{ "info": { "author": "William GP Mayner and Juan D. Gomez", "author_email": "wmayner@gmail.com, juanogo@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. 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