDR-3351)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.9.7
-Date: 2026-04-14
+Version: 1.9.8
+Date: 2026-04-18
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),
              person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",
@@ -38,7 +38,7 @@ Imports:
     stats,
     stringr,
     SummarizedExperiment,
-    qs,
+    qs2,
     utils
 Suggests:
     BiocManager,

Dockerfile

@@ -10,7 +10,7 @@ ARG GITHUB_TOKEN
 RUN mkdir -p /mnt/vol
 COPY rplatform/dependencies.yaml rplatform/.github_access_token.txt* /mnt/vol
 RUN echo "$GITHUB_TOKEN" >> /mnt/vol/.github_access_token.txt
-RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs"))'
+RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs2"))'
 RUN Rscript -e "gDRstyle::installAllDeps()"
 
 #================= Check & build package

NEWS.md

@@ -1,3 +1,7 @@
+## gDRutils 1.9.8 - 2026-04-18
+* migrate from `qs` to `qs2` package (`qs::qread` → `qs2::qs_read`, `qs::qsave` → `qs2::qs_save`)
+* update batch file extension from `.qs` to `.qs2`
+
 ## gDRutils 1.9.7 - 2026-04-14
 * add support for metadata in `merge_MAE`
 

R/combo.R

@@ -11,7 +11,7 @@
 #' @return list of data.table(s) with combo data
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs")
+#' mae <- get_synthetic_data("finalMAE_combo_matrix_small.qs2")
 #' convert_combo_data_to_dt(mae[[1]])
 #'
 #' @export

R/concatentate_SEs.R

@@ -33,7 +33,7 @@ has_nested_field <- function(asy, nested_field) {
 #' @details Revert this operation using \code{promote_fields}.
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
 #' demote_fields(se, "ReadoutValue")
@@ -96,7 +96,7 @@ demote_fields <- function(se, fields) {
 #' @seealso demote_fields
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' se <- promote_fields(se, "ReadoutValue", 2)
 #' 
@@ -218,7 +218,7 @@ promote_fields <- function(se, fields, MARGIN = c(1, 2)) {
 #' @return A \code{BumpyMatrix} object aggregated by \code{FUN}.
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' assay <- SummarizedExperiment::assay(se)
 #' aggregate_assay(assay, FUN = mean, by = c("Barcode"))

R/convert_mae_se_assay_to_dt.R

@@ -28,7 +28,7 @@
 #' @return data.table representation of the data in \code{assay_name}.
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' convert_se_assay_to_dt(se, "Metrics")
 #'
@@ -230,7 +230,7 @@ convert_se_assay_to_dt <- function(se,
 #' @seealso flatten convert_se_assay_to_dt
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' convert_mae_assay_to_dt(mae, "Metrics")
 #'
 #' @export
@@ -306,7 +306,7 @@ convert_mae_assay_to_dt <- function(mae,
 #' @return data.table representation of the data in \code{assay_name} with added information from \code{colData}.
 #'
 #' @examples
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' convert_se_assay_to_custom_dt(se, "Metrics")
 #' convert_se_assay_to_custom_dt(se, "Metrics", output_table = "Metrics_raw")
@@ -349,8 +349,8 @@ convert_se_assay_to_custom_dt <- function(se,
   }
 
   if (output_table %in% c("Metrics", "Metrics_raw")) {
-    # SE*.qs files contain 'c50' column instead of the 'ec50' in the metrics
-    # this is a temporary fix that should be removed once data (qs files) is reprocessed
+    # SE*.qs2 files contain 'c50' column instead of the 'ec50' in the metrics
+    # this is a temporary fix that should be removed once data (qs2 files) is reprocessed
     data.table::setnames(dt, "c50", "ec50", skip_absent = TRUE)
 
     groups <- c("normalization_type", "fit_source")

R/duplicates.R

@@ -31,7 +31,7 @@ has_dt_duplicated_rows <- function(dt, col_names = NULL) {
 #' 
 #' @param dt data.table with assay data
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' get_assay_req_uniq_cols(smetrics_data)
 #' @return charvec with columns required to have unique data
@@ -80,7 +80,7 @@ get_assay_req_uniq_cols <- function(dt) {
 #' @return logical flag indicating if a dt contains duplicated rows or not
 #' @keywords duplicates
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' has_assay_dt_duplicated_rows(smetrics_data)
 #' @export
@@ -142,7 +142,7 @@ get_duplicated_rows <- function(x,
 #' @param output string with the output format to be returned
 #' @return integer vector or data.table with duplicated rows
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' get_assay_dt_duplicated_rows(smetrics_data, output = "data")
 #' get_assay_dt_duplicated_rows(smetrics_data)
@@ -169,7 +169,7 @@ get_assay_dt_duplicated_rows <- function(dt, output = "index") {
 #' @param msg_f function to be used to throw the message
 #' @param preview_max_numb number of rows to preview if duplicates found
 #' @examples
-#' sdata <- get_synthetic_data("finalMAE_small")
+#' sdata <- get_synthetic_data("finalMAE_small.qs2")
 #' smetrics_data <- convert_se_assay_to_dt(sdata[[1]], "Metrics")
 #' throw_msg_if_duplicates(smetrics_data, assay_name = "Metrics", msg_f = futile.logger::flog.info)
 #' @return NULL

R/experiment_validators.R

@@ -38,7 +38,7 @@ validate_dimnames <- function(obj, obj2, skip_empty = TRUE) {
 #' @export
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' validate_se_assay_name(se, "RawTreated")
 #'
@@ -71,7 +71,7 @@ validate_se_assay_name <- function(se, name) {
 #' @export
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' validate_SE(se)
 #'
@@ -142,7 +142,7 @@ validate_SE <- function(se,
 #' @export
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' validate_MAE(mae)
 #' 
 #' @author Bartosz Czech <bartosz.czech@@contractors.roche.com>

R/fit_curves.R

@@ -444,7 +444,7 @@ predict_efficacy_from_conc <- function(c, x_inf, x_0, ec50, h) {
 #' @return A single numeric value for the predicted 'smooth' response.
 #' 
 #' @examples
-#' mae <- gDRutils::get_synthetic_data("combo_matrix")
+#' mae <- get_synthetic_data("combo_matrix")
 #' se <- mae[[gDRutils::get_supported_experiments("combo")]]
 #' dt_metrics <- gDRutils::convert_se_assay_to_dt(se[1, 1], "Metrics")[normalization_type == "RV"]
 #' predict_smooth_from_combo(conc_1 = 1.2, conc_2 = 9.8, metrics_merged = dt_metrics)

R/helpers-tests.R

@@ -11,7 +11,7 @@
 #' @export
 get_testdata <- function() {
 
-  mae <- get_synthetic_data("finalMAE_small")
+  mae <- get_synthetic_data("finalMAE_small.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)
@@ -51,7 +51,7 @@ get_testdata <- function() {
 #' @export
 get_testdata_combo <- function() {
 
-  mae <- get_synthetic_data("finalMAE_combo_matrix")
+  mae <- get_synthetic_data("finalMAE_combo_matrix.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)
@@ -91,7 +91,7 @@ get_testdata_combo <- function() {
 #' @export
 get_testdata_codilution <- function() {
 
-  mae <- get_synthetic_data("finalMAE_combo_codilution_small")
+  mae <- get_synthetic_data("finalMAE_combo_codilution_small.qs2")
   raw_data <- convert_mae_assay_to_dt(mae, "Metrics")
   drug_names <- unique(raw_data$DrugName)
   cell_line_names <- unique(raw_data$CellLineName)

R/json_convert.R

@@ -9,7 +9,7 @@
 #' @return String representation of a JSON document.
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' convert_mae_to_json(mae)
 #' convert_mae_to_json(mae, with_experiments = FALSE)
 #' 

R/json_validate.R

@@ -69,7 +69,7 @@ validate_json <- function(json, schema_path) {
 #' @return Boolean of whether or not mae is valid
 #'
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' validate_mae_with_schema(mae)
 #' 
 #' @export

R/merge_SE.R

@@ -13,8 +13,8 @@
 #' @keywords SE_operators
 #'
 #' @examples
-#' mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
-#' mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+#' mae1 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
+#' mae2 <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 #' merge_MAE(list(mae1 = mae1, mae2 = mae2), title = "Test", description = "Test MAE")
 #'
 #' @return Merged MultiAssayExperiment object.
@@ -149,7 +149,7 @@ merge_MAE <- function(MAElist,
 #' @keywords SE_operators
 #'
 #' @examples
-#' se1 <- get_synthetic_data("finalMAE_small")[[1]]
+#' se1 <- get_synthetic_data("finalMAE_small.qs2")[[1]]
 #' merge_SE(list(se1 = se1, se2 = se1))
 #'
 #' @return merged SummarizedExperiment object
@@ -248,7 +248,7 @@ merge_SE <- function(SElist,
 #' @return BumpyMatrix or list with data.table + BumpyMatrix
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise")
+#' mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
 #' 
 #' listSE <- list(
 #'   combo1 = mae[[1]], 
@@ -303,7 +303,7 @@ merge_assay <- function(SElist,
 #' @return character vector of unique names of metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' SElist <- list(
 #'   se, 
@@ -329,7 +329,7 @@ identify_unique_se_metadata_fields <- function(SElist) {
 #' @return list of merged metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' listSE <- list(
 #'   se, 

R/se_metadata.R

@@ -76,7 +76,7 @@ set_SE_experiment_raw_data <- function(se, value) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_fit_parameters(se)
 #' 
@@ -90,7 +90,7 @@ get_SE_fit_parameters <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' meta <- get_SE_processing_metadata(se)
 #' 
@@ -103,7 +103,7 @@ get_SE_processing_metadata <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_experiment_raw_data(se)
 #' 
@@ -116,7 +116,7 @@ get_SE_experiment_raw_data <- function(se) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_experiment_metadata(se)
 #' 
@@ -142,7 +142,7 @@ get_SE_keys <- function(se, key_type = NULL) {
 #' @rdname SE_metadata
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs") 
+#' mae <- get_synthetic_data("finalMAE_small.qs2") 
 #' se <- mae[[1]]
 #' get_SE_identifiers(se)
 #' 
@@ -175,7 +175,7 @@ get_SE_identifiers <- function(se, id_type = NULL, simplify = TRUE) {
 #' @return named list with identifiers for each SE
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' get_MAE_identifiers(mae)
 #' 
 #' @keywords SE_operators

R/standardize_MAE.R

@@ -8,7 +8,7 @@
 #' @return mae a MultiAssayExperiment with default gDR identifiers
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' S4Vectors::metadata(mae[[1]])$identifiers$drug <- "druug"
 #' standardize_mae(mae)
 #' 
@@ -32,7 +32,7 @@ standardize_mae <- function(mae, use_default = TRUE) {
 #' @return se a SummarizedExperiment with default gDR identifiers
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' S4Vectors::metadata(se)$identifiers$drug <- "druug"
 #' standardize_se(se)
@@ -142,7 +142,7 @@ standardize_se <- function(se, use_default = TRUE) {
 #' @return a renamed DFrame object
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' rename_DFrame(SummarizedExperiment::rowData(mae[[1]]), c("Gnumber" = "Gnumber1"))
 #' 
 #' @export
@@ -165,7 +165,7 @@ rename_DFrame <- function(df, mapping_vector) {
 #' @return a renamed BumpyMatrix object
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' se <- mae[[1]]
 #' assay <- SummarizedExperiment::assay(se)
 #' rename_bumpy(assay, c("Concentration" = "conc"))
@@ -231,7 +231,7 @@ get_optional_rowdata_fields <- function(se) {
 #' @return refined colData
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' refine_coldata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 #' 
 #' @export
@@ -263,7 +263,7 @@ refine_coldata <- function(cd, se, default_v = "Undefined") {
 #' @return refined rowData
 #' 
 #' @examples 
-#' mae <- get_synthetic_data("finalMAE_small.qs")
+#' mae <- get_synthetic_data("finalMAE_small.qs2")
 #' refine_rowdata(SummarizedExperiment::colData(mae[[1]]), mae[[1]])
 #' 
 #' @export