From bd3fffbfe75ad426efb46d688ac66a74128dd273 Mon Sep 17 00:00:00 2001
From: Artur-man <artur-man@hotmail.com>
Date: Wed, 26 Nov 2025 17:07:40 +0100
Subject: [PATCH 1/2] remove pizzarr for anndataR support

---
 DESCRIPTION | 11 ++++-------
 R/read.R    |  9 ++-------
 2 files changed, 6 insertions(+), 14 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 9e2249b..615fdc6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,13 +63,10 @@ Suggests:
     SpatialData.data,
     SpatialData.plot,
     testthat,
-    DT
-Enhances:
-    anndataR,
-    pizzarr
+    DT,
+    anndataR
 Remotes:
-    keller-mark/pizzarr,
-    keller-mark/anndataR@spatialdata,
+    keller-mark/anndataR@keller-mark/zarr,
     HelenaLC/SpatialData.data,
     HelenaLC/SpatialData.plot
 biocViews: 
@@ -82,7 +79,7 @@ biocViews:
     SingleCell,
     Spatial
 License: Artistic-2.0
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 VignetteBuilder: knitr
 URL: https://github.com/HelenaLC/SpatialData
diff --git a/R/read.R b/R/read.R
index 929fd14..3c951a8 100644
--- a/R/read.R
+++ b/R/read.R
@@ -150,15 +150,10 @@ 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\")`")
+            "`BiocManager::install(\"keller-mark/anndataR\", ref=\"keller-mark/zarr\")`")
     }
     suppressWarnings({ # suppress warnings related to hidden files
-        adata <- anndataR::read_zarr(x)
-        anndataR::to_SingleCellExperiment(adata)
+        adata <- anndataR::read_zarr(x, as = "SingleCellExperiment")
     })
 }
 

From 6b5bd3996a3575f5ab796479bbda39f57b9332fa Mon Sep 17 00:00:00 2001
From: HelenaLC <helena@crowell.eu>
Date: Wed, 26 Nov 2025 22:12:56 +0100
Subject: [PATCH 2/2] rmv pizzarr

---
 R/read.R               | 8 ++++----
 man/SpatialData.Rd     | 8 ++++----
 man/readSpatialData.Rd | 6 +++---
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/read.R b/R/read.R
index 3c951a8..83cb82f 100644
--- a/R/read.R
+++ b/R/read.R
@@ -49,8 +49,8 @@ allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7",
 #'   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`,
+#'   to use \code{anndataR} to read tables; 
+#'   defaults to FALSE in `readSpatialData`, and `readTable`,
 #'   so that pythonic \code{spatialdata} and \code{zellkonverter} are used.
 #' @param ... option arguments passed to and from other methods.
 #'
@@ -64,7 +64,7 @@ allp = c("session_info==1.0.0", "spatialdata==0.3.0", "spatialdata_io==0.1.7",
 #' library(SpatialData.data)
 #' dir.create(tf <- tempfile())
 #' base <- SpatialData.data:::.unzip_merfish_demo(tf)
-#' (x <- readSpatialData(base))
+#' (x <- readSpatialData(base, anndataR=TRUE))
 NULL
 
 readsdlayer <- function(x, ...) {
@@ -153,7 +153,7 @@ readShape <- function(x, ...) {
             "`BiocManager::install(\"keller-mark/anndataR\", ref=\"keller-mark/zarr\")`")
     }
     suppressWarnings({ # suppress warnings related to hidden files
-        adata <- anndataR::read_zarr(x, as = "SingleCellExperiment")
+        anndataR::read_zarr(x, as="SingleCellExperiment")
     })
 }
 
diff --git a/man/SpatialData.Rd b/man/SpatialData.Rd
index e760cfd..9521d85 100644
--- a/man/SpatialData.Rd
+++ b/man/SpatialData.Rd
@@ -50,8 +50,8 @@
 \alias{element,SpatialData,ANY,numeric-method}
 \alias{element,SpatialData,ANY,missing-method}
 \alias{element,SpatialData,ANY,ANY-method}
-\alias{[[<-,SpatialData,numeric,ANY-method}
-\alias{[[<-,SpatialData,character,ANY-method}
+\alias{[[<-,SpatialData,numeric,ANY,ANY-method}
+\alias{[[<-,SpatialData,character,ANY,ANY-method}
 \title{The `SpatialData` class}
 \usage{
 SpatialData(images, labels, points, shapes, tables)
@@ -88,9 +88,9 @@ SpatialData(images, labels, points, shapes, tables)
 
 \S4method{element}{SpatialData,ANY,ANY}(x, i, j)
 
-\S4method{[[}{SpatialData,numeric,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,numeric,ANY,ANY}(x, i) <- value
 
-\S4method{[[}{SpatialData,character,ANY}(x, i) <- value
+\S4method{[[}{SpatialData,character,ANY,ANY}(x, i) <- value
 }
 \arguments{
 \item{images}{list of \code{\link{ImageArray}}s}
diff --git a/man/readSpatialData.Rd b/man/readSpatialData.Rd
index 000ed43..5a3d055 100644
--- a/man/readSpatialData.Rd
+++ b/man/readSpatialData.Rd
@@ -42,8 +42,8 @@ The default, NULL, reads all elements; alternatively, may be FALSE
 to skip a layer, or a integer vector specifying which elements to read.}
 
 \item{anndataR}{logical specifying whether 
-to use \code{anndataR} to read tables; defaults to FALSE in `readSpatialData`,
-and `readTable`,
+to use \code{anndataR} to read tables; 
+defaults to FALSE in `readSpatialData`, and `readTable`,
 so that pythonic \code{spatialdata} and \code{zellkonverter} are used.}
 }
 \value{
@@ -59,5 +59,5 @@ Reading `SpatialData`
 library(SpatialData.data)
 dir.create(tf <- tempfile())
 base <- SpatialData.data:::.unzip_merfish_demo(tf)
-(x <- readSpatialData(base))
+(x <- readSpatialData(base, anndataR=TRUE))
 }