also include arrays in obsmvarm

inst/known_issues.yaml

@@ -22,3 +22,53 @@ known_issues:
     proposed_solution: Debug and fix
     to_investigate: True
     to_fix: True
+  - backend: HDF5AnnData
+    slot:
+      - obsm
+      - varm
+    dtype:
+      - boolean_array
+      - categorical
+      - categorical_missing_values
+      - categorical_ordered
+      - categorical_ordered_missing_values
+      - dense_array
+      - integer_array
+      - nullable_boolean_array
+      - nullable_integer_array
+      - string_array
+    process: [reticulate]
+    error_message: |
+      adata_r$varm[[name]] (`actual`) not equal to py_to_r(py_get_item(adata_py$varm, name)) (`expected`).
+
+      `dim(actual)` is absent
+      `dim(expected)` is an integer vector (20)
+    description: Python nd.arrays have a dimension while R vectors do not.
+    proposed_solution: Debug and fix
+    to_investigate: True
+    to_fix: True
+  - backend: HDF5AnnData
+    slot:
+      - obsm
+      - varm
+    dtype:
+      - boolean_array
+      - categorical
+      - categorical_missing_values
+      - categorical_ordered
+      - categorical_ordered_missing_values
+      - dense_array
+      - integer_array
+      - nullable_boolean_array
+      - nullable_integer_array
+      - string_array
+    process: [write]
+    error_message: |
+      Error in `if (found_dim != expected_dim) {
+          stop("dim(", label, ")[", i, "] should have shape: ", expected_dim, 
+              ", found: ", found_dim, ".")
+      }`: argument is of length zero
+    description: R vectors don't have a dimension.
+    proposed_solution: The input checking function for obsm and varm should allow the object to be a vector of the correct length instead of only a matrix or a data frame.
+    to_investigate: True
+    to_fix: True

tests/testthat/helper-expect_equal_py.R

@@ -0,0 +1,57 @@
+expect_equal_py <- function(a, b) {
+  requireNamespace("testthat")
+  requireNamespace("reticulate")
+
+  bi <- reticulate::import_builtins()
+
+  testthat::expect_equal(bi$type(a), bi$type(b)) # does this always work?
+
+  if (inherits(a, "pandas.core.frame.DataFrame")) {
+    pd <- reticulate::import("pandas")
+    testthat::expect_null(
+      pd$testing$assert_frame_equal(
+        a,
+        b,
+        check_dtype = FALSE,
+        check_exact = FALSE
+      )
+    )
+  } else if (inherits(a, "np.ndarray") || inherits(a, "scipy.sparse.base.spmatrix")) {
+    scipy <- reticulate::import("scipy")
+    np <- reticulate::import("numpy")
+
+    testthat::expect_equal(a$dtype, b$dtype)
+
+    testthat::expect_equal(
+      py_to_r_ifneedbe(a$shape),
+      py_to_r_ifneedbe(b$shape)
+    )
+
+    a_dense <-
+      if (scipy$sparse$issparse(a)) {
+        a$toarray()
+      } else {
+        a
+      }
+    b_dense <-
+      if (scipy$sparse$issparse(b)) {
+        b$toarray()
+      } else {
+        b
+      }
+
+    testthat::expect_null(
+      np$testing$assert_allclose(a_dense, b_dense)
+    )
+
+  }
+}
+
+py_to_r_ifneedbe <- function(x) {
+  if (inherits(x, "python.builtin.object")) {
+    requireNamespace("reticulate")
+    reticulate::py_to_r(x)
+  } else {
+    x
+  }
+}

tests/testthat/test-roundtrip-X.R

@@ -96,7 +96,7 @@ for (name in test_names) {
     adata_py2 <- ad$read_h5ad(file_r)
 
     # expect that the objects are the same
-    expect_py_matrix_equal(
+    expect_equal_py(
       adata_py2$X,
       adata_py$X
     )

tests/testthat/test-roundtrip-layers.R

@@ -54,7 +54,7 @@ for (name in test_names) {
     )
     expect_equal(
       adata_r$layers_keys(),
-      py_to_r(adata_py$layers$keys())
+      bi$list(adata_py$layers$keys())
     )
 
     # check that the print output is the same
@@ -100,7 +100,7 @@ for (name in test_names) {
     adata_py2 <- ad$read_h5ad(file_r)
 
     # expect that the objects are the same
-    expect_py_matrix_equal(
+    expect_equal_py(
       py_get_item(adata_py2$layers, name),
       py_get_item(adata_py$layers, name)
     )

tests/testthat/test-roundtrip-obsmvarm.R

@@ -7,16 +7,16 @@ testthat::skip_if_not(
   message = "Python dummy_anndata module not available for testing"
 )
 
-# TODO: make sure data frames in obsm / varm are also tested?
-# TODO: create a github issue for this
-
 ad <- reticulate::import("anndata", convert = FALSE)
 da <- reticulate::import("dummy_anndata", convert = FALSE)
 bi <- reticulate::import_builtins()
 
 known_issues <- read_known_issues()
 
-test_names <- names(da$matrix_generators)
+test_names <- c(
+  names(da$matrix_generators),
+  names(da$vector_generators)
+)
 
 for (name in test_names) {
   # first generate a python h5ad
@@ -57,11 +57,11 @@ for (name in test_names) {
     )
     expect_equal(
       adata_r$obsm_keys(),
-      py_to_r(adata_py$obsm$keys())
+      bi$list(adata_py$obsm$keys())
     )
     expect_equal(
       adata_r$varm_keys(),
-      py_to_r(adata_py$varm$keys())
+      bi$list(adata_py$varm$keys())
     )
 
     # check that the print output is the same
@@ -112,11 +112,11 @@ for (name in test_names) {
     adata_py2 <- ad$read_h5ad(file_r)
 
     # expect that the objects are the same
-    expect_py_matrix_equal(
+    expect_equal_py(
       py_get_item(adata_py2$obsm, name),
       py_get_item(adata_py$obsm, name)
     )
-    expect_py_matrix_equal(
+    expect_equal_py(
       py_get_item(adata_py2$varm, name),
       py_get_item(adata_py$varm, name)
     )

tests/testthat/test-roundtrip-obspvarp.R

@@ -54,11 +54,11 @@ for (name in test_names) {
     )
     expect_equal(
       adata_r$obsp_keys(),
-      py_to_r(adata_py$obsp$keys())
+      bi$list(adata_py$obsp$keys())
     )
     expect_equal(
       adata_r$varp_keys(),
-      py_to_r(adata_py$varp$keys())
+      bi$list(adata_py$varp$keys())
     )
 
     # check that the print output is the same
@@ -109,11 +109,11 @@ for (name in test_names) {
     adata_py2 <- ad$read_h5ad(file_r)
 
     # expect that the objects are the same
-    expect_py_matrix_equal(
+    expect_equal_py(
       py_get_item(adata_py2$obsp, name),
       py_get_item(adata_py$obsp, name)
     )
-    expect_py_matrix_equal(
+    expect_equal_py(
       py_get_item(adata_py2$varp, name),
       py_get_item(adata_py$varp, name)
     )

tests/testthat/test-roundtrip-obsvar.R

@@ -53,11 +53,11 @@ for (name in test_names) {
     )
     expect_equal(
       adata_r$obs_keys(),
-      py_to_r(adata_py$obs_keys())
+      bi$list(adata_py$obs_keys())
     )
     expect_equal(
       adata_r$var_keys(),
-      py_to_r(adata_py$var_keys())
+      bi$list(adata_py$var_keys())
     )
 
     # check that the print output is the same
@@ -108,7 +108,7 @@ for (name in test_names) {
     adata_py2 <- ad$read_h5ad(file_r)
 
     # expect that the objects are the same
-    expect_py_df_equal(adata_py2$obs, adata_py$obs)
-    expect_py_df_equal(adata_py2$var, adata_py$var)
+    expect_equal_py(adata_py2$obs, adata_py$obs)
+    expect_equal_py(adata_py2$var, adata_py$var)
   })
 }