error when installing hnn-core

[stephanie-r-jones]

When testing if hnn_core installed properly with 'python -c 'import hnn_core', I received the following error:

Traceback (most recent call last):
File "", line 1, in
File "/Applications/anaconda/lib/python3.6/site-packages/hnn_core/init.py", line 5, in
from .pyramidal import L2Pyr, L5Pyr
File "/Applications/anaconda/lib/python3.6/site-packages/hnn_core/pyramidal.py", line 8, in
from neuron import h
ModuleNotFoundError: No module named 'neuron'

[jasmainak]

Hi Stephanie -- did you install Neuron first? You can do:

$ pip install NEURON

[jasmainak]

We'll actually make it so that NEURON is installed automatically as part of hnn-core installation. It's in #255 . But let us know if this fixes the problem for you or you face other issues!

[stephanie-r-jones]

Hi Mainak,
Yes, I intalled the latest version of NEURON and ran a test simulation through the NEURO GUI. it worked.

[stephanie-r-jones]

And, NEURON wasn't installed automatically because I had an older version of NEURON that needed to first be removed

[stephanie-r-jones]

When I say it worked, I mean NEURON works, not hnn_core.. still issue there

[jasmainak]

how did you install NEURON? Did you use pip as I suggested above or you downloaded and installed it with the installer?

[stephanie-r-jones]

pip didn't automatically work so I used the installer... should I reinstall and try again?

[stephanie-r-jones]

I mean uninstall and try again

[jasmainak]

I think pip should be the preferred way. I have stopped using the installer for a while. What issue did you face with pip ?

[stephanie-r-jones]

Uninstalling NEURON, and then reinstalling NEURON with pip worked. Note, I first tried to just run pip install https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master and this did not install NEURON, and I think you are suggesting it should have?

[jasmainak]

If you open ipython and then do:

$ ipython

and then:

>>> import neuron

does this work? If not, I think you can safely run that pip command. No need to uninstall anything. It's possible that for the GUI, NEURON is installed in a different environment.

[jasmainak]

Note, I first tried to just run pip install https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master and this did not install NEURON

Yes, this is something to fix. We're working on it in #255 . It should really install everything with a single command but currently it doesn't. You have to install NEURON separately first

[stephanie-r-jones]

Also, installing hnn_core has broken my HNN GUI docker installation. I'm going to try now the pip install of HNN GUI and see how the goes...

[jasmainak]

I don't think a pip install of the GUI exists. The fact that it broke your installation means that you probably didn't have a docker installation. A docker installation is containerized. You probably used the scripting route to install HNN GUI. I suspect that all you need to do to fix this is to activate the hnn environment by doing:

$ conda activate hnn

and then install NEURON in that environment using pip

$ pip install NEURON