Sphinx
According to the sphinx Git page, Sphinx is a tool that makes it easy to create intelligent and beautiful documentation for Python projects (or other documents consisting of multiple reStructuredText sources). It was originally created for the new Python documentation, but it supports other languages.
Sphinx uses reStructuredText as its markup language, and many of its strengths come from the power and straightforwardness of reStructuredText and its parsing and translating suite, the Docutils.
Among its features are the following:
Output formats: HTML (including derivative formats such as HTML Help, Epub and Qt Help), plain text, manual pages and LaTeX or direct PDF output using rst2pdf
Extensive cross-references: semantic markup and automatic links for functions, classes, glossary terms and similar pieces of information
Hierarchical structure: easy definition of a document tree, with automatic links to siblings, parents and children
Automatic indices: general index as well as a module index
Code handling: automatic highlighting using the Pygments highlighter
Flexible HTML output using the Jinja 2 templating engine
Various extensions are available, e.g. for automatic testing of snippets and inclusion of appropriately formatted docstrings
Setuptools integration
Read the Docs Sphinx Theme
The sphinx_rtd_theme Git page describes Read the Docs Sphinx Theme as a theme for Sphinx that is designed to look modern and be mobile-friendly. This theme is primarily focused to be used on readthedocs.org but can work with other sphinx projects.
Resources
Sphinx and Read the Docs
reStructuredText
Work with reStructured Text Content
Good resource to understand linking