Tasks do not respect thread limt about cluster_tools HOT 3 CLOSED

This does not seem to be a general issue, but rather some workflows which do not respect the thread limit set, or use more than one thread although they should be single threaded. E.g. the watershed workflow.

from cluster_tools.

Turns out the most likely culprit is numpy:
numpy/numpy#11826
To fix it, either set the corresponding environment variables or use https://github.com/joblib/threadpoolctl.

from cluster_tools.

This is indeed the issue.
For now, the solution is to use this function and call it before the numpy import, like here.

from cluster_tools.