--- a
+++ b/docs/conf.py
@@ -0,0 +1,171 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# openomics documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun  9 13:47:02 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
+
+sys.path.insert(0, os.path.abspath('..'))
+
+import openomics
+
+# 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.autosummary',
+    'sphinx_autodoc_typehints',
+    'sphinx.ext.linkcode',
+    'sphinx.ext.napoleon',
+    'myst_parser',
+
+    # User Usability
+    'sphinx_copybutton',
+    'sphinx_inline_tabs',
+
+    'sphinx.ext.coverage',
+    'sphinx.ext.intersphinx',
+    "sphinx.ext.viewcode",
+    'sphinx_automodapi.automodapi',
+    'sphinx_automodapi.smart_resolver',
+    'sphinx.ext.graphviz',
+    'sphinx.ext.inheritance_diagram',
+]
+
+autosummary_generate = False
+autosummary_imported_members = True
+napoleon_google_docstring = True
+napoleon_use_param = True
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+exclude_patterns = ['_build', '_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'OpenOmics'
+copyright = "2019, Nhat Tran"
+author = "Jonny Tran"
+
+# 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 = openomics.__version__
+# The full version, including alpha/beta/rc tags.
+release = openomics.__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 = True
+
+# -- Options for Markdown files ----------------------------------------------
+
+myst_enable_extensions = ["colon_fence", "deflist"]
+myst_heading_anchors = 3
+
+# -- 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 = 'furo'
+
+# 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 = {
+    "sidebar_hide_name": False,
+    "light_css_variables": {
+        # "color-brand-primary": "#ff5c84",
+        # "color-brand-content": "#ff5c84",
+        # "color-admonition-background": "#33cccc",
+        # "font-stack": "Arial, sans-serif",
+        # "font-stack--monospace": "Courier, monospace",
+    },
+}
+
+html_logo = "../openomics_web/assets/openomics_logo.png"
+html_favicon = '_static/favicon.png'
+
+pygments_style = "sphinx"
+pygments_dark_style = "monokai"
+
+# 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']
+graphviz_dot = "/usr/bin/dot"
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'openomicsdoc'
+
+
+# -- 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, 'openomics',
+     u'OpenOmics Documentation',
+     [author], 1)
+]
+
+
+def linkcode_resolve(domain, info):
+    if domain != 'py':
+        return None
+    if not info['module']:
+        return None
+    filename = info['module'].replace('.', '/')
+    return "https://github.com/JonnyTran/OpenOmics/%s.py" % filename