Merge branch 'main' into rmv_arrow

Author: Artur-man

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SpatialData
 Title: Representation of Python's SpatialData in R
 Depends: R (>= 4.6)
-Version: 0.99.37
+Version: 0.99.38
 Description: R interface to Python/scverse's 'spatialdata' framework for 
     unified spatial omics data handling. Adheres to OME-NGFF standards, 
     providing lazy, on-disk representations for multiscale images and 

NAMESPACE

@@ -202,6 +202,7 @@ importFrom(sf,st_bbox)
 importFrom(sf,st_centroid)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_geometry_type)
+importFrom(sf,st_point)
 importFrom(sf,st_polygon)
 importFrom(sf,st_sf)
 importFrom(sf,st_sfc)

R/SpatialData.R

@@ -3,7 +3,7 @@
 #' 
 #' @aliases data meta 
 #' @aliases layer element element<-
-#' @aliases image label point shape table,ANY-method
+#' @aliases image label point shape table
 #' @aliases images labels points shapes tables
 #' @aliases image<- label<- point<- shape<- table<-
 #' @aliases images<- labels<- points<- shapes<- tables<-

R/methods.R

@@ -230,7 +230,8 @@ for (. in one) eval(f(.), parent.env(environment()))
 # get one ----
 
 #' @name SpatialData
-#' @exportMethod image label point shape
+#' @importFrom BiocGenerics table
+#' @exportMethod image label point shape table
 NULL
 
 .get <- \(y, i) {
@@ -249,24 +250,8 @@ NULL
     y[[i]]
 }
 
-#' @export
-#' @name SpatialData
-#' @importFrom BiocGenerics table
-setMethod("table", "ANY", \(...) {
-    l <- list(...)
-    if (!is(l[[1]], "SpatialData"))
-        return(base::table(...))
-    n <- length(l)
-    i <- if (n == 1) 1 else l[[2]]
-    m <- length(i)
-    if (n > 2 || m > 1)
-        stop("too many arguments")
-    y <- l[[1]]$tables
-    .get(y, i)
-})
-
 .set <- \(.) setMethod(., "SpatialData", \(x, i=1) .get(x[[paste0(., "s")]], i))
-for (. in setdiff(one, "table")) eval(.set(.), parent.env(environment()))
+for (. in one) eval(.set(.), parent.env(environment()))
 
 # set all ----
 

R/sdFrame.R

@@ -74,7 +74,7 @@ NULL
 
 # new ----
 
-#' @importFrom sf st_sf st_sfc st_as_sf st_polygon
+#' @importFrom sf st_sf st_sfc st_as_sf st_point st_polygon
 .df_to_sf <- \(data, type=c("POINT", "POLYGON")) {
     type <- match.arg(type)
     if (is.null(data) || isTRUE(nrow(data) == 0)) {

inst/NEWS

@@ -1,3 +1,7 @@
+changes in version 0.99.38
+
+- use BiocGenerics::table
+
 changes in version 0.99.37
 
 - fix note regarding internal '.mask' generic