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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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ImportError using topaz with python2.7 #69

Closed sbliven closed 3 years ago

sbliven commented 3 years ago

I've installed topaz with python2.7 (for use with cryosparc, so I don't think I can use 3?). I'm getting an error:

$ topaz --version
Traceback (most recent call last):
  File "/opt/psi/Programming/anaconda/2019.07/conda/envs/topaz-0.2.5/bin/topaz", line 11, in <module>
    load_entry_point('topaz-em==0.2.4', 'console_scripts', 'topaz')()
  File "/opt/psi/Programming/anaconda/2019.07/conda/envs/topaz-0.2.5/lib/python2.7/site-packages/topaz/main.py", line 68, in main
    import topaz.commands.denoise
  File "/opt/psi/Programming/anaconda/2019.07/conda/envs/topaz-0.2.5/lib/python2.7/site-packages/topaz/commands/denoise.py", line 77, in <module>
    import topaz.denoise as dn
  File "/opt/psi/Programming/anaconda/2019.07/conda/envs/topaz-0.2.5/lib/python2.7/site-packages/topaz/denoise.py", line 7, in <module>
    import torch.nn as nn
ImportError: No module named nn

Digging into this it looks like topaz.torch is shadowing pytorch's torch. Maybe torch.py should be renamed?

sbliven commented 3 years ago

This seems to be a python2/3 difference. Python 3 prefers the global package since the local one should be referenced .torch, while python2 loads the package-local file first.

tbepler commented 3 years ago

Thanks for pointing this out, I'll add this to the todo list. That said, I probably won't continue to support python 2 for much longer. I recommend using python 3 instead.

sbliven commented 3 years ago

Dropping python 2 seems very reasonable. I had originally installed following the cryosparc guide, which specifically fixes python=2.7. I later realized that there is no need to match python versions between topaz and cryosparc, so I've switched to python 3.

That said, it might still be a good idea to avoid namespace collisions with dependencies.

tbepler commented 3 years ago

This should now be resolved by commit 12f7a8a7ecc35a38c7f38fe799d549c0c82975d0