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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,95 +1,113 @@ | ||
| skip_if_no_anndata() | ||
| skip_if_not_installed("hdf5r") | ||
|
|
||
| data <- generate_dataset(10L, 20L) | ||
|
|
||
| test_names <- names(data$uns) | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[!grepl("_with_nas", test_names)] | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[!grepl("_na$", test_names)] | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[!grepl("mat_", test_names)] | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[!test_names %in% c("vec_factor", "vec_factor_ordered", "vec_logical")] | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[test_names != "list"] | ||
| # TODO: re-enable these tests | ||
| test_names <- test_names[!test_names %in% c("scalar_factor", "scalar_factor_ordered", "scalar_logical")] | ||
| 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$scalar_generators) | ||
| ) | ||
|
|
||
| for (name in test_names) { | ||
| test_that(paste0("roundtrip with uns '", name, "'"), { | ||
| # create anndata | ||
| ad <- AnnData( | ||
| obs = data$obs[, c(), drop = FALSE], | ||
| var = data$var[, c(), drop = FALSE], | ||
| uns = data$uns[name] | ||
| ) | ||
| # first generate a python h5ad | ||
| adata_py <- da$generate_dataset( | ||
| x_type = NULL, | ||
| obs_types = list(), | ||
| var_types = list(), | ||
| layer_types = list(), | ||
| obsm_types = list(), | ||
| varm_types = list(), | ||
| obsp_types = list(), | ||
| varp_types = list(), | ||
| uns_types = list(name), | ||
| nested_uns_types = list() | ||
| ) | ||
|
|
||
| # write to file | ||
| filename <- withr::local_file(tempfile(fileext = ".h5ad")) | ||
| write_h5ad(ad, filename) | ||
| # create a couple of paths | ||
| file_py <- withr::local_file(tempfile(paste0("anndata_py_", name), fileext = ".h5ad")) | ||
| file_r <- withr::local_file(tempfile(paste0("anndata_r_", name), fileext = ".h5ad")) | ||
|
|
||
| # read from file | ||
| ad_new <- read_h5ad(filename, to = "HDF5AnnData") | ||
| # write to file | ||
| adata_py$write_h5ad(file_py) | ||
|
|
||
| test_that(paste0("Reading an AnnData with uns '", name, "' works"), { | ||
| msg <- message_if_known( | ||
| backend = "HDF5AnnData", | ||
| slot = c("uns"), | ||
| dtype = name, | ||
| process = "read", | ||
| known_issues = known_issues | ||
| ) | ||
| skip_if(!is.null(msg), message = msg) | ||
|
|
||
| # expect slots are unchanged | ||
| adata_r <- read_h5ad(file_py, to = "HDF5AnnData") | ||
| expect_equal( | ||
| ad_new$uns, | ||
| data$uns[name], | ||
| ignore_attr = TRUE, | ||
| tolerance = 1e-6 | ||
| names(adata_r$uns), | ||
| bi$list(adata_py$uns$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) | ||
| }) | ||
| } | ||
|
|
||
| for (name in test_names) { | ||
| test_that(paste0("reticulate->hdf5 with uns '", name, "'"), { | ||
| # create anndata | ||
| ad <- anndata::AnnData( | ||
| obs = data$obs[, c(), drop = FALSE], | ||
| var = data$var[, c(), drop = FALSE], | ||
| uns = data$uns[name] | ||
| # maybe this test simply shouldn't be run if there is a known issue with reticulate | ||
| test_that(paste0("Comparing an anndata with uns '", name, "' with reticulate works"), { | ||
| msg <- message_if_known( | ||
| backend = "HDF5AnnData", | ||
| slot = c("uns"), | ||
| dtype = name, | ||
| process = c("read", "reticulate"), | ||
| known_issues = known_issues | ||
| ) | ||
| skip_if(!is.null(msg), message = msg) | ||
|
|
||
| # write to file | ||
| filename <- withr::local_file(tempfile(fileext = ".h5ad")) | ||
| ad$write_h5ad(filename) | ||
|
|
||
| # read from file | ||
| ad_new <- HDF5AnnData$new(filename) | ||
| adata_r <- read_h5ad(file_py, to = "HDF5AnnData") | ||
|
|
||
| # expect slots are unchanged | ||
| expect_equal( | ||
| ad_new$uns, | ||
| data$uns[name], | ||
| ignore_attr = TRUE, | ||
| tolerance = 1e-6 | ||
| adata_r$uns[[name]], | ||
| reticulate::py_to_r(adata_py$uns[[name]]) | ||
| ) | ||
| }) | ||
| } | ||
|
|
||
| for (name in test_names) { | ||
| test_that(paste0("hdf5->reticulate with uns '", name, "'"), { | ||
| # write to file | ||
| filename <- withr::local_file(tempfile(fileext = ".h5ad")) | ||
|
|
||
| # make anndata | ||
| ad <- AnnData( | ||
| obs = data$obs[, c(), drop = FALSE], | ||
| var = data$var[, c(), drop = FALSE], | ||
| uns = data$uns[name] | ||
| test_that(paste0("Writing an AnnData with uns '", name, "' works"), { | ||
| msg <- message_if_known( | ||
| backend = "HDF5AnnData", | ||
| slot = c("uns"), | ||
| dtype = name, | ||
| process = c("read", "write"), | ||
| known_issues = known_issues | ||
| ) | ||
| write_h5ad(ad, filename) | ||
| skip_if(!is.null(msg), message = msg) | ||
|
|
||
| adata_r <- read_h5ad(file_py, to = "InMemoryAnnData") | ||
| write_h5ad(adata_r, file_r) | ||
|
|
||
| # read from file | ||
| ad_new <- anndata::read_h5ad(filename) | ||
| adata_py2 <- ad$read_h5ad(file_r) | ||
|
|
||
| expect_equal( | ||
| ad_new$uns, | ||
| data$uns[name], | ||
| ignore_attr = TRUE, | ||
| tolerance = 1e-6 | ||
| # expect name is one of the keys | ||
| expect_contains( | ||
| bi$list(adata_py2$uns$keys()), | ||
| name | ||
| ) | ||
|
|
||
| # expect that the objects are the same | ||
| expect_equal_py( | ||
| py_get_item(adata_py2$uns, name), | ||
| py_get_item(adata_py$uns, name) | ||
| ) | ||
| }) | ||
| } |