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.
- numpy
- scipy
- matplotlib
- Neuron: installation instructions here: https://neuron.yale.edu/neuron/ (>=7.7)
- joblib (for simulating trials simultaneously)
- mpi4py (for simulating the cells in parallel for a single trial). Also depends on:
- openmpi or other mpi platform installed on system
- psutil
We recommend the Anaconda Python distribution. To install hnn-core, you first need to install its dependencies:
$ conda install numpy matplotlib scipy
Additionally, you would need Neuron which is available here: https://neuron.yale.edu/neuron/. It can also be installed via pip now:
$ pip install NEURON
Since hnn-core does not yet have a stable release, we recommend installing the nightly version. This may change in the future if more users start using it.
To install the latest version of the code (nightly) do:
$ pip install --upgrade https://api.github.com/repos/jonescompneurolab/hnn-core/zipball/master
To check if everything worked fine, you can do:
$ python -c 'import hnn_core'
and it should not give any error messages.
For further instructions on installation and usage of parallel backends for using more than one core, refer to parallel_backends
Use the github issue tracker to report bugs.
Read our contributing guide.