neuro-py

Analysis of neuroelectrophysiology data in Python.

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Overview

neuro_py is a Python package for analysis of neuroelectrophysiology data. It is built on top of the nelpy package, which provides core data objects. neuro_py provides a set of functions for analysis of freely moving electrophysiology, including behavior tracking utilities, neural ensemble detection, peri-event analyses, robust batch analysis tools, and more.

Tutorials are here and more will be added. The decoding tutorial and torch/lightning-backed decoders require the optional dl extra.

Installation

git clone
cd neuro_py
pip install -e .

For the optional deep-learning decoders, install the dl extra:

pip install -e .[dl]

To sync the nelpy dependency to latest version, use following instead,

pip install -e . --force-reinstall --no-cache-dir

Usage

import neuro_py as npy

Dependencies

For ease of use, this package uses nelpy core data objects. See nelpy

Testing

Use plain pytest for normal development and CI-like local runs:

pytest

To run a narrow target:

pytest tests/detectors/test_sharp_wave_ripple.py -q

If your local environment auto-loads unrelated third-party pytest plugins, use the wrapper to isolate the repo's own test environment:

python tools/run_pytest.py

This wrapper only sets PYTEST_DISABLE_PLUGIN_AUTOLOAD=1. Numba JIT and matplotlib backend behavior are exercised by the tests themselves.

CI also runs a lightweight plain-pytest smoke check against the base install so we still catch issues outside the wrapper path.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Authors

• @ryanharvey1
• @lolaBerkowitz
• @kushaangupta