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Seaborn's clustermap uses fastcluster, but not in dependencies

See original GitHub issue

Title says it all. Ran sns.clustermap earlier and got

Traceback (most recent call last):
  File "/home/users/fgrandi/.miniconda3/lib/python3.6/site-packages/seaborn/matrix.py", line 626, in calculated_linkage
    return self._calculate_linkage_fastcluster()
  File "/home/users/fgrandi/.miniconda3/lib/python3.6/site-packages/seaborn/matrix.py", line 607, in _calculate_linkage_fastcluster
    import fastcluster
ModuleNotFoundError: No module named 'fastcluster'

Is there a reason for this or should I submit a PR with that module added to setup.py?

Issue Analytics

State:
Created 6 years ago
Reactions:1
Comments:13 (5 by maintainers)

Top GitHub Comments

2reactions

MollieBakalcommented, Jun 18, 2019

I have the same error, with fastcluster throwing a ModuleNotFoundError and not falling back to scipy. Downloading fastcluster as well.

1reaction

mwaskomcommented, Dec 19, 2019

I suspect that people are getting errors during clustering and seeing the fastcluster exception because it is part of the stack trace (it gets caught and then the code moves on to use scipy), but it is not the actual cause of their problem. However, nobody has provided sufficient information to provide help beyond speculation.

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