remove geoarrow (#204)

Former-commit-id: 9c0df049157f9eebfffeac8f7247bca7c2412c55
Former-commit-id: ad68e007f8a5d4787a52f014ba5e252547050170

Author: Artur-man

DESCRIPTION

@@ -59,7 +59,6 @@ Imports:
     dplyr,
     duckspatial,
     EBImage,
-    geoarrow,
     graph,
     Matrix,
     methods,

NAMESPACE

@@ -112,7 +112,6 @@ exportMethods(tableNames)
 exportMethods(tables)
 exportMethods(transform)
 exportMethods(translation)
-import(geoarrow)
 importFrom(BiocGenerics,as.data.frame)
 importFrom(BiocGenerics,colnames)
 importFrom(BiocGenerics,combine)

R/read.R

@@ -90,7 +90,6 @@ readPoint <- function(x, ...) {
 #' @rdname readSpatialData
 #' @importFrom Rarr read_zarr_attributes
 #' @importFrom duckspatial ddbs_open_dataset
-#' @import geoarrow
 #' @export
 readShape <- function(x, ...) {
     md <- read_zarr_attributes(x)

R/tables.R

@@ -149,6 +149,7 @@ setMethod("getTable", c("SpatialData", "character"), \(x, i, j, assay=1, drop=TR
 #' @export
 setMethod("setTable", c("SpatialData", "ANY"), \(x, i, ..., name=NULL, rk="rk", ik="ik") .invalid_i())
 
+# TODO: should this comment be removed ?
 # it seems pull below dispatches to arrow, and a warning on as_vector was being produced
 #' @rdname table-utils
 #' @importFrom methods as

README.md

@@ -17,7 +17,7 @@ For more details on the framework, see [Marconato et al. (2024)](https://doi.org
 ## Key features
 
 - Out-of-memory handling of images and labels using `ZarrArray` (via the [Rarr](https://bioconductor.org/packages/Rarr) package).
-- Points and shapes are managed using [arrow](https://cran.r-project.org/package=arrow) or [duckdb](https://cran.r-project.org/package=duckdb)-backed tables.
+- Points and shapes are managed using [duckdb](https://cran.r-project.org/package=duckdb)-backed tables.
 - Functional annotations (e.g., gene expression) are represented as `SingleCellExperiment` objects, integrated via [anndataR](https://bioconductor.org/packages/anndataR).
 - A system for mapping data across multiple coordinate spaces, including support for transformation graphs.