diff --git a/NAMESPACE b/NAMESPACE index b12660bd..74d5bb21 100644 --- a/NAMESPACE +++ b/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) diff --git a/NEWS.md b/NEWS.md index a14ad143..ff41c64e 100644 --- a/NEWS.md +++ b/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 diff --git a/R/AbstractAnnData.R b/R/AbstractAnnData.R index 6673e5c6..ffe6a42c 100644 --- a/R/AbstractAnnData.R +++ b/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$as_InMemoryAnnData() - }, - #' @description #' Convert to an [`HDF5AnnData`] #' #' See [as_HDF5AnnData()] for more details on the conversion diff --git a/R/as_Seurat.R b/R/as_Seurat.R index b74148a8..ad5ca9aa 100644 --- a/R/as_Seurat.R +++ b/R/as_Seurat.R @@ -299,28 +299,6 @@ as_Seurat <- function( obj } -#' Convert an AnnData object to a Seurat object -#' -#' @description -#' `r lifecycle::badge("deprecated")` -#' -#' This function is deprecated, use `adata$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$as_Seurat()" - ) - as_Seurat(...) -} - # nolint start: object_name_linter .as_Seurat_is_atomic_character <- function(x) { # nolint end: object_name_linter diff --git a/R/as_SingleCellExperiment.R b/R/as_SingleCellExperiment.R index bcd61a95..a482e318 100644 --- a/R/as_SingleCellExperiment.R +++ b/R/as_SingleCellExperiment.R @@ -277,28 +277,6 @@ as_SingleCellExperiment <- function( sce } -#' Convert an AnnData object to a SingleCellExperiment object -#' -#' @description -#' `r lifecycle::badge("deprecated")` -#' -#' This function is deprecated, use `adata$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 diff --git a/R/from_Seurat.R b/R/from_Seurat.R index c83843a8..b1d7a8c4 100644 --- a/R/from_Seurat.R +++ b/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 diff --git a/R/from_SingleCellExperiment.R b/R/from_SingleCellExperiment.R index d286db30..20417fb6 100644 --- a/R/from_SingleCellExperiment.R +++ b/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 diff --git a/R/read_h5ad.R b/R/read_h5ad.R index e183b94b..3b4f043c 100644 --- a/R/read_h5ad.R +++ b/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") { diff --git a/man/AbstractAnnData.Rd b/man/AbstractAnnData.Rd index dbafb6e5..9839981e 100644 --- a/man/AbstractAnnData.Rd +++ b/man/AbstractAnnData.Rd @@ -61,11 +61,8 @@ Other AnnData classes: \item \href{#method-AbstractAnnData-varp_keys}{\code{AbstractAnnData$varp_keys()}} \item \href{#method-AbstractAnnData-uns_keys}{\code{AbstractAnnData$uns_keys()}} \item \href{#method-AbstractAnnData-as_SingleCellExperiment}{\code{AbstractAnnData$as_SingleCellExperiment()}} -\item \href{#method-AbstractAnnData-to_SingleCellExperiment}{\code{AbstractAnnData$to_SingleCellExperiment()}} \item \href{#method-AbstractAnnData-as_Seurat}{\code{AbstractAnnData$as_Seurat()}} -\item \href{#method-AbstractAnnData-to_Seurat}{\code{AbstractAnnData$to_Seurat()}} \item \href{#method-AbstractAnnData-as_InMemoryAnnData}{\code{AbstractAnnData$as_InMemoryAnnData()}} -\item \href{#method-AbstractAnnData-to_InMemoryAnnData}{\code{AbstractAnnData$to_InMemoryAnnData()}} \item \href{#method-AbstractAnnData-as_HDF5AnnData}{\code{AbstractAnnData$as_HDF5AnnData()}} \item \href{#method-AbstractAnnData-to_HDF5AnnData}{\code{AbstractAnnData$to_HDF5AnnData()}} \item \href{#method-AbstractAnnData-write_h5ad}{\code{AbstractAnnData$write_h5ad()}} @@ -245,28 +242,6 @@ A \code{SingleCellExperiment} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-AbstractAnnData-to_SingleCellExperiment}{}}} -\subsection{Method \code{to_SingleCellExperiment()}}{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -Deprecated, use \code{as_SingleCellExperiment()} instead -\subsection{Usage}{ -\if{html}{\out{
}}\preformatted{AbstractAnnData$to_SingleCellExperiment(...)}\if{html}{\out{
}} -} - -\subsection{Arguments}{ -\if{html}{\out{
}} -\describe{ -\item{\code{...}}{Arguments passed to \code{adata$as_SingleCellExperiment()}} -} -\if{html}{\out{
}} -} -\subsection{Returns}{ -A \code{SingleCellExperiment} object -} -} -\if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractAnnData-as_Seurat}{}}} \subsection{Method \code{as_Seurat()}}{ @@ -312,28 +287,6 @@ A \code{Seurat} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-AbstractAnnData-to_Seurat}{}}} -\subsection{Method \code{to_Seurat()}}{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -Deprecated, use \code{as_Seurat()} instead -\subsection{Usage}{ -\if{html}{\out{
}}\preformatted{AbstractAnnData$to_Seurat(...)}\if{html}{\out{
}} -} - -\subsection{Arguments}{ -\if{html}{\out{
}} -\describe{ -\item{\code{...}}{Arguments passed to \code{adata$as_Seurat()}} -} -\if{html}{\out{
}} -} -\subsection{Returns}{ -A \code{Seurat} object -} -} -\if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractAnnData-as_InMemoryAnnData}{}}} \subsection{Method \code{as_InMemoryAnnData()}}{ @@ -349,21 +302,6 @@ An \link{InMemoryAnnData} object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-AbstractAnnData-to_InMemoryAnnData}{}}} -\subsection{Method \code{to_InMemoryAnnData()}}{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -Deprecated, use \code{as_InMemoryAnnData()} instead -\subsection{Usage}{ -\if{html}{\out{
}}\preformatted{AbstractAnnData$to_InMemoryAnnData()}\if{html}{\out{
}} -} - -\subsection{Returns}{ -An \code{\link{InMemoryAnnData}} object -} -} -\if{html}{\out{
}} \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-AbstractAnnData-as_HDF5AnnData}{}}} \subsection{Method \code{as_HDF5AnnData()}}{ diff --git a/man/HDF5AnnData.Rd b/man/HDF5AnnData.Rd index ef3a2e06..4434034d 100644 --- a/man/HDF5AnnData.Rd +++ b/man/HDF5AnnData.Rd @@ -69,9 +69,6 @@ Other AnnData classes:
  • anndataR::AbstractAnnData$print()
  • anndataR::AbstractAnnData$shape()
  • anndataR::AbstractAnnData$to_HDF5AnnData()
    • -
  • anndataR::AbstractAnnData$to_InMemoryAnnData()
    • -
  • anndataR::AbstractAnnData$to_Seurat()
    • -
  • anndataR::AbstractAnnData$to_SingleCellExperiment()
  • anndataR::AbstractAnnData$uns_keys()
  • anndataR::AbstractAnnData$var_keys()
  • anndataR::AbstractAnnData$varm_keys()
    • diff --git a/man/InMemoryAnnData.Rd b/man/InMemoryAnnData.Rd index 7b5a06c1..fa8f7d3d 100644 --- a/man/InMemoryAnnData.Rd +++ b/man/InMemoryAnnData.Rd @@ -89,9 +89,6 @@ Other AnnData classes:
  • anndataR::AbstractAnnData$print()
  • anndataR::AbstractAnnData$shape()
  • anndataR::AbstractAnnData$to_HDF5AnnData()
    • -
  • anndataR::AbstractAnnData$to_InMemoryAnnData()
    • -
  • anndataR::AbstractAnnData$to_Seurat()
    • -
  • anndataR::AbstractAnnData$to_SingleCellExperiment()
  • anndataR::AbstractAnnData$uns_keys()
  • anndataR::AbstractAnnData$var_keys()
  • anndataR::AbstractAnnData$varm_keys()
    • diff --git a/man/from_Seurat.Rd b/man/from_Seurat.Rd deleted file mode 100644 index 5607de68..00000000 --- a/man/from_Seurat.Rd +++ /dev/null @@ -1,57 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/from_Seurat.R -\name{from_Seurat} -\alias{from_Seurat} -\title{Convert a Seurat object to an AnnData object} -\usage{ -from_Seurat( - seurat_obj, - assay_name = NULL, - x_mapping = NULL, - layers_mapping = TRUE, - obs_mapping = TRUE, - var_mapping = TRUE, - obsm_mapping = TRUE, - varm_mapping = TRUE, - obsp_mapping = TRUE, - varp_mapping = TRUE, - uns_mapping = TRUE, - output_class = c("InMemory", "HDF5AnnData"), - ... -) -} -\arguments{ -\item{seurat_obj}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{assay_name}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{x_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{layers_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obs_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{var_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obsm_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{varm_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obsp_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{varp_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{uns_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{output_class}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{...}{See \code{\link[=as_AnnData]{as_AnnData()}}} -} -\value{ -An \code{AnnData} object -} -\description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -This function is deprecated, use \code{\link[=as_AnnData]{as_AnnData()}} instead -} diff --git a/man/from_SingleCellExperiment.Rd b/man/from_SingleCellExperiment.Rd deleted file mode 100644 index 3e3aabd0..00000000 --- a/man/from_SingleCellExperiment.Rd +++ /dev/null @@ -1,54 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/from_SingleCellExperiment.R -\name{from_SingleCellExperiment} -\alias{from_SingleCellExperiment} -\title{Convert a SingleCellExperiment object to an AnnData object} -\usage{ -from_SingleCellExperiment( - sce, - x_mapping = NULL, - layers_mapping = TRUE, - obs_mapping = TRUE, - var_mapping = TRUE, - obsm_mapping = TRUE, - varm_mapping = TRUE, - obsp_mapping = TRUE, - varp_mapping = TRUE, - uns_mapping = TRUE, - output_class = c("InMemory", "HDF5AnnData"), - ... -) -} -\arguments{ -\item{sce}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{x_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{layers_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obs_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{var_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obsm_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{varm_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{obsp_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{varp_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{uns_mapping}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{output_class}{See \code{\link[=as_AnnData]{as_AnnData()}}} - -\item{...}{See \code{\link[=as_AnnData]{as_AnnData()}}} -} -\value{ -An \code{AnnData} object -} -\description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -This function is deprecated, use \code{\link[=as_AnnData]{as_AnnData()}} instead -} diff --git a/man/read_h5ad.Rd b/man/read_h5ad.Rd index 4c463459..fe9bd5bd 100644 --- a/man/read_h5ad.Rd +++ b/man/read_h5ad.Rd @@ -7,7 +7,6 @@ read_h5ad( path, as = c("InMemoryAnnData", "HDF5AnnData", "SingleCellExperiment", "Seurat"), - to = deprecated(), mode = c("r", "r+", "a", "w", "w-", "x"), ... ) @@ -26,8 +25,6 @@ read_h5ad( \code{\link[SeuratObject:Seurat-class]{SeuratObject::Seurat}} object }} -\item{to}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Deprecated, use \code{as} instead} - \item{mode}{The mode to open the HDF5 file. \itemize{ \item \code{a} creates a new file or opens an existing one for read/write. diff --git a/man/to_Seurat.Rd b/man/to_Seurat.Rd deleted file mode 100644 index 065562a1..00000000 --- a/man/to_Seurat.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/as_Seurat.R -\name{to_Seurat} -\alias{to_Seurat} -\title{Convert an AnnData object to a Seurat object} -\usage{ -to_Seurat(...) -} -\arguments{ -\item{...}{Arguments passed to \code{\link[=as_Seurat]{as_Seurat()}}} -} -\value{ -A \code{Seurat} object -} -\description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -This function is deprecated, use \code{adata$as_Seurat()} instead -} diff --git a/man/to_SingleCellExperiment.Rd b/man/to_SingleCellExperiment.Rd deleted file mode 100644 index ffdcb711..00000000 --- a/man/to_SingleCellExperiment.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/as_SingleCellExperiment.R -\name{to_SingleCellExperiment} -\alias{to_SingleCellExperiment} -\title{Convert an AnnData object to a SingleCellExperiment object} -\usage{ -to_SingleCellExperiment(...) -} -\arguments{ -\item{...}{Arguments passed to \code{\link[=as_SingleCellExperiment]{as_SingleCellExperiment()}}} -} -\value{ -A \code{SingleCellExperiment} object -} -\description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} - -This function is deprecated, use \code{adata$as_SingleCellExperiment()} instead -} diff --git a/tests/testthat/test-HDF5-read.R b/tests/testthat/test-HDF5-read.R index 2b68567f..5d3786d9 100644 --- a/tests/testthat/test-HDF5-read.R +++ b/tests/testthat/test-HDF5-read.R @@ -141,10 +141,3 @@ test_that("reading H5AD as Seurat works", { seurat <- read_h5ad(filename, as = "Seurat") expect_s4_class(seurat, "Seurat") }) - -test_that("deprecated to argument in read_h5ad() works", { - expect_warning( - mem_ad <- read_h5ad(filename, to = "InMemoryAnnData") - ) - expect_true(inherits(mem_ad, "InMemoryAnnData")) -}) diff --git a/tests/testthat/test-HDF5AnnData.R b/tests/testthat/test-HDF5AnnData.R index 95ff2f93..eef20294 100644 --- a/tests/testthat/test-HDF5AnnData.R +++ b/tests/testthat/test-HDF5AnnData.R @@ -187,8 +187,3 @@ test_that("writing var names works", { h5ad$var_names <- LETTERS[1:20] expect_identical(h5ad$var_names, LETTERS[1:20]) }) - -test_that("deprecated to_InMemoryAnnData() works", { - expect_warning(mem_ad <- adata$to_InMemoryAnnData()) - expect_true(inherits(mem_ad, "InMemoryAnnData")) -}) diff --git a/tests/testthat/test-InMemoryAnnData.R b/tests/testthat/test-InMemoryAnnData.R index 27b64d9d..2cebdf33 100644 --- a/tests/testthat/test-InMemoryAnnData.R +++ b/tests/testthat/test-InMemoryAnnData.R @@ -247,14 +247,3 @@ test_that("write to layers", { ad$layers <- dummy$layers expect_identical(ad$layers, dummy$layers) }) - -test_that("deprecated to_HDF5AnnData() works", { - ad <- AnnData( - X = dummy$X, - obs = dummy$obs, - var = dummy$var, - layers = dummy$layers - ) - expect_warning(h5_ad <- ad$to_HDF5AnnData(file = tempfile())) - expect_true(inherits(h5_ad, "HDF5AnnData")) -}) diff --git a/tests/testthat/test-as_Seurat.R b/tests/testthat/test-as_Seurat.R index 9e80fb22..96bd4856 100644 --- a/tests/testthat/test-as_Seurat.R +++ b/tests/testthat/test-as_Seurat.R @@ -177,8 +177,3 @@ test_that("as_Seurat works with unnamed mappings", { ) ) }) - -test_that("deprecated to_Seurat() works", { - expect_warning(seu <- ad$to_Seurat(x_mapping = "counts")) - expect_s4_class(seu, "Seurat") -}) diff --git a/tests/testthat/test-as_SingleCellExperiment.R b/tests/testthat/test-as_SingleCellExperiment.R index 7dfc7ba2..e1febf22 100644 --- a/tests/testthat/test-as_SingleCellExperiment.R +++ b/tests/testthat/test-as_SingleCellExperiment.R @@ -248,8 +248,3 @@ test_that("as_SCE works with unnamed mappings", { ) ) }) - -test_that("deprecated to_SingleCellExperiment() works", { - expect_warning(sce <- ad$to_SingleCellExperiment()) - expect_s4_class(sce, "SingleCellExperiment") -})