AssertionError: Unknown obs type is uncalled for!

[rcannood]

Report

da <- reticulate::import("dummy_anndata")

test_names <- names(da$vector_generators)

name <- test_names[[1]]

data <- da$generate_dataset(obs_types = name)

Results in

Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
  AssertionError: Unknown obs type

Version information

-----
dummy_anndata       0.0.1
session_info        1.0.0
-----
abrt_exception_handler3     NA
anndata                     0.10.3
asciitree                   NA
cloudpickle                 3.0.0
cython_runtime              NA
cytoolz                     0.12.2
dask                        2024.8.1
dateutil                    2.8.2
dill                        0.3.8
h5py                        3.10.0
jinja2                      3.1.2
markupsafe                  2.1.3
msgpack                     1.0.6
natsort                     8.4.0
numcodecs                   0.13.0
numpy                       1.26.2
packaging                   24.1
pandas                      2.2.2
paste                       NA
psutil                      5.9.8
pyarrow                     15.0.0
pydot                       2.0.0
pyparsing                   3.1.2
pytz                        2023.3.post1
scipy                       1.12.0
six                         1.16.0
sphinxcontrib               NA
tblib                       3.0.0
tlz                         0.12.2
toolz                       0.12.0
torch                       2.2.0+rocm5.7
torchgen                    NA
tqdm                        4.66.5
typing_extensions           NA
xxhash                      NA
yaml                        6.0.1
zarr                        2.18.2
-----
Python 3.12.7 (main, Oct  1 2024, 00:00:00) [GCC 14.2.1 20240912 (Red Hat 14.2.1-3)]
Linux-6.11.5-200.fc40.x86_64-x86_64-with-glibc2.39
-----
Session information updated at 2024-11-07 09:15

[LouiseDck]

These parameters (e.g. layer_types, obs_types, var_types etc) accept non-string iterables as input, meaning that you need to pass a Python list or set to them, not just one string.

I've added documentation and more informative checks in #4, does that solve your problem?

[rcannood]

I see, so I should use the following instead:

data <- da$generate_dataset(
  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()
)