automatic_sleep_staging: No module named 'lightbgm'

[18alia]

When I tried running the 5th code block in the notebook 14_automatic_sleep_staging, I got the error: ModuleNotFoundError: No module named 'lightgbm'
Here is my traceback:
ModuleNotFoundError Traceback (most recent call last)
in
1 # Getting the predicted sleep stages is now as easy as:
----> 2 y_pred = sls.predict()
3 y_pred

~\PyMOL\lib\site-packages\yasa\staging.py in predict(self, path_to_model)
425 self.fit()
426 # Load and validate pre-trained classifier
--> 427 clf = self._load_model(path_to_model)
428 # Now we make sure that the features are aligned
429 X = self.features.copy()[clf.feature_name]

~\PyMOL\lib\site-packages\yasa\staging.py in _load_model(self, path_to_model)
398 assert os.path.isfile(path_to_model), "File does not exist."
399 # Load using Joblib
--> 400 clf = joblib.load(path_to_model)
401 # Validate features
402 self._validate_predict(clf)

~\PyMOL\lib\site-packages\joblib\numpy_pickle.py in load(filename, mmap_mode)
583 return load_compatibility(fobj)
584
--> 585 obj = _unpickle(fobj, filename, mmap_mode)
586 return obj

~\PyMOL\lib\site-packages\joblib\numpy_pickle.py in _unpickle(fobj, filename, mmap_mode)
502 obj = None
503 try:
--> 504 obj = unpickler.load()
505 if unpickler.compat_mode:
506 warnings.warn("The file '%s' has been generated with a "

~\PyMOL\lib\pickle.py in load(self)
1086 raise EOFError
1087 assert isinstance(key, bytes_types)
-> 1088 dispatchkey[0]
1089 except _Stop as stopinst:
1090 return stopinst.value

~\PyMOL\lib\pickle.py in load_stack_global(self)
1383 if type(name) is not str or type(module) is not str:
1384 raise UnpicklingError("STACK_GLOBAL requires str")
-> 1385 self.append(self.find_class(module, name))
1386 dispatch[STACK_GLOBAL[0]] = load_stack_global
1387

~\PyMOL\lib\pickle.py in find_class(self, module, name)
1424 elif module in _compat_pickle.IMPORT_MAPPING:
1425 module = _compat_pickle.IMPORT_MAPPING[module]
-> 1426 import(module, level=0)
1427 if self.proto >= 4:
1428 return _getattribute(sys.modules[module], name)[0]

ModuleNotFoundError: No module named 'lightgbm'

How do I fix this error? Do I need to install something else? I already tried upgrading yasa with the commandpip install --upgrade yasa, and it told me all requirements were already satisfied

[raphaelvallat]

Hi @18alia,

You need to install the lightgbm package: https://lightgbm.readthedocs.io/en/latest/Python-Intro.html

Thanks
Raphael

[18alia]

Thank you! What else do I need to install to use YASA. I'm assuming I need the things listed on the requirements.txt file, so what is the best way to install all these if I am not GitCloning the entire project?

[raphaelvallat]

Hi @18alia,

You can pip install all of the packages in the requirements.txt file, with the exception of the entropy package that requires a manual install (via git clone / zip download).

Best,
Raphael