Add Sphinx documentation

.gitignore

@@ -5,4 +5,5 @@ freesasa.egg-info
 freesasa.c
 *.so
 __pycache__
-test.pyc
+test.pyc
+docs/build

docs/Makefile

@@ -0,0 +1,21 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = FreeSASA
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@cd ../; USE_CYTHON=1 python setup.py build_ext --inplace; cd docs;
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/classes.rst

@@ -0,0 +1,32 @@
+Classes
+=======
+
+Classifier
+----------
+
+.. autoclass:: freesasa.Classifier
+    :members:
+    :special-members:
+
+.. _config-files: http://freesasa.github.io/doxygen/Config-file.html
+
+Parameters
+----------
+
+.. autoclass:: freesasa.Parameters
+    :members:
+    :special-members:
+
+Result
+------
+
+.. autoclass:: freesasa.Result
+    :members:
+    :special-members:
+
+Structure
+---------
+
+.. autoclass:: freesasa.Structure
+    :members:
+    :special-members:

docs/source/conf.py

@@ -0,0 +1,166 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- 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
+sys.path.insert(0, os.path.abspath('../../'))
+
+# -- Project information -----------------------------------------------------
+
+project = 'FreeSASA Python Module'
+copyright = '2018, Simon Mitternacht'
+author = 'Simon Mitternacht'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '2.0.2b1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.ifconfig',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.autosummary'
+]
+
+napoleon_google_docstring = True
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- 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'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'FreeSASAdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'FreeSASA.tex', 'FreeSASA Documentation',
+     'Simon Mitternacht', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'freesasa', 'FreeSASA Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'FreeSASA', 'FreeSASA Documentation',
+     author, 'FreeSASA', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

docs/source/functions.rst

@@ -0,0 +1,25 @@
+Functions
+=============================
+.. currentmodule:: freesasa
+
+.. autosummary::
+   calc
+   calcBioPDB
+   calcCoord
+   classifyResults
+   getVerbosity
+   selectArea
+   setVerbosity
+
+.. autofunction::   calc
+.. autofunction::   calcBioPDB
+.. autofunction::   calcCoord
+.. autofunction::   classifyResults
+.. autofunction::   getVerbosity
+.. autofunction::   setVerbosity
+.. autofunction::   selectArea
+.. autofunction::   structureArray
+.. autofunction::   structureFromBioPDB
+
+.. _select-syntax: http://freesasa.github.io/doxygen/Selection.html
+.. _C API: http://freesasa.github.io/doxygen/API.html

docs/source/index.rst

@@ -0,0 +1,34 @@
+.. toctree::
+   :maxdepth: 2
+
+   intro
+   functions
+   classes
+
+FreeSASA Python Module
+======================
+
+The module provides Python bindings for the `FreeSASA C Library <https://github.com/mittinatten/freesasa>`_.
+It works with Python 2.7 and 3.4+, on Linux, Mac OS X and Windows. The source is available as a PyPi source
+distribution and on `GitHub <https://github.com/freesasa/freesasa-python>`_.
+
+Install the FreeSASA Python Module by
+
+.. code::
+
+    pip install freesasa
+
+
+Developers can clone the library, and then build the module by the following
+
+.. code::
+
+   git clone https://github.com/freesasa/freesasa-python.git
+   git submodule update --init
+   python setyp.py build
+
+Tests are run by
+
+.. code::
+
+    python setup.py test