future.utils.six not found when trying to import skbio modules

Question

I just installed numpy and scikit-bio using pip3. If I import DNASequence in an interactive session I get an error message:

>>> from skbio.sequence import DNASequence
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python3.4/site-packages/skbio/__init__.py", line 64, in <module>
    from skbio.stats.distance import DistanceMatrix
  File "/usr/local/lib/python3.4/site-packages/skbio/stats/distance/__init__.py", line 293, in <module>
    from ._base import (DissimilarityMatrixError, DistanceMatrixError,
  File "/usr/local/lib/python3.4/site-packages/skbio/stats/distance/_base.py", line 11, in <module>
    from future.utils.six import StringIO, string_types
ImportError: No module named 'future.utils.six'

Running 'pip3 list' shows me that six 1.8.0 is installed. Even more strange, if I repeat the import statement, DNASequence is loaded correctly. Any idea what's causing this behavior?

I'm running Mac OS X 10.9.5 (Mavericks), Python 3.4.1 (installed via homebrew).

Answer 1

This was an issue with a change to the future package in version 0.14.0 (the removal of future.utils.six, as noted here).

We have this fixed in the development version of scikit-bio, but in the meantime you can get this working again with the release versions as follows:

pip uninstall future pip install future==0.13.1

See here for some more discussion of the issue if you're interested.