Remove deprecated functionality

NAMESPACE

@@ -4,12 +4,8 @@ S3method(as_AnnData,Seurat)
 S3method(as_AnnData,SingleCellExperiment)
 export(AnnData)
 export(as_AnnData)
-export(from_Seurat)
-export(from_SingleCellExperiment)
 export(generate_dataset)
 export(read_h5ad)
-export(to_Seurat)
-export(to_SingleCellExperiment)
 export(write_h5ad)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,sparseMatrix)

NEWS.md

@@ -1,6 +1,8 @@
 # anndataR 0.99.0
 
-- Bump required R version to 4.5 in preparation of Bioconductor submission
+- Bump required R version to 4.5 in preparation for Bioconductor submission
+  (PR #309)
+- Remove deprecated functions and arguments (PR #311)
 
 # anndataR 0.2.0
 

R/AbstractAnnData.R

@@ -204,23 +204,6 @@ AbstractAnnData <- R6::R6Class(
       )
     },
     #' @description
-    #' `r lifecycle::badge('deprecated')`
-    #'
-    #' Deprecated, use `as_SingleCellExperiment()` instead
-    #'
-    #' @param ... Arguments passed to `adata$as_SingleCellExperiment()`
-    #'
-    #' @return A `SingleCellExperiment` object
-    to_SingleCellExperiment = function(...) {
-      lifecycle::deprecate_warn(
-        "0.1.0",
-        "to_SingleCellExperiment()",
-        "as_SingleCellExperiment()"
-      )
-
-      self$as_SingleCellExperiment(...)
-    },
-    #' @description
     #' Convert to `Seurat`
     #'
     #' See [as_Seurat()] for more details on the conversion
@@ -258,23 +241,6 @@ AbstractAnnData <- R6::R6Class(
       )
     },
     #' @description
-    #' `r lifecycle::badge('deprecated')`
-    #'
-    #' Deprecated, use `as_Seurat()` instead
-    #'
-    #' @param ... Arguments passed to `adata$as_Seurat()`
-    #'
-    #' @return A `Seurat` object
-    to_Seurat = function(...) {
-      lifecycle::deprecate_warn(
-        "0.1.0",
-        "to_Seurat()",
-        "as_Seurat()"
-      )
-
-      self$as_Seurat(...)
-    },
-    #' @description
     #' Convert to an [`InMemoryAnnData`]
     #'
     #' See [as_InMemoryAnnData()] for more details on the conversion
@@ -284,21 +250,6 @@ AbstractAnnData <- R6::R6Class(
       as_InMemoryAnnData(self)
     },
     #' @description
-    #' `r lifecycle::badge('deprecated')`
-    #'
-    #' Deprecated, use `as_InMemoryAnnData()` instead
-    #'
-    #' @return An [`InMemoryAnnData`] object
-    to_InMemoryAnnData = function() {
-      lifecycle::deprecate_warn(
-        "0.1.0",
-        "to_InMemoryAnnData()",
-        "as_InMemoryAnnData()"
-      )
-
-      self$as_InMemoryAnnData()
-    },
-    #' @description
     #' Convert to an [`HDF5AnnData`]
     #'
     #' See [as_HDF5AnnData()] for more details on the conversion

R/as_Seurat.R

@@ -299,28 +299,6 @@ as_Seurat <- function(
   obj
 }
 
-#' Convert an AnnData object to a Seurat object
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is deprecated, use `adata$as_Seurat()` instead
-#'
-#' @param ... Arguments passed to [as_Seurat()]
-#'
-#' @return A `Seurat` object
-#' @export
-# nolint start: object_name_linter
-to_Seurat <- function(...) {
-  # nolint end: object_name_linter
-  lifecycle::deprecate_warn(
-    when = "0.1.0",
-    what = "to_Seurat()",
-    with = "adata$as_Seurat()"
-  )
-  as_Seurat(...)
-}
-
 # nolint start: object_name_linter
 .as_Seurat_is_atomic_character <- function(x) {
   # nolint end: object_name_linter

R/as_SingleCellExperiment.R

@@ -277,28 +277,6 @@ as_SingleCellExperiment <- function(
   sce
 }
 
-#' Convert an AnnData object to a SingleCellExperiment object
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is deprecated, use `adata$as_SingleCellExperiment()` instead
-#'
-#' @param ... Arguments passed to [as_SingleCellExperiment()]
-#'
-#' @return A `SingleCellExperiment` object
-#' @export
-# nolint start: object_name_linter
-to_SingleCellExperiment <- function(...) {
-  # nolint end: object_name_linter
-  lifecycle::deprecate_warn(
-    when = "0.1.0",
-    what = "to_SingleCellExperiment()",
-    with = "adata$as_SingleCellExperiment()"
-  )
-  as_SingleCellExperiment(...)
-}
-
 # nolint start: object_length_linter object_name_linter
 .as_SCE_guess_all <- function(adata, slot) {
   # nolint end: object_length_linter object_name_linter

R/from_Seurat.R

@@ -1,10 +1,5 @@
 #' Convert a Seurat object to an AnnData object
 #'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is deprecated, use [as_AnnData()] instead
-#'
 #' @param seurat_obj See [as_AnnData()]
 #' @param assay_name See [as_AnnData()]
 #' @param x_mapping See [as_AnnData()]
@@ -20,7 +15,7 @@
 #' @param ... See [as_AnnData()]
 #'
 #' @return An `AnnData` object
-#' @export
+#' @noRd
 # nolint start: object_name_linter
 from_Seurat <- function(
   # nolint end: object_name_linter

R/from_SingleCellExperiment.R

@@ -1,10 +1,5 @@
 #' Convert a SingleCellExperiment object to an AnnData object
 #'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is deprecated, use [as_AnnData()] instead
-#'
 #' @param sce See [as_AnnData()]
 #' @param x_mapping See [as_AnnData()]
 #' @param layers_mapping See [as_AnnData()]
@@ -19,7 +14,7 @@
 #' @param ... See [as_AnnData()]
 #'
 #' @return An `AnnData` object
-#' @export
+#' @noRd
 # nolint start: object_name_linter
 from_SingleCellExperiment <- function(
   # nolint end: object_name_linter

R/read_h5ad.R

@@ -12,7 +12,6 @@
 #'     [`SingleCellExperiment::SingleCellExperiment`] object
 #'   * `"Seurat"`: Read the H5AD file as a
 #'     [`SeuratObject::Seurat`] object
-#' @param to `r lifecycle::badge('deprecated')` Deprecated, use `as` instead
 #' @param mode The mode to open the HDF5 file.
 #'
 #'   * `a` creates a new file or opens an existing one for read/write.
@@ -43,23 +42,12 @@
 read_h5ad <- function(
   path,
   as = c("InMemoryAnnData", "HDF5AnnData", "SingleCellExperiment", "Seurat"),
-  to = deprecated(),
   mode = c("r", "r+", "a", "w", "w-", "x"),
   ...
 ) {
   as <- match.arg(as)
   mode <- match.arg(mode)
 
-  if (lifecycle::is_present(to)) {
-    lifecycle::deprecate_warn(
-      when = "0.1.0",
-      what = "read_h5ad(to = )",
-      with = "read_h5ad(as = )",
-      details = "Overwriting `as` with `to`."
-    )
-    as <- to
-  }
-
   hdf5_adata <- HDF5AnnData$new(path, mode = mode)
 
   if (as == "HDF5AnnData") {