scverse · rcannood · Aug 5, 2025 · Aug 4, 2025 · Aug 4, 2025 · Aug 4, 2025
diff --git a/NEWS.md b/NEWS.md
@@ -2,7 +2,8 @@
 
 - Bump required R version to 4.5 in preparation for Bioconductor submission
   (PR #309)
-- Remove deprecated functions and arguments (PR #311)
+- Remove deprecated functions and arguments (PR #311, PR #313)
+- Minor cleanups and improvements (PR #313).
 
 # anndataR 0.2.0
 

diff --git a/R/AbstractAnnData.R b/R/AbstractAnnData.R
@@ -272,23 +272,6 @@ AbstractAnnData <- R6::R6Class(
       )
     },
     #' @description
-    #' `r lifecycle::badge('deprecated')`
-    #'
-    #' Deprecated, use `as_HDF5AnnData()` instead
-    #'
-    #' @param ... Arguments passed to `adata$as_HDF5AnnData()`
-    #'
-    #' @return An [`HDF5AnnData`] object
-    to_HDF5AnnData = function(...) {
-      lifecycle::deprecate_warn(
-        "0.1.0",
-        "to_HDF5AnnDAta()",
-        "as_HDF5AnnData()",
-      )
-
-      self$as_HDF5AnnData(...)
-    },
-    #' @description
     #' Write the `AnnData` object to an H5AD file
     #'
     #' See [write_h5ad()] for details

diff --git a/R/generate_dataset.R b/R/generate_dataset.R
@@ -24,11 +24,6 @@
 #'
 #' @examples
 #' dummy <- generate_dataset()
-#' \dontrun{
-#' dummy <- generate_dataset(format = "AnnData")
-#' dummy <- generate_dataset(format = "SingleCellExperiment")
-#' dummy <- generate_dataset(format = "Seurat")
-#' }
 generate_dataset <- function(
   n_obs = 10L,
   n_vars = 20L,

diff --git a/man/AbstractAnnData.Rd b/man/AbstractAnnData.Rd
diff --git a/man/HDF5AnnData.Rd b/man/HDF5AnnData.Rd
diff --git a/man/InMemoryAnnData.Rd b/man/InMemoryAnnData.Rd
diff --git a/man/generate_dataset.Rd b/man/generate_dataset.Rd
diff --git a/tests/testthat/helper-expect_equal_py.R b/tests/testthat/helper-expect_equal_py.R
@@ -4,7 +4,8 @@ expect_equal_py <- function(a, b) {
 
   bi <- reticulate::import_builtins()
 
-  testthat::expect_equal(bi$str(bi$type(a)), bi$str(bi$type(b))) # does this always work?
+  # ↓ does this always work?
+  testthat::expect_equal(bi$str(bi$type(a)), bi$str(bi$type(b)))
 
   if (inherits(a, "pandas.core.frame.DataFrame")) {
     pd <- reticulate::import("pandas")

diff --git a/tests/testthat/test-roundtrip-X.R b/tests/testthat/test-roundtrip-X.R
@@ -64,7 +64,6 @@ for (name in test_names) {
     expect_equal(str_r, str_py)
   })
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0("Comparing an anndata with X '", name, "' with reticulate works"),
     {

diff --git a/tests/testthat/test-roundtrip-layers.R b/tests/testthat/test-roundtrip-layers.R
@@ -70,7 +70,6 @@ for (name in test_names) {
 
   gc()
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0(
       "Comparing an anndata with layer '",

diff --git a/tests/testthat/test-roundtrip-obsmvarm.R b/tests/testthat/test-roundtrip-obsmvarm.R
@@ -92,7 +92,6 @@ for (name in test_names) {
     }
   )
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0(
       "Comparing an anndata with obsm and varm '",

diff --git a/tests/testthat/test-roundtrip-obspvarp.R b/tests/testthat/test-roundtrip-obspvarp.R
@@ -75,7 +75,6 @@ for (name in test_names) {
     }
   )
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0(
       "Comparing an anndata with obsp and varp '",

diff --git a/tests/testthat/test-roundtrip-obsvar.R b/tests/testthat/test-roundtrip-obsvar.R
@@ -72,7 +72,6 @@ for (name in test_names) {
     expect_equal(str_r, str_py)
   })
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0(
       "Comparing an anndata with obs and var '",

diff --git a/tests/testthat/test-roundtrip-uns-nested.R b/tests/testthat/test-roundtrip-uns-nested.R
@@ -66,7 +66,6 @@ for (name in test_names) {
     expect_equal(str_r, str_py)
   })
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0(
       "Comparing an anndata with uns_nested '",

diff --git a/tests/testthat/test-roundtrip-uns.R b/tests/testthat/test-roundtrip-uns.R
@@ -66,7 +66,6 @@ for (name in test_names) {
     expect_equal(str_r, str_py)
   })
 
-  # maybe this test simply shouldn't be run if there is a known issue with reticulate
   test_that(
     paste0("Comparing an anndata with uns '", name, "' with reticulate works"),
     {

diff --git a/vignettes/known_issues.Rmd b/vignettes/known_issues.Rmd
@@ -10,8 +10,8 @@ vignette: >
 This document lists known issues with the package and suggests possible solutions.
 
 ```{r known-issues, echo=FALSE, results="asis"}
-# how to get a file from a package
-data <- yaml::read_yaml(system.file("known_issues.yaml", package = "anndataR"))$known_issues
+known_issues_path <- system.file("known_issues.yaml", package = "anndataR")
+data <- yaml::read_yaml(known_issues_path)$known_issues
 
 for (i in seq_along(data)) {
   str <- paste0(
-Original file line number
+Diff line change
@@ Expand Up / @@ -70,7 +70,6 @@ for (name in test_names) { @@
       gc()
-      # maybe this test simply shouldn't be run if there is a known issue with reticulate
       test_that(
         paste0(
           "Comparing an anndata with layer '",
@@ Expand Down @@