Cherry-pick Bioc3.22 updates into devel (#411)

* Cherry-pick dd6b69c

Update email for release 3.22 (#410)

* Update email Robrecht

* update news

* Git cherry-pick: Fix linting issues (#412)

* remove explicit returns

* changed %>% into |>

* bump version

* Git cherry-pick: Fix tests (#413)

* fix roundtrip test

* fix dataset generator

* update news

* fix test

Author: rcannood

DESCRIPTION

@@ -2,7 +2,7 @@ Package: anndataR
 Title: AnnData interoperability in R
 Version: 1.1.0
 Authors@R: c(
-    person("Robrecht", "Cannoodt", , "robrecht@data-intuitive.com", role = c("aut", "cre"),
+    person("Robrecht", "Cannoodt", , "rcannood@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
     person("Luke", "Zappia", , "luke@lazappi.id.au", role = "aut",
            comment = c(ORCID = "0000-0001-7744-8565", github = "lazappi")),

NEWS.md

@@ -2,6 +2,13 @@
 
 - Bioconductor 3.23 devel
 
+# anndataR 1.0.1
+
+- Update author email address (PR #410).
+- Fix linting issues (PR #412).
+- Fix roundtrip test; ensure that `X` is always 2-dimensional (PR #413).
+- Fix HDF5 write test; make sure to only pass CsparseMatrix to Seurat (PR #413).
+
 # anndataR 1.0.0
 
 - Bioconductor 3.22 release (October 2025)

R/AnnDataView.R

@@ -70,10 +70,10 @@ AnnDataView <- R6::R6Class(
           result <- result[, private$.var_subset, drop = FALSE]
         }
 
-        return(result)
+        result
+      } else {
+        x
       }
-
-      x
     },
 
     # Apply subsetting to vectors
@@ -367,7 +367,6 @@ convert_to_indices <- function(
         "Logical subset of {context_name} must have length {max_length}"
       )
     }
-
     which(subset)
   } else if (is.integer(subset) || is.numeric(subset)) {
     subset <- as.integer(subset)
@@ -376,7 +375,6 @@ convert_to_indices <- function(
         "Integer indices for {context_name} must be between 1 and {max_length}"
       )
     }
-
     subset
   } else if (is.character(subset)) {
     if (is.null(names_vector)) {
@@ -395,7 +393,6 @@ convert_to_indices <- function(
         "Names of {context_name} not found: {paste(missing_names, collapse = ', ')}"
       )
     }
-
     indices
   } else {
     cli_abort(

R/generate_dataset.R

@@ -311,6 +311,11 @@ generate_dataset <- function(
   colnames(X) <- dataset_list$obs_names
   rownames(X) <- dataset_list$var_names
 
+  # Convert to sparse matrix to avoid Seurat warning about coercing dense matrix
+  if (!inherits(X, "sparseMatrix")) {
+    X <- as(X, "CsparseMatrix")
+  }
+
   seurat <- SeuratObject::CreateSeuratObject(X)
 
   for (layer in names(dataset_list$layers)) {

tests/testthat/test-generate_dataset.R

@@ -21,16 +21,10 @@ test_that("generating dummy SingleCellExperiment works", {
 test_that("generating dummy Seurat works", {
   skip_if_not_installed("SeuratObject")
 
-  expect_warning(
-    dummy <- generate_dataset(format = "Seurat"),
-    "Data is of class matrix"
-  )
+  dummy <- generate_dataset(format = "Seurat")
   expect_s4_class(dummy, "Seurat")
 
-  expect_warning(
-    dummy <- generate_dataset(format = "Seurat", example = TRUE),
-    "Data is of class matrix"
-  )
+  dummy <- generate_dataset(format = "Seurat", example = TRUE)
   expect_s4_class(dummy, "Seurat")
 })
 

tests/testthat/test-roundtrip-X.R

@@ -11,6 +11,10 @@ known_issues <- read_known_issues()
 
 test_names <- names(da$matrix_generators)
 
+# X must always be 2-dimensional in AnnData
+# -> https://github.com/scverse/anndata/blob/2a2c0e3198c298a5c80a73ac343c63203b5ca133/src/anndata/_core/anndata.py#L2164-L2172 # nolint
+test_names <- test_names[!grepl("_3d$", test_names)]
+
 for (name in test_names) {
   # first generate a python h5ad
   adata_py <- da$generate_dataset(