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JSchlensok / VespaG

Expert-Guided Protein Language Models enable Accurate and Blazingly Fast Fitness Prediction
GNU General Public License v3.0
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No module named 'src.vespag.runner.embeddings' #4

Closed gavinmdouglas closed 6 months ago

gavinmdouglas commented 6 months ago

Hi there,

I just ran into this problem when running the predict command (python -m src.vespag.runner.predict) with the latest developmental version:

Traceback (most recent call last):
  File "/home6/gmdougla/local/miniforge3/envs/vespag/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home6/gmdougla/local/miniforge3/envs/vespag/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/home6/gmdougla/local/prg/VespaG/src/vespag/runner/predict.py", line 13, in <module>
    from src.vespag.runner.embeddings import get_esm2_embeddings
ModuleNotFoundError: No module named 'src.vespag.runner.embeddings

It looks like embeddings.py was moved to src/vespa/data, but also that the get_esm2_embeddings function was removed or renamed and put elsewhere.

I can confirm that that running python -m src.vespag.runner.predict -h works as expected when I revert to an earlier commit (3a781ade47c526d00530582f6447f182e81089e8).

Cheers,

Gavin

JSchlensok commented 6 months ago

Hi Gavin, thanks for reporting this! There was still some work ongoing on the repository this week with a submission deadline ahead, sorry for that! Should be good to go now - let me know if the error persists.

Please note that invocation has changed to python -m vespag predict ... now and some parameter names have slightly changed!

gavinmdouglas commented 6 months ago

Hi @JSchlensok , no worries -- I figured!

Thanks -- it seems to be working now.

Cheers,

Gavin