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 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.

Testing

OSS-DBS has two types of tests:

Unit Tests (tests/): Fast, isolated tests that run on every push/PR.

pytest                    # Run all unit tests
pytest --cov              # With coverage

Simulation Tests (input_test_cases/): Full simulation tests that validate the complete pipeline. These run only on pull requests to avoid slowing down regular development.

pytest input_test_cases/test_simulations.py -m simulation      # All simulation tests
pytest input_test_cases/test_simulations.py -m "simulation and not slow"  # Fast only

See input_test_cases/README.md for detailed documentation on the simulation test suite, including how to add new tests.

Directory Structure

• tests/ - Unit tests (run on every commit)
• input_test_cases/ - Simulation tests (run on PR only)
• input_files/ - Reference input files
• examples/ - Example code for users (may be resource-intensive)