This is a leaner and cleaner version of the code based off the HNN repository. However, a Graphical User Interface is not supported at the moment in this repository.

It is early Work in Progress. Contributors are very welcome.

• Neuron: installation instructions here: https://neuron.yale.edu/neuron/
• scipy
• numpy
• matplotlib
• joblib (optional for parallel processing)

We recommend the Anaconda Python distribution. To install hnn-core, you first need to install its dependencies:

$ conda install numpy matplotlib scipy

For joblib, you can do:

$ pip install joblib

Additionally, you would need Neuron which is available here: https://neuron.yale.edu/neuron/

If you want to install the latest version of the code (nightly) use:

$ pip install https://api.github.com/repos/hnnsolver/hnn-core/zipball/master

If you do not have admin privileges on the computer, use the --user flag with pip. To upgrade, use the --upgrade flag provided by pip.

To check if everything worked fine, you can do:

$ python -c 'import hnn_core'

and it should not give any error messages.

A final step to the installation process is to compile custom ionic channel mechanisms using nrnivmodl from Neuron. To do this, simple do:

$ make

It should create a directory with the compiled mechanisms.

Use the github issue tracker to report bugs.