https://github.com/wmayner/pyphi
A toolbox for integrated information theory.
https://github.com/wmayner/pyphi
causality causation information integrated-information modeling neuroscience
Last synced: 8 days ago
JSON representation
A toolbox for integrated information theory.
- Host: GitHub
- URL: https://github.com/wmayner/pyphi
- Owner: wmayner
- License: other
- Created: 2014-04-08T05:31:10.000Z (about 11 years ago)
- Default Branch: feature/iit-4.0
- Last Pushed: 2024-09-24T19:32:19.000Z (8 months ago)
- Last Synced: 2024-10-30T16:51:47.953Z (6 months ago)
- Topics: causality, causation, information, integrated-information, modeling, neuroscience
- Language: Python
- Homepage: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006343
- Size: 22.3 MB
- Stars: 376
- Watchers: 38
- Forks: 96
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
Awesome Lists containing this project
README
[](https://pyphi.readthedocs.io/)
[](https://coveralls.io/github/wmayner/pyphi?branch=develop)
[](https://wiki.python.org/moin/Python2orPython3)
PyPhi is a Python library for computing integrated information (𝚽), and the
associated quantities and objects.
**If you use this code, please cite the paper:**
---
Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)
[PyPhi: A toolbox for integrated information
theory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational
Biology 14(7): e1006343.
---
An [illustrated tutorial on how Φ is calculated](https://doi.org/10.1371/journal.pcbi.1006343.s001) is available as a supplement to the paper.
## Usage, Examples, and API documentation
- [Documentation for the latest stable
release](http://pyphi.readthedocs.io/en/stable/)
- [Documentation for the latest (potentially unstable) development
version](http://pyphi.readthedocs.io/en/latest/).
- Documentation is also available within the Python interpreter with the `help`
function.
## Installation
Set up a Python 3 virtual environment and install with
```bash
pip install pyphi
```
To install the latest development version, which is a work in progress and may
have bugs, run:
```bash
pip install "git+https://github.com/wmayner/pyphi@develop#egg=pyphi"
```
**Note:** this software is only supported on Linux and macOS. However, if you
use Windows, you can run it by using the [Anaconda
Python](https://www.anaconda.com/what-is-anaconda/) distribution and
[installing PyPhi with conda](https://anaconda.org/wmayner/pyphi):
```bash
conda install -c wmayner pyphi
```
### Detailed installation guide for Mac OS X
[See here](https://github.com/wmayner/pyphi/blob/develop/INSTALLATION.rst).
## User group
For discussion about the software or integrated information theory in general,
you can join the [pyphi-users
group](https://groups.google.com/forum/#!forum/pyphi-users).
For technical issues with PyPhi or feature requests, please use the [issues
page](https://github.com/wmayner/pyphi/issues).
## Contributing
To help develop PyPhi, fork the project on GitHub and install the requirements
with
```bash
pip install -r requirements.txt
```
The `Makefile` defines some tasks to help with development:
```bash
make test
```
runs the unit tests every time you change the source code.
```bash
make benchmark
```
runs performance benchmarks.
```bash
make docs
```
builds the HTML documentation.
### Developing on Linux
Make sure you install the C headers for Python 3, SciPy, and NumPy
before installing the requirements:
```bash
sudo apt-get install python3-dev python3-scipy python3-numpy
```
### Developing on Windows
If you're just looking for an editable install, pip may work better than the conda develop utility included in the conda-build package. When using pip on Windows, the build of pyemd may fail. The simplest solution to this is to obtain pyemd through conda.
```bash
conda create -n pyphi_dev
conda activate pyphi_dev
conda install -c wmayner pyemd
cd path/to/local/editable/copy/of/pyphi
pip install -e .
```
Unfortunately, pip isn't great at managing the DLLs that some packages (especially scipy) rely on. If you have missing DLL errors, try reinstalling the offending package (here, scipy) with conda.
```bash
conda activate pyphi_dev
pip uninstall scipy
conda install scipy
```
## Credit
### Please cite these papers if you use this code:
Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)
[PyPhi: A toolbox for integrated information
theory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational
Biology 14(7): e1006343.
```
@article{mayner2018pyphi,
title={PyPhi: A toolbox for integrated information theory},
author={Mayner, William GP and Marshall, William and Albantakis, Larissa and Findlay, Graham and Marchman, Robert and Tononi, Giulio},
journal={PLoS Computational Biology},
volume={14},
number={7},
pages={e1006343},
year={2018},
publisher={Public Library of Science},
doi={10.1371/journal.pcbi.1006343},
url={https://doi.org/10.1371/journal.pcbi.1006343}
}
```
Albantakis L, Oizumi M, Tononi G (2014). [From the Phenomenology to the
Mechanisms of Consciousness: Integrated Information Theory
3.0](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003588).
PLoS Comput Biol 10(5): e1003588. doi: 10.1371/journal.pcbi.1003588.
```
@article{iit3,
title={From the Phenomenology to the Mechanisms of Consciousness:
author={Albantakis, Larissa AND Oizumi, Masafumi AND Tononi, Giulio},
Integrated Information Theory 3.0},
journal={PLoS Comput Biol},
publisher={Public Library of Science},
year={2014},
month={05},
volume={10},
pages={e1003588},
number={5},
doi={10.1371/journal.pcbi.1003588},
url={http://dx.doi.org/10.1371%2Fjournal.pcbi.1003588}
}
```
This project is inspired by a [previous
project](https://github.com/albantakis/iit) written in Matlab by L. Albantakis,
M. Oizumi, A. Hashmi, A. Nere, U. Olcese, P. Rana, and B. Shababo.
Correspondence regarding this code and the PyPhi paper should be directed to
Will Mayner, at [](mailto:[email protected]). Correspondence
regarding the Matlab code and the IIT 3.0 paper should be directed to Larissa
Albantakis, PhD, at [](mailto:[email protected]).