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dpeerlab / Palantir

Single cell trajectory detection
https://palantir.readthedocs.io
GNU General Public License v2.0
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ImportError: cannot import name 'config' from 'jax.config' (/home/william/mambaforge/envs/palantir/lib/python3.12/site-packages/jax/config.py) #136

Closed wbrett87 closed 4 months ago

wbrett87 commented 4 months ago

Hello!

Upon creating a new conda environment and installing the newest Palantir version using pip, I get the following error after importing palantir in jupyter:

image

Any help would be greatly appreciated!

katosh commented 4 months ago

This seems to be a change of the jax library that broke the dependency Mellon. I will make a new version of Mellon soon. For a quick fix you can install it from the current main branhc by

pip install --upgrade 'git+https://github.com/settylab/Mellon.git'

Please let me know if this does not fix the issue or if you have any further questions!

katosh commented 4 months ago

This can be traced back to the deprecation of jax.config.config in jax v0.4.25 just two days ago. I finished a new release of Mellon v1.4.2 which is available through conda and pypi with

pip install --upgrade mellon
wbrett87 commented 4 months ago

Wow thanks for the quick action. This fixed it!