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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Nose not installed by default #131

Open joshim5 opened 8 years ago

joshim5 commented 8 years ago

Calling from pyensembl import EnsemblRelease gives ImportError: No module named nose.

Solution: This is corrected by calling pip install nose from the command line. Nose should be pip installed by default.

iskandr commented 8 years ago

Strange, I wonder how a dependency on nose sneaks in.

@tavinathanson Do tests get packaged up with each release? If so, I guess we should add nose back to setup.py.

tavinathanson commented 8 years ago

@joshim5 Sorry for the much delayed reply to this! I'm curious how you got into this state, as it appears that scikit-bio requires nose (https://github.com/biocore/scikit-bio/blob/master/setup.py#L123), so I'd expect nose to be installed already. When I install pyensembl in a new environment, I can't reproduce the issue; though when I uninstall nose after scikit-bio installs it during that pyensembl installation in a new environment, I do get this error:

/Users/tavi/.virtualenvs/pe2/lib/python2.7/site-packages/skbio/util/_testing.py in <module>()
     17 import six
     18 import pandas as pd
---> 19 import nose
     20
     21 import numpy as np

ImportError: No module named nose

@iskandr We do package up tests, though I don't think that's the issue?