conf.py

# -*- coding: utf-8 -*-
#
# transcriptic documentation build configuration file, created by
# sphinx-quickstart on Tue Oct 27 15:01:12 2015.
#
# 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.

import sys
import os
from mock import Mock as MagicMock

class Mock(MagicMock):
    @classmethod
    def __getattr__(cls, name):
            return Mock()

# All imported modules containing C components must be mocked (added to the
# MOCK_MODULES list below)
MOCK_MODULES = ['numpy', 'scipy', 'matplotlib', 'matplotlib.pyplot',
                'sklearn.grid_search', 'sklearn.externals', 'plotly',
                'plotly.graph_objs', 'matplotlib.gridspec', 'scikit-learn',
                'pandas', 'plotly.plotly', 'plotly.tools', 'Ipython.display']
sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)


# 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.
sys.path.insert(0, os.path.abspath('../transcriptic'))
sys.path.insert(0, os.path.abspath('../transcriptic/analysis'))

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '1.3'

# 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.viewcode',
    'sphinx.ext.napoleon'
]

# Napoleon settings
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = True
napoleon_use_admonition_for_examples = False
napoleon_use_admonition_for_notes = True
napoleon_use_admonition_for_references = False
napoleon_use_ivar = False
napoleon_use_param = True
napoleon_use_rtype = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The encoding of source files.
#source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'TxPy'
copyright = u'2016, Max Hodak, Tali Herzka, Jeremy Apthorp, Yang Choo, Peter Lee'


exec(open('../transcriptic/version.py').read())
# 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 = __version__
# The full version, including alpha/beta/rc tags.
release = __version__

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']

# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
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 = 'default'

# A shorter title for the navigation bar.  Default is the same as html_title.
html_short_title = "TxPy Docs"

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
html_logo = "transcriptic.svg"

# The name of an image file (within the static path) to use as favicon of the
# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
html_favicon = "favicon.ico"

# 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']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []

# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True

# If false, no index is generated.
#html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False

# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'TxPydoc'


# -- 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': '',
}

# 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 = [
  ('index', 'transcriptic.tex', u'transcriptic Documentation',
   u'Max Hodak, Tali Herzka, Jeremy Apthorp, Yang Choo, Peter Lee', 'manual'),
]

# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False

# If true, show page references after internal links.
#latex_show_pagerefs = False

# If true, show URL addresses after external links.
#latex_show_urls = False

# Documents to append as an appendix to all manuals.
#latex_appendices = []

# If false, no module index is generated.
#latex_domain_indices = True


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    ('index', 'transcriptic', u'transcriptic Documentation',
     [u'Max Hodak, Tali Herzka, Jeremy Apthorp, Yang Choo, Peter Lee'], 1)
]

# If true, show URL addresses after external links.
#man_show_urls = False


# -- 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 = [
  ('index', 'transcriptic', u'transcriptic Documentation',
   u'Max Hodak, Tali Herzka, Jeremy Apthorp, Yang Choo, Peter Lee', 'transcriptic', 'One line description of project.',
   'Miscellaneous'),
]

# Documents to append as an appendix to all manuals.
#texinfo_appendices = []

# If false, no module index is generated.
#texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False


# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'http://docs.python.org/': None}


# on_rtd is whether we are on readthedocs.org
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

if not on_rtd:  # only import and set the theme if we're building docs locally
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

    def setup(app):
        app.add_stylesheet('transcriptic.css')

else:
    html_context = {
        'css_files': [
            'https://media.readthedocs.org/css/sphinx_rtd_theme.css',
            'https://media.readthedocs.org/css/readthedocs-doc-embed.css',
            '_static/transcriptic.css'
        ]
    }


# otherwise, readthedocs.org uses their theme by default, so no need to specify it
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []

# If false, no module index is generated.
#texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False