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/conf.py

@@ -0,0 +1,69 @@
+# -*- coding: utf-8 -*-
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+# make sure sphinx always uses the current branch
+sys.path.insert(0, os.path.abspath('../..'))
+
+# https://sphinx-rtd-theme.readthedocs.io/en/stable/
+import sphinx_rtd_theme
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'PROPKA 3'
+copyright = '2020, Jan H. Jensen, Chresten R. Søndergaard, Mats H. M. Olsson, Michał Rostkowski, Nathan A. Baker, Matvey Adzhigirey, Oliver Beckstein, Jimmy Charnley Kromann, Mike Beachy, Toni G, Thomas Holder'
+author = 'Jan H. Jensen, Chresten R. Søndergaard, Mats H. M. Olsson, Michał Rostkowski, Nathan A. Baker, Matvey Adzhigirey, Oliver Beckstein, Jimmy Charnley Kromann, Mike Beachy, Toni G, Thomas Holder'
+
+# The full version, including alpha/beta/rc tags
+release = '3.2.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx',
+              'sphinx.ext.mathjax', 'sphinx.ext.viewcode',
+              'sphinx.ext.napoleon', 'sphinx.ext.todo',
+##              'sphinx_sitemap',
+              'sphinx_rtd_theme']
+
+mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+
+# for sitemap with https://github.com/jdillard/sphinx-sitemap
+# change if we put it under a custom domain; for right now, assume RTD
+##site_url = "https://propka.readthedocs.io"
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']