Future.utils.six not found while 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 the "pip3 list" shows me that six 1.8.0 are installed. Even stranger, if I repeat the import statement, DNASequence loads correctly. Any idea what causes this behavior?

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

Answer 1

This was a problem with changing the future package in version 0.14.0 (removing future.utils.six , as noted here ).

We have fixed this in the scikit-bio development version, but for now you can work with release versions again as follows:

pip uninstall future pip install future==0.13.1

See here for a more detailed discussion of the issue if you are interested.