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Genentech / gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
https://genentech.github.io/gReLU/
MIT License
230 stars 23 forks source link

Loading models from the checkpoint leads to package version conflicts #28

Open MuhammedHasan opened 4 months ago

MuhammedHasan commented 4 months ago

I downloaded grelu from the github and try to load the borzoi model

from grelu.resources import load_model
fold=0
borzoi = load_model(project="borzoi", model_name=f"human_state_dict_fold{fold}")

The loading of the model the checkpoint leads to error below:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[28], [line 2](vscode-notebook-cell:?execution_count=28&line=2)
      [1](vscode-notebook-cell:?execution_count=28&line=1) fold=0
----> [2](vscode-notebook-cell:?execution_count=28&line=2) borzoi = load_model(project="borzoi", model_name=f"human_state_dict_fold{fold}")

File ~/Projects/gReLU/src/grelu/resources/__init__.py:136, in load_model(project, model_name, alias, checkpoint_file)
    [134](https://vscode-remote+ssh-002dremote-002brosalind.vscode-resource.vscode-cdn.net/gstore/home/celikm5/Projects/borzoi-variant-effect-pred/.snakemake/scripts/~/Projects/gReLU/src/grelu/resources/__init__.py:134) with TemporaryDirectory() as d:
    [135](https://vscode-remote+ssh-002dremote-002brosalind.vscode-resource.vscode-cdn.net/gstore/home/celikm5/Projects/borzoi-variant-effect-pred/.snakemake/scripts/~/Projects/gReLU/src/grelu/resources/__init__.py:135)     art.download(d)
--> [136](https://vscode-remote+ssh-002dremote-002brosalind.vscode-resource.vscode-cdn.net/gstore/home/celikm5/Projects/borzoi-variant-effect-pred/.snakemake/scripts/~/Projects/gReLU/src/grelu/resources/__init__.py:136)     model = LightningModel.load_from_checkpoint(Path(d) / checkpoint_file)
    [138](https://vscode-remote+ssh-002dremote-002brosalind.vscode-resource.vscode-cdn.net/gstore/home/celikm5/Projects/borzoi-variant-effect-pred/.snakemake/scripts/~/Projects/gReLU/src/grelu/resources/__init__.py:138) return model

AttributeError: module 'pytorch_lightning' has no attribute 'utilities'

Problem is due to version difference of pytorch_lightning.