ctheodoris

/

Geneformer

like 194

Minimum amount of code required to generate the error:

from geneformer import Classifier
cc = Classifier(classifier="cell",
                cell_state_dict = {"state_key": "Rx", "states": "all"},
                #filter_data=filter_data_dict,
                #training_args=training_args,
                max_ncells=None,
                freeze_layers = 2,
                num_crossval_splits = 1,
                forward_batch_size=200,
                nproc=16)

Traceback:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/hy374/.conda/envs/py310/lib/python3.10/site-packages/geneformer/classifier.py", line 236, in __init__
    with open(token_dictionary_file, "rb") as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType

I tried reinstall using pip, is the file corrupted or is the path just weird?
edit: triedtoken_dictionary_file = None, as well, same error