-
-
Notifications
You must be signed in to change notification settings - Fork 11
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* add uns_keys function * add extra check to unit tests * update the uns rountrip tests * add uns-nested roundtrip test
- Loading branch information
Showing
8 changed files
with
352 additions
and
71 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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) | ||
| ) | ||
| }) | ||
| } |
Oops, something went wrong.