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Merged
Artur-man merged 2 commits into from
May 19, 2026
+2 −4
Merged

remove geoarrow #204

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415ddef
remove geoarrow
Artur-man May 19, 2026
b35642d
Merge branch 'main' into rmv_arrow
Artur-man May 19, 2026
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1 change: 0 additions & 1 deletion DESCRIPTION
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Expand Up @@ -59,7 +59,6 @@ Imports:
dplyr,
duckspatial,
EBImage,
geoarrow,
graph,
Matrix,
methods,
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1 change: 0 additions & 1 deletion NAMESPACE
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Expand Up @@ -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)
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1 change: 0 additions & 1 deletion R/read.R
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Expand Up @@ -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)
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1 change: 1 addition & 0 deletions R/tables.R
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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.

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