initial sphinx docs

starts #69

- basic structure
- RTD theme
- installation
- quickstart (more to do)
- references
- added start page with license and links to repo and issues
- authors in docs: papers and repo contributors (to be discussed)

docs/source/index.rst

@@ -0,0 +1,86 @@
+.. -*- coding: utf-8 -*-
+.. PROPKA 3 documentation master file, created by
+   sphinx-quickstart on Fri Jun 19 11:12:18 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. |pKa| replace:: :math:`\text{p}K_\text{a}`
+
+====================================
+PROPKA 3: Heuristic |pKa| prediction
+====================================
+
+:Release: |release|
+:Date: |today|
+
+
+PROPKA 3 predicts the |pKa| values of ionizable groups in proteins
+[Sondergaard2011]_ and protein-ligand complexes based on the 3D
+structure [Olsson2011]_.
+
+   
+License and source code
+=======================
+
+PROPKA 3 is released under the `GNU Lesser General Public License v2.1`_ (see the
+files *LICENSE* in the repository for details).
+
+Source code is available in the public GitHub repository
+https://github.com/jensengroup/propka.
+
+
+   
+Getting help
+============
+
+Please report *bugs and feature requests* for PROPKA through the
+`Issue Tracker`_.
+
+
+
+Contributing
+============
+
+PROPKA welcomes new contributions. To contribute code, submit a *pull
+request* against the master branch in the `propka repository`_.
+
+
+Citation
+========
+
+If you use PROPKA 3 in published work please cite [Sondergaard2011]_ and [Olsson2011]_.
+
+
+   
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+.. links
+
+.. _`GNU Lesser General Public License v2.1`:
+   https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html   
+.. _propka repository: https://github.com/jensengroup/propka   
+.. _issue tracker: https://github.com/jensengroup/propka/issues
+   
+
+.. Hide the contents from the front page because they are already in
+.. the side bar in the rtd sphinx style
+
+.. Contents
+.. ========
+
+   
+.. toctree::
+   :maxdepth: 3
+   :numbered:
+   :hidden:      
+
+   installation
+   quickstart
+   references
+
+