Different order in sys.path list after importing pkg_resources

Hi,

I was having problems importing a module with ipython when I noticed that the output of sys.path is different whether is called from ipython or python. And the problem in ipython appears after importing pkg_resources by path module (ipython: __init__.py <-- embed.py <-- Ipython.core.interactiveshell <-- pickleshare <-- path <-- pkg-resources).

Running with setuptools 20.6.7 installed with conda 4.0.5 from its default channel:

#!/usr/bin/env python
import sys
print(sys.path)
import pkg_resources
print(sys.path)

this is what I get:

['', '/home/diego/Myusr/src/MyGitHub/AquaLab', '/home/diego/Myusr/src/MyGitHub/MyLab', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python35.zip', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/plat-linux', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/lib-dynload', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/Sphinx-1.3.5-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/pyEMMA-2.1-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg']

['', '/home/diego/Myusr/src/MyGitHub/AquaLab', '/home/diego/Myusr/src/MyGitHub/MyLab', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python35.zip', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/plat-linux', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/lib-dynload', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/Sphinx-1.3.5-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/pyEMMA-2.1-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages']

Before importing pkg_resources the path /.../site-packages appears before any /.../site-packages/*.egg.
After importing pkg_resources the path /.../site-packages appears after every /.../site-packages/*.egg affecting the way they are imported. Example:

#!/usr/bin/env python
import sys
import pybel
print(sys.path)
print(pybel.__spec__)

['', '/home/diego/Myusr/src/MyGitHub/AquaLab', '/home/diego/Myusr/src/MyGitHub/MyLab', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python35.zip', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/plat-linux', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/lib-dynload', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/Sphinx-1.3.5-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/pyEMMA-2.1-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg']
ModuleSpec(name='pybel', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7f6bee5169b0>, origin='/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/pybel.py')

And

#!/usr/bin/env python
import sys
import pkg_resources
import pybel
print(sys.path)
print(pybel.__spec__)

['', '/home/diego/Myusr/src/MyGitHub/AquaLab', '/home/diego/Myusr/src/MyGitHub/MyLab', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python35.zip', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/plat-linux', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/lib-dynload', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/PROPKA-3.1-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/Sphinx-1.3.5-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/pyEMMA-2.1-py3.5-linux-x86_64.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/setuptools-20.6.7-py3.5.egg', '/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages']
ModuleSpec(name='pybel', loader=<zipimporter object "/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg">, origin='/home/diego/Myopt/anaconda2/envs/mylab3/lib/python3.5/site-packages/openbabel-1.8.3-py3.5-linux-x86_64.egg/pybel.py')

Which at the end means pybel does not work properly under ipython.

Why is this?
Is this solved with setuptools 20.6.8?
Is this a problem a bug in the way conda installs setuptool 20.6.7?
Can anyone reproduce this problem with conda 4.0.5?

conda create --name test python=3
source activate test
conda install -c https://conda.anaconda.org/omnia openbabel
conda install ipython

Thanks

Start by running the supplied minimal Python script and the conda reproduction to compare sys.path before and after importing pkg_resources. Then trace the pkg_resources import path and its interaction with the egg entries, using the pybel examples to verify the effect. Done means determining whether setuptools or conda causes the reorder and documenting a reproducible resolution.