www.neuron.yale.edu

Posted: **Thu Dec 11, 2014 4:44 pm**

When I execute

nrniv -python

then

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import sys
sys.path

i get:

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['', '', '', '/Users/milsteina', '/Applications/NEURON-7.3/nrn/lib/python', '/anaconda/lib', '/usr/lib/python27.zip', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-darwin', '/usr/lib/python2.7/plat-mac', '/usr/lib/python2.7/plat-mac/lib-scriptpackages', '/usr/Extras/lib/python', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/Library/Python/2.7/site-packages', '/Applications/NEURON-7.3/nrn/share/nrn/lib/python']

but when i just execute

Code: Select all

python

then

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import sys
sys.path

i get

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['', '/Users/milsteina', '/Applications/NEURON-7.3/nrn/lib/python', '/anaconda/lib', '/anaconda/lib/python27.zip', '/anaconda/lib/python2.7', '/anaconda/lib/python2.7/plat-darwin', '/anaconda/lib/python2.7/plat-mac', '/anaconda/lib/python2.7/plat-mac/lib-scriptpackages', '/anaconda/lib/python2.7/lib-tk', '/anaconda/lib/python2.7/lib-old', '/anaconda/lib/python2.7/lib-dynload', '/anaconda/lib/python2.7/site-packages', '/anaconda/lib/python2.7/site-packages/PIL', '/anaconda/lib/python2.7/site-packages/Sphinx-1.2.3-py2.7.egg', '/anaconda/lib/python2.7/site-packages/runipy-0.1.1-py2.7.egg', '/anaconda/lib/python2.7/site-packages/setuptools-7.0-py2.7.egg']

i need to be able to access the modules that are installed in the anaconda python, which seems configured correctly in my .bash_profile

Posted: **Thu Dec 11, 2014 5:13 pm**

Note:
I can get around this by first executing:

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python

then

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from neuron import gui
import sys
sys.path

which then gives me the access that i need

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['', '/Users/milsteina', '/Applications/NEURON-7.3/nrn/lib/python', '/anaconda/lib', '/anaconda/lib/python27.zip', '/anaconda/lib/python2.7', '/anaconda/lib/python2.7/plat-darwin', '/anaconda/lib/python2.7/plat-mac', '/anaconda/lib/python2.7/plat-mac/lib-scriptpackages', '/anaconda/lib/python2.7/lib-tk', '/anaconda/lib/python2.7/lib-old', '/anaconda/lib/python2.7/lib-dynload', '/anaconda/lib/python2.7/site-packages', '/anaconda/lib/python2.7/site-packages/PIL', '/anaconda/lib/python2.7/site-packages/Sphinx-1.2.3-py2.7.egg', '/anaconda/lib/python2.7/site-packages/runipy-0.1.1-py2.7.egg', '/anaconda/lib/python2.7/site-packages/setuptools-7.0-py2.7.egg']

but i'm still curious where the other sys.path defaults come from. thanks.

Posted: **Fri Dec 12, 2014 6:10 pm**

First a few questions.
Are you running NEURON under MSWin, Linux, or OS X?
Did you build NEURON from source code using --with-nrnpython, or did you install from a binary distribution i.e. a dmg or rpm?

Posted: **Sat Dec 13, 2014 10:44 am**

ted wrote:First a few questions.
Are you running NEURON under MSWin, Linux, or OS X?

OS X

ted wrote:Did you build NEURON from source code using --with-nrnpython?

Yes. Come to think of it, I did not install the anaconda build of python until after I had installed NEURON. Is it now hard coded to refer to the previous python?

Posted: **Sat Dec 13, 2014 6:19 pm**

Either that, or else some post-compilation configuration script has done something that depends on the non-anaconda python. Looking at nrn/configure, I see

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  --with-nrnpython=desired python binary or 'dynamic'
                          Python interpreter can be used (default is NO)
                          Probably need to set PYLIBDIR to find libpython...
                          and PYINCDIR to find Python.h

which suggests you need to throw away what you built, then do
make clean
then set the indicated environment variables, and finally
./configure . . . other options . . . --with-nrnpython=pathtodesiredpythonbinary
make
make install

But you may want to wait to see if Robert McDougal or Michael Hines have other suggestions.

Posted: **Sun Dec 14, 2014 12:56 am**

Did you build NEURON from source code using --with-nrnpython?
Yes. Come to think of it, I did not install the anaconda build of python until after I had installed NEURON. Is it now hard coded to refer to the previous python?

Yes. You need to rebuild if you installed from sources using --with-nrnpython.

www.neuron.yale.edu

What sets the sys.path for nrniv -python?

What sets the sys.path for nrniv -python?

Re: What sets the sys.path for nrniv -python?

Re: What sets the sys.path for nrniv -python?

Re: What sets the sys.path for nrniv -python?

Re: What sets the sys.path for nrniv -python?

Re: What sets the sys.path for nrniv -python?