olgabot/after_make_html.rst

## after_make_html.rst

      
    Raw
  

              after_make_html.rst
            
          
flotilla


API Reference

General use plots


toctree
generated/


Study.plot_gene Study.plot_event

Interactive plots


toctree
generated/


Study.interactive_pca Study.interactive_classifier Study.interactive_graph Study.interactive_pooled_inconsistent

Machine learning plots


toctree
generated/


Study.plot_pca Study.plot_classifier Study.plot_graph

Splicing-specific plots


toctree
generated/


Study.plot_pooled_inconsistent


## before_make_html.rst

      
    Raw
  

              before_make_html.rst
            
          
flotilla


API Reference

General use plots


Study.plot_gene Study.plot_event

Interactive plots


Study.interactive_pca Study.interactive_classifier Study.interactive_graph Study.interactive_pooled_inconsistent

Machine learning plots


Study.plot_pca Study.plot_classifier Study.plot_graph

Splicing-specific plots


Study.plot_pooled_inconsistent


## conf.py
# -*- coding: utf-8 -*-
#
# flotilla documentation build configuration file, created by
# sphinx-quickstart on Thu Jul 10 08:32:34 2014.
#
# 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

import matplotlib as mpl
import sphinx_bootstrap_theme


mpl.use('Agg')


# 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('.'))
sys.path.insert(0, os.path.abspath('..{}flotilla'.format(os.sep)))
sys.path.insert(0, os.path.abspath('sphinxext'.format(os.sep)))

# -- 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.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.autosummary',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'numpydoc',
    'plot_generator',
    'ipython_directive',
    'ipython_console_highlighting',
]

# Generate the API documentation when building
autosummary_generate = True
numpydoc_show_class_members = False

# 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'flotilla'
copyright = u'2014, Olga Botvinnik, Michael Lovci, Patrick Liu, Yan Song, ' \
            u'and Gene Yeo'

# 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.
sys.path.insert(0, os.path.abspath(os.path.pardir))
import flotilla

version = flotilla.__version__
# The full version, including alpha/beta/rc tags.
release = flotilla.__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 = []

# 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


# -- 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'
html_theme = 'bootstrap'
html_theme_path = sphinx_bootstrap_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 = {}
# (Optional) Logo. Should be small enough to fit the navbar (ideally 24x24).
# Path should be relative to the ``_static`` files directory.
#html_logo = "my_logo.png"

# Theme options are theme-specific and customize the look and feel of a
# theme further.
html_theme_options = {
    # Navigation bar title. (Default: ``project`` value)
    'navbar_title': "Flotilla",

    # Tab name for entire site. (Default: "Site")
    'navbar_site_name': "Site",

    # A list of tuples containing pages or urls to link to.
    # Valid tuples should be in the following forms:
    #    (name, page)                 # a link to a page
    #    (name, "/aa/bb", 1)          # a link to an arbitrary relative url
    #    (name, "http://example.com", True) # arbitrary absolute url
    # Note the "1" or "True" value above as the third argument to indicate
    # an arbitrary url.
    'navbar_links': [
        ("Tutorial", "tutorial"),
        ("Gallery", "gallery"),
        ("YeoLab@UCSD", "http://yeolab.ucsd.edu", True),
    ],

    # Render the next and previous page links in navbar. (Default: true)
    'navbar_sidebarrel': True,

    # Render the current pages TOC in the navbar. (Default: true)
    'navbar_pagenav': True,

    # Global TOC depth for "site" navbar tab. (Default: 1)
    # Switching to -1 shows all levels.
    'globaltoc_depth': 2,

    # Include hidden TOCs in Site navbar?
    #
    # Note: If this is "false", you cannot have mixed ``:hidden:`` and
    # non-hidden ``toctree`` directives in the same page, or else the build
    # will break.
    #
    # Values: "true" (default) or "false"
    'globaltoc_includehidden': "true",

    # HTML navbar class (Default: "navbar") to attach to <div> element.
    # For black navbar, do "navbar navbar-inverse"
    'navbar_class': "navbar",

    # Fix navigation bar to top of page?
    # Values: "true" (default) or "false"
    'navbar_fixed_top': "true",

    # Location of link to source.
    # Options are "nav" (default), "footer" or anything else to exclude.
    'source_link_position': "nav",

    # Bootswatch (http://bootswatch.com/) theme.
    #
    # Options are nothing with "" (default) or the name of a valid theme
    # such as "amelia" or "cosmo".
    'bootswatch_theme': "paper",  # "united",

    # Choose Bootstrap version.
    # Values: "3" (default) or "2" (in quotes)
    'bootstrap_version': "3",
}

# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
#html_title = None

# A shorter title for the navigation bar.  Default is the same as html_title.
#html_short_title = None

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

# 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 = None

# 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 = 'flotilladoc'


# -- 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', 'flotilla.tex', u'flotilla Documentation',
     u'Olga Botvinnik, Michael Lovci', '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', 'flotilla', u'flotilla Documentation',
     [u'Olga Botvinnik, Michael Lovci'], 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', 'flotilla', u'flotilla Documentation',
     u'Olga Botvinnik, Michael Lovci', 'flotilla',
     '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}
	# -- coding: utf-8 --
	#
	# flotilla documentation build configuration file, created by
	# sphinx-quickstart on Thu Jul 10 08:32:34 2014.
	#
	# 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

	import matplotlib as mpl
	import sphinx_bootstrap_theme


	mpl.use('Agg')



	# 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('.'))
	sys.path.insert(0, os.path.abspath('..{}flotilla'.format(os.sep)))
	sys.path.insert(0, os.path.abspath('sphinxext'.format(os.sep)))

	# -- 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.intersphinx',
	'sphinx.ext.todo',
	'sphinx.ext.autosummary',
	'sphinx.ext.coverage',
	'sphinx.ext.mathjax',
	'sphinx.ext.ifconfig',
	'sphinx.ext.viewcode',
	'numpydoc',
	'plot_generator',
	'ipython_directive',
	'ipython_console_highlighting',
	]

	# Generate the API documentation when building
	autosummary_generate = True
	numpydoc_show_class_members = False

	# 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'flotilla'
	copyright = u'2014, Olga Botvinnik, Michael Lovci, Patrick Liu, Yan Song, ' \
	u'and Gene Yeo'

	# 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.
	sys.path.insert(0, os.path.abspath(os.path.pardir))
	import flotilla

	version = flotilla.__version__
	# The full version, including alpha/beta/rc tags.
	release = flotilla.__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 = []

	# 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


	# -- 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'
	html_theme = 'bootstrap'
	html_theme_path = sphinx_bootstrap_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 = {}
	# (Optional) Logo. Should be small enough to fit the navbar (ideally 24x24).
	# Path should be relative to the ``_static`` files directory.
	#html_logo = "my_logo.png"

	# Theme options are theme-specific and customize the look and feel of a
	# theme further.
	html_theme_options = {
	# Navigation bar title. (Default: ``project`` value)
	'navbar_title': "Flotilla",

	# Tab name for entire site. (Default: "Site")
	'navbar_site_name': "Site",

	# A list of tuples containing pages or urls to link to.
	# Valid tuples should be in the following forms:
	# (name, page) # a link to a page
	# (name, "/aa/bb", 1) # a link to an arbitrary relative url
	# (name, "http://example.com", True) # arbitrary absolute url
	# Note the "1" or "True" value above as the third argument to indicate
	# an arbitrary url.
	'navbar_links': [
	("Tutorial", "tutorial"),
	("Gallery", "gallery"),
	("YeoLab@UCSD", "http://yeolab.ucsd.edu", True),
	],

	# Render the next and previous page links in navbar. (Default: true)
	'navbar_sidebarrel': True,

	# Render the current pages TOC in the navbar. (Default: true)
	'navbar_pagenav': True,

	# Global TOC depth for "site" navbar tab. (Default: 1)
	# Switching to -1 shows all levels.
	'globaltoc_depth': 2,

	# Include hidden TOCs in Site navbar?
	#
	# Note: If this is "false", you cannot have mixed ``:hidden:`` and
	# non-hidden ``toctree`` directives in the same page, or else the build
	# will break.
	#
	# Values: "true" (default) or "false"
	'globaltoc_includehidden': "true",

	# HTML navbar class (Default: "navbar") to attach to <div> element.
	# For black navbar, do "navbar navbar-inverse"
	'navbar_class': "navbar",

	# Fix navigation bar to top of page?
	# Values: "true" (default) or "false"
	'navbar_fixed_top': "true",

	# Location of link to source.
	# Options are "nav" (default), "footer" or anything else to exclude.
	'source_link_position': "nav",

	# Bootswatch (http://bootswatch.com/) theme.
	#
	# Options are nothing with "" (default) or the name of a valid theme
	# such as "amelia" or "cosmo".
	'bootswatch_theme': "paper", # "united",

	# Choose Bootstrap version.
	# Values: "3" (default) or "2" (in quotes)
	'bootstrap_version': "3",
	}

	# Add any paths that contain custom themes here, relative to this directory.
	#html_theme_path = []

	# The name for this set of Sphinx documents. If None, it defaults to
	# "<project> v<release> documentation".
	#html_title = None

	# A shorter title for the navigation bar. Default is the same as html_title.
	#html_short_title = None

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

	# 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 = None

	# 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 = 'flotilladoc'


	# -- 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', 'flotilla.tex', u'flotilla Documentation',
	u'Olga Botvinnik, Michael Lovci', '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', 'flotilla', u'flotilla Documentation',
	[u'Olga Botvinnik, Michael Lovci'], 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', 'flotilla', u'flotilla Documentation',
	u'Olga Botvinnik, Michael Lovci', 'flotilla',
	'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}