Convert README to markdown

MANIFEST.in

@@ -1,4 +1,4 @@
-include README.rst
+include README.md
 include INSTALLATION.rst
 include CACHING.rst
 include LICENSE.md

Makefile

@@ -56,7 +56,7 @@ benchmark:
 	cd $(benchmarks) && asv continuous develop
 
 check-dist:
-	python setup.py check --restructuredtext --strict
+	python setup.py check --strict
 
 dist: build-dist check-dist
 	twine upload $(dist_dir)/*

README.md

@@ -0,0 +1,165 @@
+<a href="http://pyphi.readthedocs.io/">
+  <img alt="PyPhi logo" src="https://github.com/wmayner/pyphi/raw/develop/docs/_static/pyphi-logo-text-760x180.png" height="90px" width="380px" style="max-width:100%;">
+</a>
+
+[![Documentation badge](https://readthedocs.org/projects/pyphi/badge/?style=flat-square&maxAge=600)](https://pyphi.readthedocs.io/)
+[![Travis build badge](https://img.shields.io/travis/wmayner/pyphi.svg?style=flat-square&maxAge=600)](https://travis-ci.org/wmayner/pyphi)
+[![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)
+[![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)
+[![Python versions badge](https://img.shields.io/pypi/pyversions/pyphi.svg?style=flat-square&maxAge=86400)](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 manuscript:**
+
+---
+
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G (2017).
+[PyPhi: A toolbox for integrated
+information](https://arxiv.org/abs/1712.09644). arXiv:1712.09644 \[q-bio.NC\].
+
+---
+
+The manuscript is available at <https://arxiv.org/abs/1712.09644>.
+
+
+## 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
+```
+
+
+## Credit
+
+### Please cite these papers if you use this code:
+
+Mayner WGP, Marshall W, Albantakis L, Findlay G, Marchman R, Tononi G (2017).
+[PyPhi: A toolbox for integrated
+information](https://arxiv.org/abs/1712.09644). arXiv:1712.09644 \[q-bio.NC\].
+
+```
+@article{mayner2017pyphi,
+  title={PyPhi: A toolbox for integrated information},
+  author={Mayner, William, Gerald Paul AND Marshall, William AND 
+          Albantakis, Larissa AND Findlay, Graham AND 
+          Marchman, Robert AND Tononi, Giulio},
+  journal={arXiv:1712.09644 [q-bio.NC]},
+  year={2017},
+  month={12},
+  url={https://arxiv.org/abs/1712.09644}
+}
+```
+
+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. Olces, P. Rana, and B. Shababo.
+
+Correspondence regarding this code and the PyPhi paper should be directed to
+Will Mayner, at [<mayner@wisc.edu>](mailto:mayner@wisc.edu). Correspondence
+regarding the Matlab code and the IIT 3.0 paper should be directed to Larissa
+Albantakis, PhD, at [<albantakis@wisc.edu>](mailto:albantakis@wisc.edu).

setup.py

@@ -6,7 +6,7 @@
 # Use a consistent encoding
 from codecs import open
 
-with open('README.rst', encoding='utf-8') as f:
+with open('README.md', encoding='utf-8') as f:
     readme = f.read()
 
 about = {}
@@ -36,6 +36,7 @@
     url=about['__url__'],
     license=about['__license__'],
     long_description=readme,
+    long_description_content_type='text/markdown',
     install_requires=install_requires,
     keywords=('causality causal-modeling causation iit information integrated '
               'integrated-information modeling neuroscience theory'),