experiment with new dummy anndata (#193)

* refactor obsvar test

* make sure dummy-anndata is installed

* add nolint

* use fix

* avoid reticulate conversion

* also test a couple of things in R

* split up tests

.github/workflows/R-CMD-check.yaml

@@ -61,7 +61,7 @@ jobs:
           if (!reticulate:::miniconda_exists()) {
             reticulate::install_miniconda()
           }
-          reticulate::py_install(c("anndata", "scanpy"), pip = TRUE)
+          reticulate::py_install(c("anndata", "scanpy", "dummy-anndata"), pip = TRUE)
         shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2

tests/testthat/test-roundtrip-obsvar.R

@@ -1,104 +1,100 @@
 skip_if_no_anndata()
-skip_if_not_installed("hdf5r")
+skip_if_not_installed("reticulate")
 
-data <- generate_dataset(10L, 20L)
+library(reticulate)
+testthat::skip_if_not(
+  reticulate::py_module_available("dummy_anndata"),
+  message = "Python dummy_anndata module not available for testing"
+)
 
-test_names <- names(data$obs)
+ad <- reticulate::import("anndata", convert = FALSE)
+da <- reticulate::import("dummy_anndata", convert = FALSE)
+pd <- reticulate::import("pandas", convert = FALSE)
+bi <- reticulate::import_builtins()
 
-# TODO: re-enable tests
-test_names <- test_names[!grepl("_with_nas", test_names)]
-
-# TODO: re-enable tests
-# NOTE: I think this doesn't work in cran anndata
-test_names <- test_names[test_names != "logical_with_nas"]
+test_names <- names(da$vector_generators)
 
 for (name in test_names) {
-  test_that(paste0("roundtrip with obs and var '", name, "'"), {
-    # create anndata
-    ad <- AnnData(
-      X = data$X,
-      obs = data$obs[, name, drop = FALSE],
-      var = data$var[, name, drop = FALSE]
-    )
-
-    # write to file
-    filename <- withr::local_file(tempfile(fileext = ".h5ad"))
-    write_h5ad(ad, filename)
-
-    # read from file
-    ad_new <- read_h5ad(filename, to = "HDF5AnnData")
-
-    # expect slots are unchanged
+  # first generate a python h5ad
+  adata_py <- da$generate_dataset(
+    x_type = "generate_float_matrix",
+    obs_types = list(name),
+    var_types = list(name),
+    layer_types = list(),
+    obsm_types = list(),
+    varm_types = list(),
+    obsp_types = list(),
+    varp_types = list(),
+    uns_types = list()
+  )
+  # remove uns - workaround for https://github.com/data-intuitive/dummy-anndata/issues/2
+  adata_py$uns <- bi$dict()
+  # TODO: remove X
+
+  # 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$write_h5ad(file_py)
+
+  test_that(paste0("reading an AnnData with obs and var '", name, "' works"), {
+    adata_r <- read_h5ad(file_py, to = "HDF5AnnData")
     expect_equal(
-      ad_new$obs[[name]],
-      data$obs[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
+      adata_r$shape(),
+      unlist(reticulate::py_to_r(adata_py$shape))
     )
     expect_equal(
-      ad_new$var[[name]],
-      data$var[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
-    )
-  })
-}
-
-for (name in test_names) {
-  test_that(paste0("reticulate->hdf5 with obs and var '", name, "'"), {
-    ad <- anndata::AnnData(
-      obs = data$obs[, name, drop = FALSE],
-      var = data$var[, name, drop = FALSE]
-    )
-
-    # write to file
-    filename <- withr::local_file(tempfile(fileext = ".h5ad"))
-    ad$write_h5ad(filename)
-
-    # read from file
-    ad_new <- HDF5AnnData$new(filename)
-
-    # expect slots are unchanged
-    expect_equal(
-      ad_new$obs[[name]],
-      data$obs[[name]],
-      tolerance = 1e-6
+      adata_r$obs_keys(),
+      py_to_r(adata_py$obs_keys())
     )
     expect_equal(
-      ad_new$var[[name]],
-      data$var[[name]],
-      tolerance = 1e-6
+      adata_r$var_keys(),
+      py_to_r(adata_py$var_keys())
     )
-  })
-}
 
-for (name in test_names) {
-  test_that(paste0("hdf5->reticulate with obs and var '", name, "'"), {
-    # write to file
-    filename <- withr::local_file(tempfile(fileext = ".h5ad"))
+    # 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)
+
+    # 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
+  })
 
-    # create anndata
-    ad <- AnnData(
-      obs = data$obs[, name, drop = FALSE],
-      var = data$var[, name, drop = FALSE]
-    )
-    write_h5ad(ad, filename)
+  test_that(paste0("Writing an AnnData with obs and var '", name, "' works"), {
+    adata_r <- read_h5ad(file_py, to = "InMemoryAnnData")
+    write_h5ad(adata_r, file_r)
 
     # read from file
-    ad_new <- anndata::read_h5ad(filename)
-
-    # expect slots are unchanged
-    expect_equal(
-      ad_new$obs[[name]],
-      data$obs[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
+    adata_py2 <- ad$read_h5ad(file_r)
+
+    # expect that the objects are the same
+    zz <- pd$testing$assert_frame_equal(
+      adata_py2$obs,
+      adata_py$obs,
+      check_dtype = FALSE,
+      check_exact = FALSE
     )
-    expect_equal(
-      ad_new$var[[name]],
-      data$var[[name]],
-      ignore_attr = TRUE,
-      tolerance = 1e-6
+    expect_null(reticulate::py_to_r(zz))
+    pd$testing$assert_frame_equal(
+      adata_py2$var,
+      adata_py$var,
+      check_dtype = FALSE,
+      check_exact = FALSE
     )
+    expect_null(reticulate::py_to_r(zz))
   })
 }