Comments (5)
from imcsegmentationpipeline.
Hi Vito, thanks for your quick reply!
In the screenshot you can see that I executed "activate imctools" then I executed the jupyter notebook from the activated imctools env.
I also just tried this with "conda activate imctools" then jupyter notebook and the error persists.
Steve
from imcsegmentationpipeline.
Hey,
A sorry, I looked at it on a mobile phone - you sure are doing things right!
Two things to try:
a) Reinstall the imctools environment (first use conda env remove imctools
) then install it again using using: conda env create -f conda_imctools.yml
- are there any errors during installation?
b) try within the environment pip install git+https://github.com/BodenmillerGroup/imctools.git@develop-test
Are there any errors?
c) register the conda kernel as ipython kernel for jupyter specifically : activate imctools environment, then `python -m ipykernel install --user --name imctools --display-name "Python (imctools) " then select this env as active kernel in the notebook.
Let me know if/what helped!
Best, Vito
from imcsegmentationpipeline.
Hi Vito, thanks so much.
It tried option A first and that alone did not work. However I then tried B & C and now the issue is resolved.
Thanks for your help!
Enjoy the rest of your vacation,
Steve
from imcsegmentationpipeline.
Hm strange! I tested this several times on Ubuntu & Windows and everything seemed to work just with the conda install - I guess I need to investigate further and figure a procedure that works more reliable.
Glad that it worked after all!
from imcsegmentationpipeline.
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