Spyder dependency bug: # Mandatory: jellyfish >=0.7 : None (NOK)

Question:

Long term Spyder user (Python IDE angled toward data science).

Persistent issue:

You have missing dependencies!

# Mandatory: jellyfish >=0.7 : None (NOK)

Jellyfish is installed for this specific conda environment (2.2.10).

Stuff I’ve tried:

conda update --strict-channel-priority --all
conda update --all
conda update conda
conda update -n base -c defaults conda
conda update jellyfish

Finally,

import jellyfish

ModuleNotFoundError: No module named ‘jellyfish’

Also tried removing conda remove jellyfish and reinstalling.

Spyder version 5.2.2

Asked By: M__

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Source

Answers:

Its a package name conflict issue with jellyfish between the conda channels condo-forge and bioconda. Thus the solution is:

conda install -c conda-forge jellyfish

This will install jellyfish 0.9.0 and that’s what is wanted. Its a string searching package.

jellyfish 2.2.0 concerns DNA k-mers.

Perhaps Spyder could name the channel in the dependency error log?

Otherwise, I think the question can be deleted because its unlikely to be of general interest given the solution is unique to my setup.

Answered By: M__