add uns-nested roundtrip test

inst/known_issues.yaml

@@ -75,6 +75,7 @@ known_issues:
   - backend: HDF5AnnData
     slot:
       - uns
+      - uns_nested
     dtype:
       - empty
       - none
@@ -91,21 +92,7 @@ known_issues:
   - backend: HDF5AnnData
     slot:
       - uns
-    dtype:
-      - boolean_array
-    process: [reticulate]
-    error_message: |
-      adata_r$uns[[name]] (`actual`) not equal to reticulate::py_to_r(adata_py$uns[[name]]) (`expected`).
-
-      `dim(actual)` is absent
-      `dim(expected)` is an integer vector (10)
-    description: The python object has a dimension while the R object does not.
-    proposed_solution: Think about whether this is a problem or not. If it isn't, fix the unit test.
-    to_investigate: True
-    to_fix: True
-  - backend: HDF5AnnData
-    slot:
-      - uns
+      - uns_nested
     dtype:
       - boolean_array
       - dense_array
@@ -124,6 +111,7 @@ known_issues:
   - backend: HDF5AnnData
     slot:
       - uns
+      - uns_nested
     dtype:
       - categorical
       - categorical_missing_values
@@ -155,6 +143,7 @@ known_issues:
   - backend: HDF5AnnData
     slot:
       - uns
+      - uns_nested
     dtype:
       - nullable_boolean_array
       - nullable_integer_array
@@ -171,6 +160,7 @@ known_issues:
   - backend: HDF5AnnData
     slot:
       - uns
+      - uns_nested
     dtype:
       - boolean
       - char

tests/testthat/test-roundtrip-uns-nested.R

@@ -0,0 +1,113 @@
+skip_if_no_anndata()
+skip_if_not_installed("reticulate")
+
+library(reticulate)
+testthat::skip_if_not(
+  reticulate::py_module_available("dummy_anndata"),
+  message = "Python dummy_anndata module not available for testing"
+)
+
+ad <- reticulate::import("anndata", convert = FALSE)
+da <- reticulate::import("dummy_anndata", convert = FALSE)
+bi <- reticulate::import_builtins()
+
+known_issues <- read_known_issues()
+
+test_names <- c(
+  names(da$matrix_generators),
+  names(da$vector_generators),
+  names(da$scalar_generators)
+)
+
+for (name in test_names) {
+  # first generate a python h5ad
+  adata_py <- da$generate_dataset(
+    x_type = NULL,
+    obs_types = list(),
+    var_types = list(),
+    layer_types = list(),
+    obsm_types = list(),
+    varm_types = list(),
+    obsp_types = list(),
+    varp_types = list(),
+    uns_types = list(),
+    nested_uns_types = list(name)
+  )
+
+  # create a couple of paths
+  file_py <- withr::local_file(tempfile(paste0("anndata_py_", name), fileext = ".h5ad"))
+  file_r <- withr::local_file(tempfile(paste0("anndata_r_", name), fileext = ".h5ad"))
+
+  # write to file
+  adata_py$write_h5ad(file_py)
+
+  test_that(paste0("Reading an AnnData with uns_nested '", name, "' works"), {
+    msg <- message_if_known(
+      backend = "HDF5AnnData",
+      slot = c("uns_nested"),
+      dtype = name,
+      process = "read",
+      known_issues = known_issues
+    )
+    skip_if(!is.null(msg), message = msg)
+
+    adata_r <- read_h5ad(file_py, to = "HDF5AnnData")
+    expect_equal(
+      names(adata_r$uns$nested),
+      bi$list(adata_py$uns$nested$keys())
+    )
+
+    # check that the print output is the same
+    str_r <- capture.output(print(adata_r))
+    str_py <- capture.output(print(adata_py))
+    expect_equal(str_r, str_py)
+  })
+
+  # maybe this test simply shouldn't be run if there is a known issue with reticulate
+  test_that(paste0("Comparing an anndata with uns_nested '", name, "' with reticulate works"), {
+    msg <- message_if_known(
+      backend = "HDF5AnnData",
+      slot = c("uns_nested"),
+      dtype = name,
+      process = c("read", "reticulate"),
+      known_issues = known_issues
+    )
+    skip_if(!is.null(msg), message = msg)
+
+    adata_r <- read_h5ad(file_py, to = "HDF5AnnData")
+
+    expect_equal(
+      adata_r$uns[["nested"]][[name]],
+      reticulate::py_to_r(adata_py$uns$nested[[name]])
+    )
+  })
+
+  test_that(paste0("Writing an AnnData with uns_nested '", name, "' works"), {
+    msg <- message_if_known(
+      backend = "HDF5AnnData",
+      slot = c("uns_nested"),
+      dtype = name,
+      process = c("read", "write"),
+      known_issues = known_issues
+    )
+    skip_if(!is.null(msg), message = msg)
+
+    adata_r <- read_h5ad(file_py, to = "InMemoryAnnData")
+    write_h5ad(adata_r, file_r)
+
+    # read from file
+    adata_py2 <- ad$read_h5ad(file_r)
+
+    # expect name is one of the keys
+    expect_contains(
+      bi$list(adata_py2$uns$nested$keys()),
+      name
+    )
+
+    # expect that the objects are the same
+    expect_equal_py(
+      py_get_item(adata_py2$uns$nested, name),
+      py_get_item(adata_py$uns$nested, name)
+    )
+  })
+}