added documentation

3 files changed, 257 insertions, 0 deletions

diff --git a/docs/Makefile b/docs/Makefile
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+++ b/docs/Makefile
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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = GenSVM
+SOURCEDIR     = .
+BUILDDIR      = ../../gensvm_docs
+
+# 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 $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..a5c06ea
--- /dev/null
+++ b/docs/conf.py
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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# GenSVM documentation build configuration file, created by
+# sphinx-quickstart on Tue Sep 26 00:11:33 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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
+import sphinx_rtd_theme
+
+from unittest.mock import MagicMock
+
+sys.path.insert(0, os.path.abspath('..'))
+
+# mock out C extensions for ReadTheDocs 
+# (http://docs.readthedocs.io/en/latest/faq.html)
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+        return MagicMock()
+
+MOCK_MODULES = ['gensvm.wrapper']
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+
+
+# -- 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.doctest',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx'
+    ]
+
+# intersphinx mappings (https://kev.inburke.com/kevin/sphinx-interlinks/)
+# https://stackoverflow.com/q/46080681
+intersphinx_mapping = {
+        'sklearn': ('http://scikit-learn.org/stable', None)
+        }
+
+
+# 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'
+
+# General information about the project.
+project = 'GenSVM'
+copyright = '2017, Gertjan van den Burg'
+author = 'Gertjan van den Burg'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+#version = '0.1.0'
+# The full version, including alpha/beta/rc tags.
+#release = '0.1.0'
+__version__ = "1.0.0"
+try:
+    pth = os.path.realpath(__file__)
+    dr = os.path.dirname(pth)
+    init_pth = os.path.realpath(os.path.join(dr, '..', 'gensvm', 
+        '__init__.py'))
+    line = open(init_pth).readlines()[0]
+    __version__ = line.split('=')[-1].strip("\n '")
+except:
+    pass
+
+version = __version__
+release = version
+
+# 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 patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# 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.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'GenSVMdoc'
+
+
+# -- 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, 'GenSVM.tex', 'GenSVM Documentation',
+     'Gertjan van den Burg', '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, 'gensvm', 'GenSVM 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, 'GenSVM', 'GenSVM Documentation',
+     author, 'GenSVM', 'Implementation of the GenSVM classifier in Python',
+     'Miscellaneous'),
+]
diff --git a/docs/index.rst b/docs/index.rst
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index 0000000..d8f8425
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+++ b/docs/index.rst
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+.. GenSVM documentation master file, created by
+   sphinx-quickstart on Tue Sep 26 00:11:33 2017.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+.. include:: ../README.rst
+
+Classes
+=======
+
+The complete documentation of the available GenSVM classes is presented below.  
+
+GenSVM
+------
+
+.. autoclass:: gensvm.core.GenSVM
+
+GenSVMGridSearchCV
+------------------
+
+.. autoclass:: gensvm.gridsearch.GenSVMGridSearchCV
+
+
+.. include:: ../CHANGELOG.rst