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# -*- coding: utf-8 -*-
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# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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# Copyright [2016-2021] EMBL-European Bioinformatics Institute
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# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
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#
# ehive_user_manual documentation build configuration file, created by
# sphinx-quickstart on Thu Dec 15 12:59:35 2016.
#
# 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
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import datetime
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import sphinx_rtd_theme
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# 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.
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sys.path.insert(0, os.path.abspath('.'))

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from xhive import setup_if_needed
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# -- 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.coverage',
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    'sphinx.ext.imgmath',
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    'sphinx.ext.graphviz',
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    'sphinxcontrib.doxylink',
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    'xhive.code_doc',
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    'xhive.analysis_diagram',
    'xhive.misc',
    'xhive.pipeline',
    'xhive.sql_schema',
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]

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

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# Add markdown support
from recommonmark.parser import CommonMarkParser

source_parsers = {
    '.md': CommonMarkParser,
}

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authors = [u'Ensembl']
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# The suffix of source filenames.
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source_suffix = ['.rst', '.md']
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# The encoding of source files.
#source_encoding = 'utf-8-sig'

# The master toctree document.
master_doc = 'index'

# General information about the project.
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project = u'eHive user manual'
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project_lc = project.replace(' ', '_').lower()

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copyright_owner = u'EMBL-European Bioinformatics Institute'
copyright_dates = u'[2016-%d]' % datetime.datetime.now().year
copyright = copyright_dates + ' ' + copyright_owner
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# 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.
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import re
version = re.sub('^(heads|remotes/origin)/', '', os.popen('git describe --all').read().strip())
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# The full version, including alpha/beta/rc tags.
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release = version + '/' + os.popen('git rev-parse --short HEAD').read().strip()
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doxygen_target = setup_if_needed(release, True)
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doxylink = {
    'doxehive': (os.path.join(doxygen_target, "ensembl-hive.tag"), 'perl/'),
}


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# 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.
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today_fmt = '%B %d, %Y'
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# 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


# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
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html_theme = 'sphinx_rtd_theme'
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# 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 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.
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html_extra_path = ['_build/doxygen/', 'presentations/']
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# 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.
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htmlhelp_basename = project_lc
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# -- 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.
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'preamble': r'''
\usepackage{pdflscape}
\usepackage{charter}
\usepackage[defaultsans]{lato}
\usepackage{inconsolata}
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\usepackage{verbatim}
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''',
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}

# 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 = [
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  (master_doc, project_lc+'.tex', project,
   authors[0], 'manual'),
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]

# 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 = [
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    (master_doc, project_lc, project,
     authors, 1)
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]

# 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 = [
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  (master_doc, project_lc, project,
   authors[0], project_lc, 'One line description of project.',
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   '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


# -- Options for Epub output ----------------------------------------------

# Bibliographic Dublin Core info.
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epub_title = project
epub_author = authors[0]
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epub_publisher = copyright_owner
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epub_copyright = copyright
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# The basename for the epub file. It defaults to the project name.
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epub_basename = project_lc
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# The HTML theme for the epub output. Since the default themes are not optimized
# for small screen space, using the same theme for HTML and epub output is
# usually not wise. This defaults to 'epub', a theme designed to save visual
# space.
#epub_theme = 'epub'

# The language of the text. It defaults to the language option
# or en if the language is not set.
#epub_language = ''

# The scheme of the identifier. Typical schemes are ISBN or URL.
#epub_scheme = ''

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#epub_identifier = ''

# A unique identification for the text.
#epub_uid = ''

# A tuple containing the cover image and cover page html template filenames.
#epub_cover = ()

# A sequence of (type, uri, title) tuples for the guide element of content.opf.
#epub_guide = ()

# HTML files that should be inserted before the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_pre_files = []

# HTML files shat should be inserted after the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#epub_post_files = []

# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']

# The depth of the table of contents in toc.ncx.
#epub_tocdepth = 3

# Allow duplicate toc entries.
#epub_tocdup = True

# Choose between 'default' and 'includehidden'.
#epub_tocscope = 'default'

# Fix unsupported image types using the PIL.
#epub_fix_images = False

# Scale large images.
#epub_max_image_width = 0

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

# If false, no index is generated.
#epub_use_index = True
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# Add overriding stylesheets, searching in html_static_path
# (see https://github.com/rtfd/sphinx_rtd_theme/issues/117)
def setup(app):
    app.add_stylesheet("theme_overrides.css")
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