pinellolab / simba

SIMBA: SIngle-cell eMBedding Along with features
https://simba-bio.readthedocs.io
BSD 3-Clause "New" or "Revised" License
54 stars 7 forks source link

AttributeError: 'ConfigFileLoader' object has no attribute 'load_config_simba' #8

Closed mvinyard closed 2 years ago

mvinyard commented 2 years ago

From the Multiomics integration tutorial. Running the notebook with the example data without changing any parameters.

simba.tl.pbg_train(pbg_params=dict_config, auto_wd=True, save_wd=True, output="model")
Auto-estimated weight decay is 0.00026
`.settings.pbg_params['wd']` has been updated to 0.00026
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_15400/277741414.py in <module>
----> 1 simba.tl.pbg_train(pbg_params = dict_config, auto_wd=True, save_wd=True, output='model')

~/github/simba/simba/tools/_pbg.py in pbg_train(dirname, pbg_params, output, auto_wd, save_wd)
    621 
    622     loader = ConfigFileLoader()
--> 623     config = loader.load_config_simba(pbg_params)
    624     set_logging_verbosity(config.verbose)
    625 

AttributeError: 'ConfigFileLoader' object has no attribute 'load_config_simba'

It seems that the function, load_config_simba() is not natively defined as part of the ConfigFileLoader() class from torchbiggraph.config. I'm wondering if the following import is meant to be from simba_pbg ?

from torchbiggraph.config import (
    add_to_sys_path,
    ConfigFileLoader
)
mvinyard commented 2 years ago

Actually, I found that reinstalling simba_pbg fixed this. Closing - thanks!