Replace pizzarr support with Rarr for importing tables (anndataR) (#139)

Author: Artur-man

DESCRIPTION

@@ -46,12 +46,12 @@ Imports:
     ZarrArray,
     RBGL,
     reticulate,
+    anndataR,
     sf,
     S4Arrays,
     S4Vectors,
     SingleCellExperiment,
-    SummarizedExperiment,
-    zellkonverter
+    SummarizedExperiment
 Suggests:
     BiocStyle,
     ggnewscale,
@@ -63,11 +63,7 @@ Suggests:
     SpatialData.plot,
     testthat,
     DT
-Enhances:
-    anndataR,
-    pizzarr
 Remotes:
-    keller-mark/pizzarr,
     keller-mark/anndataR@spatialdata,
     HelenaLC/SpatialData.data,
     HelenaLC/SpatialData.plot,

NAMESPACE

@@ -80,6 +80,7 @@ exportMethods(tableNames)
 exportMethods(tables)
 exportMethods(translation)
 exportMethods(valTable)
+import(anndataR)
 import(geoarrow)
 importClassesFrom(S4Arrays,Array)
 importClassesFrom(S4Vectors,DFrame)
@@ -149,4 +150,3 @@ importFrom(sf,st_sfc)
 importFrom(utils,.DollarNames)
 importFrom(utils,head)
 importFrom(utils,tail)
-importFrom(zellkonverter,AnnData2SCE)

R/read.R

@@ -27,10 +27,10 @@
 # "zarr==2.18.4", "zict==3.0.0")
 allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0", 
          "spatialdata_plot==0.2.14", "setuptools==75.8.0")
-# notes from VJC -- readSpatialData was modified below so
-# that if anndataR = FALSE, spatialdata.read_zarr is used
+# notes from VJC/AM -- readSpatialData was modified below so
+# that if anndataR = FALSE, anndata.read_zarr is used
 # to get the whole zarr store, and then the tables are
-# transformed via zellkonverter.  this gives a 10x speedup
+# transformed via anndataR. This gives a 10x speedup
 # for ingesting the visium_hd_3.0.0 example but fails on
 # the blobs dataset in example("table-utils") because
 # of matters related to metadata/hasTable behavior
@@ -51,9 +51,9 @@ allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0",
 #'   The default, NULL, reads all elements; alternatively, may be FALSE 
 #'   to skip a layer, or a integer vector specifying which elements to read.
 #' @param anndataR logical specifying whether 
-#'   to use \code{anndataR} to read tables; defaults to FALSE in `readSpatialData`,
-#'   and `readTable`,
-#'   so that pythonic \code{spatialdata} and \code{zellkonverter} are used.
+#'   to use \code{anndataR} to read tables; 
+#'   defaults to FALSE in `readSpatialData`, and `readTable`,
+#'   so that pythonic \code{anndata} are used.
 #' @param ... option arguments passed to and from other methods.
 #'
 #' @return 
@@ -67,6 +67,9 @@ allp = c("zarr==3.1.5", "spatialdata==0.7.0", "spatialdata_io==0.6.0",
 #' dir.create(tf <- tempfile())
 #' base <- SpatialData.data:::.unzip_merfish_demo(tf)
 #' (x <- readSpatialData(base))
+#' 
+#' # import tables using anndataR
+#' (x <- readSpatialData(base, anndataR=TRUE))
 NULL
 
 #' @importFrom ZarrArray ZarrArray
@@ -123,9 +126,9 @@ readShape <- function(x, ...) {
     packages=c( "python==3.13.0"),
     pip=allp)
 
+#' @import anndataR
 #' @importFrom reticulate import
 #' @importFrom S4Vectors metadata
-#' @importFrom zellkonverter AnnData2SCE
 #' @importFrom SingleCellExperiment int_metadata
 #' @importFrom basilisk basiliskStart basiliskStop basiliskRun
 .readTables_basilisk <- function(x) {
@@ -141,7 +144,7 @@ readShape <- function(x, ...) {
                                    full.names = FALSE)
       lapply(ts, \(z) {
         zs <- sd$read_zarr(file.path(x, "tables", z))
-        se <- AnnData2SCE(zs)
+        se <- zs$as_SingleCellExperiment()
         nm <- "spatialdata_attrs"
         md <- metadata(se)[[nm]]
         int_metadata(se)[[nm]] <- md
@@ -152,16 +155,12 @@ readShape <- function(x, ...) {
 }
 .readTable_anndataR <- function(x) {
     if (!requireNamespace('anndataR', quietly=TRUE)) {
-        stop("To use this function, install the 'anndataR' package via\n",
-            "`BiocManager::install(\"keller-mark/anndataR\", ref=\"spatialdata\")`")
-    }
-    if (!requireNamespace('pizzarr', quietly=TRUE)) {
-        stop("To use this function, install the 'pizzarr' package via\n",
-            "`BiocManager::install(\"keller-mark/pizzarr\")`")
+        message("To make sure 'anndataR' package works as intended, ", 
+                "install the development version via\n",
+                "`BiocManager::install(\"keller-mark/anndataR\", ref=\"spatialdata\")`")
     }
     suppressWarnings({ # suppress warnings related to hidden files
-        adata <- anndataR::read_zarr(x)
-        anndataR::to_SingleCellExperiment(adata)
+        anndataR::read_zarr(x, as="SingleCellExperiment")
     })
 }
 

inst/NEWS

@@ -1,3 +1,11 @@
+changes in version 0.99.24
+
+- ZarrArray imported by Bioconductor/ZarrArray
+- Rarr replaces pizzarr for importing tables via anndataR
+- anndataR replaces zellkonverter
+- update basilisk env to spatialdata==0.7.0
+- replace spatialdata.read with anndata.read_zarr to read tables
+
 changes in version 0.99.22
 
 - split off 'SpatialData.data'