PsychRNN 1.0.0
Easy-to-use package for the modeling and analysis of neural network dynamics, directed towards cognitive neuroscientists.
License: MIT
Keywords: neuroscience,modeling,analysis,neural networks

# PsychRNN
[![Build Status](https://api.travis-ci.com/murraylab/PsychRNN.svg?branch=master)](https://api.travis-ci.com/murraylab/PsychRNN)
[![codecov](https://codecov.io/gh/murraylab/PsychRNN/branch/master/graph/badge.svg)](https://codecov.io/gh/murraylab/PsychRNN)
[![Documentation Status](https://readthedocs.org/projects/psychrnn/badge/?version=latest)](https://psychrnn.readthedocs.io/en/latest/?badge=latest)

**Paper:**

Ehrlich, D. B.<sup>\*</sup>, Stone, J. T.<sup>\*</sup>, Brandfonbrener, D., Atanasov, A., & Murray, J. D. (2021). PsychRNN: An Accessible and Flexible Python Package for Training Recurrent Neural Network Models on Cognitive Tasks. *ENeuro, 8*(1). [\[DOI\]](https://doi.org/10.1523/ENEURO.0427-20.2020)

## Overview

Full documentation is available at [psychrnn.readthedocs.io](https://psychrnn.readthedocs.io/).

This package is intended to help cognitive scientists easily translate task designs from human or primate behavioral experiments into a form capable of being used as training data for a recurrent neural network.

We have isolated the front-end task design, in which users can intuitively describe the conditional logic of their task from the backend where gradient descent based optimization occurs. This is intended to facilitate researchers who might otherwise not have an easy implementation available to design and test hypothesis regarding the behavior of recurrent neural networks in different task environements.

Release announcments are posted on the [psychrnn mailing list](https://www.freelists.org/list/psychrnn>) and on [GitHub](https://github.com/murraylab/PsychRNN)

Code is written and upkept by: [Daniel B. Ehrlich](https://github.com/dbehrlich>), [Jasmine T. Stone](https://github.com/syncrostone/), [David Brandfonbrener](https://github.com/davidbrandfonbrener), and [Alex Atanasov](https://github.com/ABAtanasov).

Contact: psychrnn@gmail.com 

## Getting Started

Start with [Hello World](https://psychrnn.readthedocs.io/en/latest/notebooks/Minimal_Example.html) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/murraylab/PsychRNN/blob/master/docs/notebooks/Minimal_Example.ipynb) to get a quick sense of what PsychRNN does. Then go through the [Simple Example](https://psychrnn.readthedocs.io/en/latest/notebooks/PerceptualDiscrimination.html) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/murraylab/PsychRNN/blob/master/docs/notebooks/PerceptualDiscrimination.ipynb) to get a feel for how to customize PsychRNN. The rest of [Getting Started](https://psychrnn.readthedocs.io/en/quickstart.html) will help guide you through using available features, defining your own task, and even defining your own model.

## Install

### Dependencies

- python = 2.7 or python >= 3.4
- [numpy](http://www.numpy.org/)
- [tensorflow](https://www.tensorflow.org/) >= 1.13.1

- For notebook demos, [jupyter](https://jupyter.org/)
- For notebook demos, [ipython](https://ipython.org/)
- For plotting features, [matplotlib](https://matplotlib.org/)

PsychRNN was developed to work with both Python 2.7 and 3.4+ using TensorFlow 1.13.1+. It is currently being tested on Python 2.7 and 3.4-3.8 with TensorFlow 1.13.1-2.2.

**Note:** TensorFlow 2.2 does not support Python < 3.5. Only TensorFlow 1.13.1-1.14 are compatible with Python 3.4. Python 3.8 is only supported by TensorFlow 2.2.

### Installation

Normally, you can install with:

	pip install psychrnn

Alternatively, you can download and extract the source files from the [GitHub release](https://github.com/murraylab/psychrnn/releases/). Within the downloaded PsychRNN folder, run:

        python setup.py install

[THIS OPTION IS NOT RECOMMENDED FOR MOST USERS] To get the most recent (not necessarily stable) version from the github repo, clone the repository and install:

        git clone https://github.com/murraylab/PsychRNN.git
        cd PsychRNN
        python setup.py install

## Contributing

Please report bugs to https://github.com/murraylab/psychrnn/issues.  This
includes any problems with the documentation.  Fixes (in the form of
pull requests) for bugs are greatly appreciated.

Feature requests are welcome but may or may not be accepted due to limited
resources. If you implement the feature yourself we are open
to accepting it in PsychRNN.  If you implement a new feature in PsychRNN,
please do the following before submitting a pull request on GitHub:

- Make sure your code is clean and well commented
- If appropriate, update the official documentation in the ``docs/``
  directory
- Write unit tests and optionally integration tests for your new
  feature in the ``tests/`` folder.
- Ensure all existing tests pass (``pytest`` returns without
  error)

For all other questions or comments, contact psychrnn@gmail.com.

## License

All code is available under the MIT license. See LICENSE for more information.