switch from Rarr to ZarrArray

Author: Artur-man

DESCRIPTION

@@ -43,7 +43,7 @@ Imports:
     jsonlite,
     Matrix,
     methods,
-    Rarr,
+    ZarrArray,
     RBGL,
     reticulate,
     sf,
@@ -70,7 +70,8 @@ Remotes:
     keller-mark/pizzarr,
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,
-    HelenaLC/SpatialData.plot
+    HelenaLC/SpatialData.plot,
+    Bioconductor/ZarrArray
 biocViews: 
     DataImport, 
     DataRepresentation, 

NAMESPACE

@@ -91,7 +91,6 @@ importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseVector)
 importFrom(Matrix,t)
 importFrom(RBGL,sp.between)
-importFrom(Rarr,ZarrArray)
 importFrom(S4Arrays,as.array.Array)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,coolcat)
@@ -107,6 +106,7 @@ importFrom(SingleCellExperiment,int_metadata)
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
+importFrom(ZarrArray,ZarrArray)
 importFrom(arrow,open_dataset)
 importFrom(basilisk,BasiliskEnvironment)
 importFrom(basilisk,basiliskRun)

R/ImageArray.R

@@ -2,7 +2,7 @@
 #' @title The `ImageArray` class
 #' 
 #' @param x \code{ImageArray}
-#' @param data list of \code{\link[Rarr]{ZarrArray}}s
+#' @param data list of \code{\link[ZarrArray]{ZarrArray}}s
 #' @param meta \code{\link{Zattrs}}
 #' @param metadata optional list of arbitrary 
 #'   content describing the overall object.

R/LabelArray.R

@@ -14,7 +14,7 @@
 #' }
 #'
 #' @param x \code{LabelArray}
-#' @param data list of \code{\link[Rarr]{ZarrArray}}s
+#' @param data list of \code{\link[ZarrArray]{ZarrArray}}s
 #' @param meta \code{\link{Zattrs}}
 #' @param metadata optional list of arbitrary 
 #'   content describing the overall object.

R/read.R

@@ -69,15 +69,15 @@ allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0",
 #' (x <- readSpatialData(base))
 NULL
 
+#' @importFrom ZarrArray ZarrArray
 readsdlayer <- function(x, ...) {
   md <- fromJSON(file.path(x, ".zattrs"))
   ps <- .get_multiscales_dataset_paths(md)
-  list(array = lapply(ps, \(.) ZarrArray(file.path(x, as.character(.)))), 
+  list(array = lapply(ps, \(.) ZarrArray::ZarrArray(file.path(x, as.character(.)))), 
        md = md)
 }
 
 #' @rdname readSpatialData
-#' @importFrom Rarr ZarrArray
 #' @importFrom jsonlite fromJSON
 #' @export
 readImage <- function(x, ...) {
@@ -86,7 +86,6 @@ readImage <- function(x, ...) {
 }
 
 #' @rdname readSpatialData
-#' @importFrom Rarr ZarrArray
 #' @importFrom jsonlite fromJSON
 #' @export
 readLabel <- function(x, ...) {