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# -*- coding: utf-8 -*- |
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# |
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# ODDT documentation build configuration file, created by |
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# sphinx-quickstart on Mon Aug 25 13:49:30 2014. |
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# |
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# This file is execfile()d with the current directory set to its |
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# containing dir. |
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# |
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# Note that not all possible configuration values are present in this |
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# autogenerated file. |
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# |
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# All configuration values have a default; values that are commented out |
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# serve to show the default. |
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import sys |
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import os |
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# If extensions (or modules to document with autodoc) are in another directory, |
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# add these directories to sys.path here. If the directory is relative to the |
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# 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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# -- General configuration ------------------------------------------------ |
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# If your documentation needs a minimal Sphinx version, state it here. |
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#needs_sphinx = '1.0' |
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# Add any Sphinx extension module names here, as strings. They can be |
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom |
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# ones. |
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extensions = [ |
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'sphinx.ext.autodoc', |
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'sphinx.ext.autosummary', |
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'sphinx.ext.doctest', |
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'sphinx.ext.mathjax', |
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'sphinx.ext.intersphinx', |
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'sphinx.ext.viewcode', |
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'numpydoc', |
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] |
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autosummary_generate = True |
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autodoc_default_flags = ['members', 'inherited-members', 'imported-members'] |
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autoclass_content = 'init' |
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# Add any paths that contain templates here, relative to this directory. |
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templates_path = ['_templates'] |
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# The suffix of source filenames. |
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source_suffix = '.rst' |
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# The encoding of source files. |
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#source_encoding = 'utf-8-sig' |
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# The master toctree document. |
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master_doc = 'index' |
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# General information about the project. |
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project = u'Open Drug Discovery Toolkit' |
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copyright = u'2015, Maciej Wojcikowski' |
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# The version info for the project you're documenting, acts as replacement for |
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# |version| and |release|, also used in various other places throughout the |
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# built documents. |
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# |
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from oddt import __version__ as VERSION |
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# The short X.Y version. |
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version = VERSION |
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# The full version, including alpha/beta/rc tags. |
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release = VERSION |
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# The language for content autogenerated by Sphinx. Refer to documentation |
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# for a list of supported languages. |
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#language = None |
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# There are two options for replacing |today|: either, you set today to some |
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# non-false value, then it is used: |
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#today = '' |
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# 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 |
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# directories to ignore when looking for source files. |
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exclude_patterns = ['_build'] |
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# The reST default role (used for this markup: `text`) to use for all |
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# documents. |
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#default_role = None |
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# If true, '()' will be appended to :func: etc. cross-reference text. |
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#add_function_parentheses = True |
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# If true, the current module name will be prepended to all description |
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# unit titles (such as .. function::). |
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#add_module_names = True |
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# If true, sectionauthor and moduleauthor directives will be shown in the |
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# output. They are ignored by default. |
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#show_authors = False |
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# The name of the Pygments (syntax highlighting) style to use. |
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pygments_style = 'sphinx' |
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# A list of ignored prefixes for module index sorting. |
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#modindex_common_prefix = [] |
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# If true, keep warnings as "system message" paragraphs in the built documents. |
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#keep_warnings = False |
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# -- Options for HTML output ---------------------------------------------- |
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# The theme to use for HTML and HTML Help pages. See the documentation for |
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# a list of builtin themes. |
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html_theme = 'default' |
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# Theme options are theme-specific and customize the look and feel of a theme |
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# further. For a list of options available for each theme, see the |
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# documentation. |
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#html_theme_options = {} |
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# Add any paths that contain custom themes here, relative to this directory. |
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#html_theme_path = [] |
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# The name for this set of Sphinx documents. If None, it defaults to |
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# "<project> v<release> documentation". |
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#html_title = None |
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# A shorter title for the navigation bar. Default is the same as html_title. |
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#html_short_title = None |
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# The name of an image file (relative to this directory) to place at the top |
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# of the sidebar. |
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#html_logo = None |
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# The name of an image file (within the static path) to use as favicon of the |
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# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 |
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# pixels large. |
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#html_favicon = None |
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# Add any paths that contain custom static files (such as style sheets) here, |
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# relative to this directory. They are copied after the builtin static files, |
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# so a file named "default.css" will overwrite the builtin "default.css". |
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html_static_path = ['_static'] |
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# Add any extra paths that contain custom files (such as robots.txt or |
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# .htaccess) here, relative to this directory. These files are copied |
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# directly to the root of the documentation. |
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#html_extra_path = [] |
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# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, |
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# using the given strftime format. |
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#html_last_updated_fmt = '%b %d, %Y' |
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# If true, SmartyPants will be used to convert quotes and dashes to |
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# typographically correct entities. |
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#html_use_smartypants = True |
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# Custom sidebar templates, maps document names to template names. |
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#html_sidebars = {} |
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# Additional templates that should be rendered to pages, maps page names to |
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# template names. |
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#html_additional_pages = {} |
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# If false, no module index is generated. |
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#html_domain_indices = True |
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# If false, no index is generated. |
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#html_use_index = True |
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# If true, the index is split into individual pages for each letter. |
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#html_split_index = False |
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# If true, links to the reST sources are added to the pages. |
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#html_show_sourcelink = True |
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# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. |
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#html_show_sphinx = True |
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# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. |
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#html_show_copyright = True |
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# If true, an OpenSearch description file will be output, and all pages will |
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# contain a <link> tag referring to it. The value of this option must be the |
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# base URL from which the finished HTML is served. |
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#html_use_opensearch = '' |
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# This is the file name suffix for HTML files (e.g. ".xhtml"). |
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#html_file_suffix = None |
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# Output file base name for HTML help builder. |
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htmlhelp_basename = 'ODDTdoc' |
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# -- Options for LaTeX output --------------------------------------------- |
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latex_elements = { |
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# The paper size ('letterpaper' or 'a4paper'). |
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#'papersize': 'letterpaper', |
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# The font size ('10pt', '11pt' or '12pt'). |
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#'pointsize': '10pt', |
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# Additional stuff for the LaTeX preamble. |
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#'preamble': '', |
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} |
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# Grouping the document tree into LaTeX files. List of tuples |
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# (source start file, target name, title, |
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# author, documentclass [howto, manual, or own class]). |
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latex_documents = [ |
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('index', 'ODDT.tex', u'ODDT Documentation', |
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u'Maciej Wojcikowski', 'manual'), |
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] |
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# The name of an image file (relative to this directory) to place at the top of |
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# the title page. |
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#latex_logo = None |
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# For "manual" documents, if this is true, then toplevel headings are parts, |
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# not chapters. |
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#latex_use_parts = False |
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# If true, show page references after internal links. |
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#latex_show_pagerefs = False |
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# If true, show URL addresses after external links. |
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#latex_show_urls = False |
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# Documents to append as an appendix to all manuals. |
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#latex_appendices = [] |
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# If false, no module index is generated. |
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#latex_domain_indices = True |
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# -- Options for manual page output --------------------------------------- |
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# One entry per manual page. List of tuples |
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# (source start file, name, description, authors, manual section). |
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man_pages = [ |
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('index', 'Open Drug Discovery Toolkit', u'ODDT Documentation', |
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[u'Maciej Wojcikowski'], 1) |
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] |
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# If true, show URL addresses after external links. |
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#man_show_urls = False |
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# -- Options for Texinfo output ------------------------------------------- |
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# Grouping the document tree into Texinfo files. List of tuples |
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# (source start file, target name, title, author, |
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# dir menu entry, description, category) |
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texinfo_documents = [ |
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('index', 'Open Drug Discovery Toolkit', u'ODDT Documentation', |
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u'Maciej Wojcikowski', 'Open Drug Discovery Toolkit', 'One line description of project.', |
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'Miscellaneous'), |
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] |
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# Documents to append as an appendix to all manuals. |
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#texinfo_appendices = [] |
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# If false, no module index is generated. |
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#texinfo_domain_indices = True |
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# How to display URL addresses: 'footnote', 'no', or 'inline'. |
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#texinfo_show_urls = 'footnote' |
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# If true, do not generate a @detailmenu in the "Top" node's menu. |
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#texinfo_no_detailmenu = False |
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# -- Options for Epub output ---------------------------------------------- |
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# Bibliographic Dublin Core info. |
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epub_title = u'Open Drug Discovery Toolkit' |
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epub_author = u'Maciej Wojcikowski' |
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epub_publisher = u'Maciej Wojcikowski' |
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epub_copyright = u'2015, Maciej Wojcikowski' |
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# The basename for the epub file. It defaults to the project name. |
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#epub_basename = u'Open Drug Discovery Toolkit' |
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# The HTML theme for the epub output. Since the default themes are not optimized |
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# for small screen space, using the same theme for HTML and epub output is |
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# usually not wise. This defaults to 'epub', a theme designed to save visual |
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# space. |
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#epub_theme = 'epub' |
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# The language of the text. It defaults to the language option |
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# or en if the language is not set. |
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#epub_language = '' |
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# The scheme of the identifier. Typical schemes are ISBN or URL. |
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#epub_scheme = '' |
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# The unique identifier of the text. This can be a ISBN number |
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# or the project homepage. |
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#epub_identifier = '' |
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# A unique identification for the text. |
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#epub_uid = '' |
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# A tuple containing the cover image and cover page html template filenames. |
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#epub_cover = () |
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# A sequence of (type, uri, title) tuples for the guide element of content.opf. |
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#epub_guide = () |
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# HTML files that should be inserted before the pages created by sphinx. |
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# The format is a list of tuples containing the path and title. |
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#epub_pre_files = [] |
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# HTML files shat should be inserted after the pages created by sphinx. |
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# The format is a list of tuples containing the path and title. |
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#epub_post_files = [] |
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# A list of files that should not be packed into the epub file. |
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epub_exclude_files = ['search.html'] |
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# The depth of the table of contents in toc.ncx. |
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#epub_tocdepth = 3 |
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# Allow duplicate toc entries. |
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#epub_tocdup = True |
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# Choose between 'default' and 'includehidden'. |
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#epub_tocscope = 'default' |
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# Fix unsupported image types using the PIL. |
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#epub_fix_images = False |
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# Scale large images. |
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#epub_max_image_width = 0 |
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# How to display URL addresses: 'footnote', 'no', or 'inline'. |
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#epub_show_urls = 'inline' |
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# If false, no index is generated. |
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#epub_use_index = True |
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# Example configuration for intersphinx: refer to the Python standard library. |
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intersphinx_mapping = {} |
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intersphinx_mapping['sklearn'] = ('http://scikit-learn.org/stable', None) |
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intersphinx_mapping['numpy'] = ('http://docs.scipy.org/doc/numpy/', None) |
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intersphinx_mapping['scipy'] = ('http://docs.scipy.org/doc/scipy/reference/', None) |
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# Ignore some modules during documentation building on readthedocs.org |
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if os.environ.get('READTHEDOCS', None) == 'True': |
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# Invoke sphinx-apidoc |
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os.system("sphinx-apidoc -f -o rst/ ../oddt") |
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try: |
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from unittest.mock import patch, MagicMock # Python 3.3 |
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except ImportError: |
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from mock import patch, MagicMock |
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pybel = MagicMock() |
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openbabel = MagicMock() |
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rdkit = MagicMock() |
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modules = { |
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# OpenBabel |
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'pybel': pybel, |
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'openbabel' : openbabel, |
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# RDK |
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'rdkit': rdkit, |
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'rdkit.Chem': rdkit.Chem, |
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'rdkit.DataStructs': rdkit.DataStructs, |
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'rdkit.Chem.MACCSkeys': rdkit.Chem.MACCSkeys, |
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'rdkit.Chem.AtomPairs': rdkit.Chem.AtomPairs, |
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'rdkit.Chem.AtomPairs.Pairs': rdkit.Chem.AtomPairs.Pairs, |
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'rdkit.Chem.AtomPairs.Torsions': rdkit.Chem.AtomPairs.Torsions, |
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'rdkit.Chem.Lipinski': rdkit.Chem.Lipinski, |
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'rdkit.Chem.AllChem': rdkit.Chem.AllChem, |
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'rdkit.Chem.Pharm2D': rdkit.Chem.Pharm2D, |
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} |
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p = patch.dict('sys.modules', modules) |
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p.start() |