ossdbs 0.5.1

OSS-DBS v2: faster and modular open-source code for deep brain stimulation

OSS-DBSv2

This is the development version of the OSS-DBS rewrite. Use with caution and please wait for the first official release before deploying it. Bug reports are highly welcome, though!

Installation

OSS-DBS is tested with Python 3.8, 3.9, 3.10, and 3.11.

Windows users and Mac users with Python 3.8: Please install NEURON separately before installing OSS-DBS. The instructions can be found here.

All other users can run

pip install ossdbs

Developers

To install OSS-DBS, clone it into a local directory, cd into this directory and run

pip install -e .

To also run the test suite of OSS-DBS, run

pip install -e ".[test]"

To develop OSS-DBS, run

pip install -e ".[dev]"

To locally build the docs of OSS-DBS, run

pip install -e ".[doc]"

To do everything of the above, run

pip install -e ".[all]"

Run OSS-DBS

To run OSS-DBS, cd into the input_files directory, insert your parameters in the input.json and start the simulation with

ossdbs input.json

Also check out the examples directory and the documentation.

Development

The code uses the input_files and tests directories to check the functionality upon each commit. If you add a new feature, please add a test to tests. Make sure that the test does not run long and does not consume much memory. It shall be rather a unit test than a full simulation run. Likewise, only change input_files after opening an issue.

The examples directory is meant for users to understand what has been implemented. Place heavy and/or experimental code there (e.g., code that may crash or consume many resources).

The code development follows different coding styles that are checked by git pre-commit hooks. Install pre-commit via pip install pre-commit and run pre-commit install to activate it.