Add anndata v0.10.2 environment

theislab · Oct 16, 2023 · 253179e · 253179e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: zellkonverter
 Title: Conversion Between scRNA-seq Objects
-Version: 1.11.3
-Date: 2023-10-02
+Version: 1.11.4
+Date: 2023-10-16
 Authors@R: 
     c(person(given = "Luke",
              family = "Zappia",

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,10 @@
 
 * Bioconductor 3.18, October 2023
 
+## zellkonverter 1.11.4 (2023-10-16)
+
+* Add environment for **anndata** v0.10.2
+
 ## zellkonverter 1.11.3 (2023-10-2)
 
 * Add environment for **anndata** v0.9.2

diff --git a/R/basilisk.R b/R/basilisk.R
@@ -61,7 +61,7 @@ NULL
 #' version strings.
 #'
 #' @export
-.AnnDataVersions <- c("0.9.2", "0.8.0", "0.7.6")
+.AnnDataVersions <- c("0.10.2", "0.9.2", "0.8.0", "0.7.6")
 
 #' @rdname AnnData-Environment
 #'
@@ -114,6 +114,17 @@ AnnDataDependencies <- function(version = .AnnDataVersions) {
             "pandas==2.1.1",
             "python==3.11.5",
             "scipy==1.11.3"
+        ),
+        "0.10.2" = c(
+            "anndata==0.10.2",
+            "h5py==3.10.0",
+            "hdf5==1.14.2",
+            "natsort==8.4.0",
+            "numpy==1.26.0",
+            "packaging==23.2",
+            "pandas==2.1.1",
+            "python==3.11.5",
+            "scipy==1.11.3"
         )
     )
 }
@@ -143,3 +154,4 @@ zellkonverterAnnDataEnv <- function(version = .AnnDataVersions) {
 anndata_env_0.7.6 <- zellkonverterAnnDataEnv(version = "0.7.6")
 anndata_env_0.8.0 <- zellkonverterAnnDataEnv(version = "0.8.0")
 anndata_env_0.9.2 <- zellkonverterAnnDataEnv(version = "0.9.2")
+anndata_env_0.9.2 <- zellkonverterAnnDataEnv(version = "0.10.2")
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -5,8 +5,8 @@
   \subsection{Major changes}{
   \itemize{
     \item{
-      Add an environment for \bold{anndata} v0.9.2. This is now the default
-      envrionment for the Python reader/writer.
+      Add environments for \bold{anndata} v0.9.2 and v0.10.2. Version 0.10.20 is
+      now the default envrionment for the Python reader/writer.
     }
   }}
   \subsection{Minor changes}{

diff --git a/tests/testthat/test-read.R b/tests/testthat/test-read.R
@@ -11,6 +11,14 @@ test_that("Reading H5AD works", {
     expect_identical(colnames(colData(sce)), "cell_type")
 })
 
+test_that("Reading H5AD works with version 0.9.2", {
+    sce <- readH5AD(file, version = "0.9.2")
+    expect_s4_class(sce, "SingleCellExperiment")
+
+    expect_identical(assayNames(sce), "X")
+    expect_identical(colnames(colData(sce)), "cell_type")
+})
+
 test_that("Reading H5AD works with version 0.8.0", {
     sce <- readH5AD(file, version = "0.8.0")
     expect_s4_class(sce, "SingleCellExperiment")

diff --git a/tests/testthat/test-write.R b/tests/testthat/test-write.R
@@ -35,6 +35,37 @@ test_that("writeH5AD works as expected", {
     expect_identical(col_data, colData(sce))
 })
 
+test_that("writeH5AD works as expected with version 0.9.2", {
+    temp <- tempfile(fileext = ".h5ad")
+    writeH5AD(sce, temp, version = "0.9.2")
+    expect_true(file.exists(temp))
+
+    # Reading it back out again. Hopefully we didn't lose anything important.
+    out <- readH5AD(temp, version = "0.9.2")
+
+    expect_identical(dimnames(out), dimnames(sce))
+    expect_equal(assay(out), assay(sce))
+    expect_identical(reducedDims(out), reducedDims(sce))
+
+    # Need to coerce the factors back to strings.
+    row_data <- rowData(out)
+    for (i in seq_len(ncol(row_data))) {
+        if (is.factor(row_data[[i]])) {
+            row_data[[i]] <- as.character(row_data[[i]])
+        }
+    }
+    expect_identical(row_data, rowData(sce))
+
+    col_data <- colData(out)
+    for (i in seq_len(ncol(col_data))) {
+        if (is.factor(col_data[[i]])) {
+            col_data[[i]] <- as.character(col_data[[i]])
+        }
+    }
+    names(col_data) <- names(colData(sce))
+    expect_identical(col_data, colData(sce))
+})
+
 test_that("writeH5AD works as expected with version 0.8.0", {
     temp <- tempfile(fileext = ".h5ad")
     writeH5AD(sce, temp, version = "0.8.0")