Conflicting Dependencies + Failure to Run

[sgoldenlab]

Conflicting Dependencies + Failure to Run

[akh8zm]

oh my gosh it worked! Thank you so much.
For posterity, I created a new environment and did:

conda install shapely
pip install simba-uw-no-tf
pip install h5py
simba

[sgoldenlab]

Hi @akh8zm - this is most likely a Shapely issue - the same issue and error msg has been reported and solved a few times in the past and unrelated to imblearn / scikit.

#12 (comment)

#11 (comment)

#33 (comment)

I think it relates to some modules of the Shapely package not meant to be run in python.

I'd try some of the following to see if you can get it started: Remove shapely if installed: conda remove shapely and install it again conda install shapely and see if that works.

Otherwise, the fix that has been working for me is the second link above - download the wheel yourself and install it.

Let me know if that helps!

[akh8zm]

Thanks for the prompt reply! I removed and reinstalled shapely as you said using conda, didn't work and produced new error message. I'm gonna post the error message just for completeness.

Traceback (most recent call last):
File "c:\programdata\anaconda3\envs\new_env\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec)
File "c:\programdata\anaconda3\envs\new_env\lib\runpy.py", line 85, in _run_code exec(code, run_globals)
File "C:\ProgramData\Anaconda3\envs\new_env\Scripts\simba.exe\__main__.py", line 4, in <module>
File "c:\programdata\anaconda3\envs\new_env\lib\site-packages\simba\SimBA.py", line 90, in <module> from simba.sleap_bottom_up_convert import importSLEAPbottomUP
File "c:\programdata\anaconda3\envs\new_env\lib\site-packages\simba\sleap_bottom_up_convert.py", line 1, in <module> import h5py
ModuleNotFoundError: No module named 'h5py'

I next tried to download the wheel directly from the link you said, installed it using pip and reinstalled simba. Running simba results in the same error message as above.

In the install documentation for simba-no-tf it says "This does not require a GPU, or local installations of DeepLabCut, DeepPoseKit, or SLEAP.", but since I'm getting an error missing a module, is there something else I need to install? I'm gonna keep trying to troubleshoot with my limited skills 😄

• removing and reinstalling shapely with conda-forge doesn't fix it..
• created fresh environment and as per this comment, installed shapely with conda first, then installed simba using pip. Getting the same h5py error when trying to run simba
• tried to use method 2, installing by cloning from github. Seemed to work with a few warning messages about incompatible packages, but running python simBA.py in the simba folder produces the following error message traceback:

C:\ProgramData\Anaconda3\envs\test\lib\site-packages\sklearn\ensemble\weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed in a future NumPy release.
  from numpy.core.umath_tests import inner1d
Traceback (most recent call last):
  File "simBA.py", line 23, in <module>
    from sklearn_DLC_RF_train_model import RF_trainmodel
  File "C:\ProgramData\Anaconda3\simba\simba\sklearn_DLC_RF_train_model.py", line 19, in <module>
    from imblearn.combine import SMOTEENN
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\__init__.py", line 37, in <module>
    from . import combine
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\combine\__init__.py", line 5, in <module>
    from ._smote_enn import SMOTEENN
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\combine\_smote_enn.py", line 10, in <module>
    from ..base import BaseSampler
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\base.py", line 15, in <module>
    from .utils import check_sampling_strategy, check_target_type
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\utils\__init__.py", line 7, in <module>
    from ._validation import check_neighbors_object
  File "C:\ProgramData\Anaconda3\envs\test\lib\site-packages\imblearn\utils\_validation.py", line 15, in <module>
    from sklearn.neighbors._base import KNeighborsMixin
ModuleNotFoundError: No module named 'sklearn.neighbors._base'

[sgoldenlab]

@akh8zm You are almost there! For some reason h5py hasn't installed in your environment either.

You fixed the shapely error. Once that is done, run:

pip install h5py

and try and launch SimBA again and let me know if that fixes it!

[sgoldenlab]

Great - let me know if you get into any more issues @akh8zm