Merge pull request #124 from tidyomics/use-tidy-from-generics

Use tidy from generics

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.19.3
+Version: 1.19.4
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="mangiolastefano@gmail.com",
@@ -42,7 +42,8 @@ Imports:
     cli,
     fansi,
     Matrix,
-    stats
+    stats,
+    generics
 Suggests:
     BiocStyle,
     testthat,

NAMESPACE

@@ -47,7 +47,6 @@ S3method(unite,SingleCellExperiment)
 S3method(unnest,tidySingleCellExperiment_nested)
 export("%>%")
 export(join_transcripts)
-export(tidy)
 export(unnest_single_cell_experiment)
 exportMethods(join_features)
 importFrom(Matrix,rowSums)
@@ -101,6 +100,7 @@ importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_used)
 importFrom(fansi,strwrap_ctl)
+importFrom(generics,tidy)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,ggplot)
 importFrom(lifecycle,deprecate_warn)

R/methods.R

@@ -93,11 +93,11 @@ setMethod("join_features", "SingleCellExperiment", function(.data,
     }
 })
 
-#' @name tidy
-#' @rdname tidy
 #' @title (DEPRECATED) tidy for `SingleCellExperiment`
+#' @name tidy.SingleCellExperiment
 #'
-#' @param object A `SingleCellExperiment` object.
+#' @param x A `SingleCellExperiment` object.
+#' @param ... Additional arguments passed to `generics::tidy`. (Unused.)
 #' @return A `tidySingleCellExperiment` object. (DEPRECATED - not needed anymore)
 #'
 #' @examples
@@ -107,23 +107,18 @@ setMethod("join_features", "SingleCellExperiment", function(.data,
 #' @references
 #' Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2
 #'
-#' @export
-tidy <- function(object) {
-    UseMethod("tidy", object)
-}
-
-#' @rdname tidy
+#' @importFrom generics tidy
 #' @importFrom lifecycle deprecate_warn
 #' @export
-tidy.SingleCellExperiment <- function(object) {
+tidy.SingleCellExperiment <- function(x, ...) {
 
     # DEPRECATE
     deprecate_warn(
         when="1.1.1",
         what="tidy()",
         details="tidySingleCellExperiment says: tidy() is not needed anymore.")
 
-    return(object)
+    return(x)
 }
 
 #' @name aggregate_cells