avoid reticulate conversion

tests/testthat/test-roundtrip-obsvar.R

@@ -6,8 +6,10 @@ testthat::skip_if_not(
   message = "Python dummy_anndata module not available for testing"
 )
 
-ad <- reticulate::import("anndata")
-da <- reticulate::import("dummy_anndata")
+ad <- reticulate::import("anndata", convert = FALSE)
+da <- reticulate::import("dummy_anndata", convert = FALSE)
+pd <- reticulate::import("pandas", convert = FALSE)
+bi <- reticulate::import_builtins()
 
 test_names <- names(da$vector_generators)
 
@@ -25,29 +27,30 @@ for (name in test_names) {
       uns_types = list()
     )
     # remove uns
-    adata_py$uns <- NULL
+    adata_py$uns <- bi$dict()
     # TODO: remove X
 
     # write to file
     filename <- withr::local_file(tempfile(fileext = ".h5ad"))
     adata_py$write_h5ad(filename)
 
     # read from file
-    adata_r <- read_h5ad(filename, to = "HDF5AnnData")
+    adata_r <- read_h5ad(filename, to = "InMemoryAnnData")
 
-    # expect slots are unchanged
-    expect_equal(
-      adata_r$obs[[name]],
-      adata_py$obs[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
-    )
-    expect_equal(
-      adata_r$var[[name]],
-      adata_py$var[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
-    )
+    # if we would test the objects at this stage,
+    # we're also testing reticulate's conversion
+    # nolint start
+    # expect_equal(
+    #   adata_r$obs[[name]],
+    #   py_to_r(adata_py$obs[[name]]),
+    #   tolerance = 1e-6
+    # )
+    # expect_equal(
+    #   adata_r$var[[name]],
+    #   py_to_r(adata_py$var[[name]]),
+    #   tolerance = 1e-6
+    # )
+    # nolint end
 
     # write back to file
     filename2 <- withr::local_file(tempfile(fileext = ".h5ad"))
@@ -56,19 +59,25 @@ for (name in test_names) {
     # read from file
     adata_py2 <- ad$read_h5ad(filename2)
 
-    # expect slots are unchanged
     expect_equal(
-      adata_py2$obs[[name]],
-      adata_py$obs[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
+      reticulate::py_to_r(adata_py2$shape),
+      reticulate::py_to_r(adata_py$shape)
     )
 
-    expect_equal(
-      adata_py2$var[[name]],
-      adata_py$var[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
+    # expect slots are unchanged
+    zz <- pd$testing$assert_frame_equal(
+      adata_py$obs,
+      adata_py2$obs,
+      check_dtype = FALSE,
+      check_exact = FALSE
+    )
+    expect_null(reticulate::py_to_r(zz))
+    pd$testing$assert_frame_equal(
+      adata_py$var,
+      adata_py2$var,
+      check_dtype = FALSE,
+      check_exact = FALSE
     )
+    expect_null(reticulate::py_to_r(zz))
   })
 }