YASS: Yet Another Spike Sorter
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edublancas Cleanup (#270)
* adds some notes to detect files

* updated docs for preprocess code

* adds note on cli

* example for building custom pipeline

* documentation updates

* updates readme

* some notes on the current codebase state
Latest commit cc54164 Nov 6, 2018

README.rst

YASS: Yet Another Spike Sorter

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Note: YASS is in an early stage of development. Although it is stable, it has only been tested with the data in our lab, but we are working to make it more flexible. Feel free to send feedback through Gitter. Expect a lot of API changes in the near future.

Reference

Lee, J. et al. (2017). YASS: Yet another spike sorter. Neural Information Processing Systems. Available in biorxiv: https://www.biorxiv.org/content/early/2017/06/19/151928

Installation

Installing the last stable version:

pip install yass-algorithm

If you are feeling adventurous, you can install from the master branch:

pip install git+git://github.com/paninski-lab/yass@master

Example

We are currently updating our documentation, this section will be updated once we have an example with publicly available data.

Documentation

Documentation hosted at https://yass.readthedocs.io

Running tests

Note: this is indented only for YASS developers, our testing data is not publicly available.

Before running the tests, download the testing data:

export YASS_TESTING_DATA_URL=[URL-TO-TESTING-DATA]

make download-test-data

make test

To run tests and flake8 checks (from the root folder):

pip install -r requirements.txt

make test

Building documentation

You need to install graphviz to build the graphs included in the documentation. On macOS:

brew install graphviz

To build the docs (from the root folder):

pip install -r requirements.txt

make docs

Contributors

Peter Lee, Eduardo Blancas, Nishchal Dethe, Shenghao Wu, Hooshmand Shokri, Calvin Tong, Catalin Mitelut