Package: pyphi
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. PLOS Computational
Biology 14(7): e1006343.https://doi.org/10.1371/journal.pcbi.1006343Usage, Examples, and API documentationDocumentation for the latest stable
releaseDocumentation for the latest (potentially unstable) development
version.Documentation is also available within the Python interpreter with thehelpfunction.InstallationSet up a Python 3 virtual environment and install withpipinstallpyphiTo install the latest development version, which is a work in progress and may
have bugs, run:pipinstall"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 theAnaconda
Pythondistribution andinstalling PyPhi with conda:condainstall-cwmaynerpyphiDetailed installation guide for Mac OS XSee here.User groupFor discussion about the software or integrated information theory in general,
you can join thepyphi-users
group.For technical issues with PyPhi or feature requests, please use theissues
page.ContributingTo help develop PyPhi, fork the project on GitHub and install the requirements
withpipinstall-rrequirements.txtTheMakefiledefines some tasks to help with development:maketestruns the unit tests every time you change the source code.makebenchmarkruns performance benchmarks.makedocsbuilds the HTML documentation.Developing on LinuxMake sure you install the C headers for Python 3, SciPy, and NumPy
before installing the requirements:sudoapt-getinstallpython3-devpython3-scipypython3-numpyDeveloping on WindowsIf 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.condacreate-npyphi_dev
condaactivatepyphi_dev
condainstall-cwmaynerpyemdcdpath/to/local/editable/copy/of/pyphi
pipinstall-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.condaactivatepyphi_dev
pipuninstallscipy
condainstallscipyCreditPlease 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. PLOS Computational
Biology 14(7): e1006343.https://doi.org/10.1371/journal.pcbi.1006343@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.
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 aprevious
projectwritten in Matlab by L. Albantakis,
M. Oizumi, A. Hashmi, A. Nere, U. Olces, P. Rana, and B. Shababo.Correspondence regarding this code and the PyPhi paper should be directed to
Will Mayner, atmayner@wisc.edu. Correspondence
regarding the Matlab code and the IIT 3.0 paper should be directed to Larissa
Albantakis, PhD, atalbantakis@wisc.edu.