{ "info": { "author": "William GP Mayner", "author_email": "wmayner@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Natural Language :: English", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering" ], "description": "

\n \n \"PyPhi\n \n

\n\n[![Documentation badge](https://readthedocs.org/projects/pyphi/badge/?style=flat-square&maxAge=600)](https://pyphi.readthedocs.io/)\n[![Travis build badge](https://img.shields.io/travis/wmayner/pyphi.svg?style=flat-square&maxAge=600)](https://travis-ci.org/wmayner/pyphi)\n[![Coveralls.io badge](https://img.shields.io/coveralls/wmayner/pyphi/develop.svg?style=flat-square&maxAge=600)](https://coveralls.io/github/wmayner/pyphi?branch=develop)\n[![License badge](https://img.shields.io/github/license/wmayner/pyphi.svg?style=flat-square&maxAge=86400)](https://github.com/wmayner/pyphi/blob/master/LICENSE.md)\n[![Python versions badge](https://img.shields.io/pypi/pyversions/pyphi.svg?style=flat-square&maxAge=86400)](https://wiki.python.org/moin/Python2orPython3)\n\nPyPhi is a Python library for computing integrated information (\ud835\udebd), and the\nassociated quantities and objects.\n\n**If you use this code, please cite the paper:**\n\n---\n\nMayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)\n[PyPhi: A toolbox for integrated information\ntheory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational\nBiology 14(7): e1006343. \n\n---\n\n\n## Usage, Examples, and API documentation\n\n- [Documentation for the latest stable\n release](http://pyphi.readthedocs.io/en/stable/)\n- [Documentation for the latest (potentially unstable) development\n version](http://pyphi.readthedocs.io/en/latest/).\n- Documentation is also available within the Python interpreter with the `help`\n function.\n\n\n## Installation\n\nSet up a Python 3 virtual environment and install with\n\n```bash\npip install pyphi\n```\n\nTo install the latest development version, which is a work in progress and may\nhave bugs, run:\n\n```bash\npip install \"git+https://github.com/wmayner/pyphi@develop#egg=pyphi\"\n```\n\n**Note:** this software is only supported on Linux and macOS. However, if you\nuse Windows, you can run it by using the [Anaconda\nPython](https://www.anaconda.com/what-is-anaconda/) distribution and\n[installing PyPhi with conda](https://anaconda.org/wmayner/pyphi):\n\n```bash\nconda install -c wmayner pyphi\n```\n\n### Detailed installation guide for Mac OS X\n\n[See here](https://github.com/wmayner/pyphi/blob/develop/INSTALLATION.rst).\n\n\n## User group\n\nFor discussion about the software or integrated information theory in general,\nyou can join the [pyphi-users\ngroup](https://groups.google.com/forum/#!forum/pyphi-users).\n\nFor technical issues with PyPhi or feature requests, please use the [issues\npage](https://github.com/wmayner/pyphi/issues).\n\n\n## Contributing\n\nTo help develop PyPhi, fork the project on GitHub and install the requirements\nwith\n\n```bash\npip install -r requirements.txt\n```\n\nThe `Makefile` defines some tasks to help with development:\n\n```bash\nmake test\n```\n\nruns the unit tests every time you change the source code.\n\n```bash\nmake benchmark\n```\n\nruns performance benchmarks.\n\n```bash\nmake docs\n```\n\nbuilds the HTML documentation.\n\n### Developing on Linux\n\nMake sure you install the C headers for Python 3, SciPy, and NumPy\nbefore installing the requirements:\n\n```bash\nsudo apt-get install python3-dev python3-scipy python3-numpy\n```\n\n### Developing on Windows\n\nIf 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. \n\n```bash\nconda create -n pyphi_dev\nconda activate pyphi_dev\nconda install -c wmayner pyemd\ncd path/to/local/editable/copy/of/pyphi\npip install -e .\n```\n\nUnfortunately, 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. \n\n```bash\nconda activate pyphi_dev\npip uninstall scipy\nconda install scipy\n```\n\n## Credit\n\n### Please cite these papers if you use this code:\n\nMayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G. (2018)\n[PyPhi: A toolbox for integrated information\ntheory](https://doi.org/10.1371/journal.pcbi.1006343). PLOS Computational\nBiology 14(7): e1006343. \n\n```\n@article{mayner2018pyphi,\n title={PyPhi: A toolbox for integrated information theory},\n author={Mayner, William GP and Marshall, William and Albantakis, Larissa and Findlay, Graham and Marchman, Robert and Tononi, Giulio},\n journal={PLoS Computational Biology},\n volume={14},\n number={7},\n pages={e1006343},\n year={2018},\n publisher={Public Library of Science},\n doi={10.1371/journal.pcbi.1006343},\n url={https://doi.org/10.1371/journal.pcbi.1006343}\n}\n```\n\nAlbantakis L, Oizumi M, Tononi G (2014). [From the Phenomenology to the\nMechanisms of Consciousness: Integrated Information Theory\n3.0](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003588).\nPLoS Comput Biol 10(5): e1003588. doi: 10.1371/journal.pcbi.1003588.\n\n```\n@article{iit3,\n title={From the Phenomenology to the Mechanisms of Consciousness:\n author={Albantakis, Larissa AND Oizumi, Masafumi AND Tononi, Giulio},\n Integrated Information Theory 3.0},\n journal={PLoS Comput Biol},\n publisher={Public Library of Science},\n year={2014},\n month={05},\n volume={10},\n pages={e1003588},\n number={5},\n doi={10.1371/journal.pcbi.1003588},\n url={http://dx.doi.org/10.1371%2Fjournal.pcbi.1003588}\n}\n```\n\nThis project is inspired by a [previous\nproject](https://github.com/albantakis/iit) written in Matlab by L. Albantakis,\nM. Oizumi, A. Hashmi, A. Nere, U. Olces, P. Rana, and B. Shababo.\n\nCorrespondence regarding this code and the PyPhi paper should be directed to\nWill Mayner, at [](mailto:mayner@wisc.edu). 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