This error is caused by a version incompatibility between transformers and huggingface_hub.

[yaotingsun]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of omicverse.
• (optional) I have confirmed this bug exists on the main branch of omicverse.

What happened?

This error is caused by a version incompatibility between transformers and huggingface_hub.

When importing omicverse in a conda environment on macOS (Apple Silicon, M3), the import fails with the following error:
ImportError: cannot import name 'HfFolder' from 'huggingface_hub'

Full:
python -c "import omicverse"
/Users/miniforge3/envs/omicverse/lib/python3.10/site-packages/torch/cuda/init.py:58: FutureWarning: The pynvml package is deprecated. Please install nvidia-ml-py instead. If you did not install pynvml directly, please report this to the maintainers of the package that installed pynvml for you.
import pynvml # type: ignore[import]
Traceback (most recent call last):
File "", line 1, in
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/init.py", line 41, in
from . import bulk, single, utils, bulk2single, pp, space, pl, llm
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/bulk/init.py", line 44, in
from ._Deseq2 import pyDEG,deseq2_normalize,estimateSizeFactors,estimateDispersions,Matrix_ID_mapping,data_drop_duplicates_index
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/bulk/_Deseq2.py", line 15, in
from ..pl import volcano
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/pl/init.py", line 58, in
from ._cpdb import *
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/pl/_cpdb.py", line 12, in
from ..single import cpdb_exact_target,cpdb_exact_source
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/single/init.py", line 53, in
from ._mofa import (
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/single/_mofa.py", line 1, in
from ..external import mofapy2
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/external/init.py", line 62, in
from . import (scSLAT,CEFCON,mofapy2,GNTD,spaceflow,STT,
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/external/scMulan/init.py", line 1, in
from .model.model import MulanConfig, scMulanModel
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/omicverse/external/scMulan/model/model.py", line 8, in
from transformers.generation.utils import SampleDecoderOnlyOutput
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/transformers/init.py", line 30, in
from . import dependency_versions_check
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/transformers/dependency_versions_check.py", line 36, in
from .file_utils import is_tokenizers_available
File "/Users/ysun/miniforge3/envs/omicverse/lib/python3.10/site-packages/transformers/file_utils.py", line 51, in
from huggingface_hub import HfFolder, Repository, create_repo, list_repo_files, whoami
ImportError: cannot import name 'HfFolder' from 'huggingface_hub' (/Users/miniforge3/envs/omicverse/lib/python3.10/site-packages/huggingface_hub/init.py)

Minimal code sample

NA

Error output

Versions

Details

[ansarahmadjaved]

Any solution for this ? I am facing same error

[superrray]

ImportError: cannot import name 'SampleDecoderOnlyOutput' from 'transformers.generation.utils'

[Starlitnightly]

i want to know which version of omicverse and transformer you installed?