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Initial addition of docs.
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‎docs/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line.
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SPHINXOPTS = -W
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SPHINXBUILD = sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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DOXYGEN_XML=doxygen/xml
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all: ${DOXYGEN_XML}
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@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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${DOXYGEN_XML}: ../c/kastore.h
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cd doxygen && doxygen
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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# .PHONY: help Makefile
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# # Catch-all target: route all unknown targets to Sphinx using the new
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# # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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# %: Makefile
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# @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/c-api.rst‎

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.. _sec_c_api:
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===================
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C API Documentation
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===================
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This is the C API documentation for kastore.
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.. todo:: Give a short example program.
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******************
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General principles
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******************
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--------------
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Error handling
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--------------
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Functions return 0 to indicate success or an
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:ref:`error code <sec_c_api_error_codes>` to indicate a failure condition.
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Thus, the return value of all functions must be checked to ensure safety.
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-------------
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Array lengths
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-------------
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The length of arrays is specified in terms of the number of elements not bytes.
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*********
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Top level
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*********
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.. doxygenstruct:: kastore_t
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.. doxygenfunction:: kastore_open
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.. doxygenfunction:: kastore_close
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.. doxygenfunction:: kas_strerror
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.. _sec_c_api_get:
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*************
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Get functions
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*************
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Get functions provide the interface for querying a store. The most general interface
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is :c:func:`kastore_get`, but it is usually more convenient to use one of the
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:ref:`typed get functions <sec_c_api_typed_get>`.
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.. doxygenfunction:: kastore_get
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.. doxygenfunction:: kastore_gets
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.. _sec_c_api_typed_get:
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----------
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Typed gets
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----------
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The functions listed here provide a convenient short-cut for accessing arrays
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where the key is a standard NULL terminated C string and the type of the
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array is known in advance.
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.. doxygengroup:: TYPED_GETS_GROUP
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:content-only:
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.. _sec_c_api_put:
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*************
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Put functions
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*************
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Put functions provide the interface for inserting data into store. The most
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general interface is :c:func:`kastore_put` which allows keys to be arbitrary
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bytes, but it is usually more convenient to use one of the :ref:`typed put
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functions <sec_c_api_typed_put>`.
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.. doxygenfunction:: kastore_put
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.. doxygenfunction:: kastore_puts
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.. _sec_c_api_typed_put:
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----------
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Typed puts
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----------
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The functions listed here provide a convenient short-cut for inserting
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key-array pairs where the key is a standard NULL terminated C string and the
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type of the array is known in advance.
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.. doxygengroup:: TYPED_PUTS_GROUP
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:content-only:
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*********
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Constants
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*********
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.. _sec_c_api_error_codes:
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------
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Errors
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------
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.. doxygengroup:: ERROR_GROUP
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:content-only:
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-----
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Types
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-----
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.. doxygengroup:: TYPE_GROUP
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:content-only:
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-------------------
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Version information
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-------------------
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.. doxygengroup:: API_VERSION_GROUP
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:content-only:
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.. doxygengroup:: FILE_VERSION_GROUP
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:content-only:
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***********************
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Miscellaneous functions
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***********************
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.. doxygenstruct:: kas_version_t
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:members:
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.. doxygenfunction:: kas_version
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.. doxygenfunction:: kas_dynamic_api_init
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‎docs/changelogs.rst‎

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.. _sec_changelogs:
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==========
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Changelogs
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==========
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******
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Python
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******
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.. include:: ../python/CHANGELOG.rst
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*****
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C API
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*****
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.. include:: ../c/CHANGELOG.rst

‎docs/conf.py‎

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# -*- coding: utf-8 -*-
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#
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# Configuration file for the Sphinx documentation builder.
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#
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# This file does only contain a selection of the most common options. For a
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# full list see the documentation:
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# http://www.sphinx-doc.org/en/master/config
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# -- Path setup --------------------------------------------------------------
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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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#
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import subprocess
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import os
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import sys
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sys.path.insert(0, os.path.abspath('../python'))
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read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
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if read_the_docs_build:
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subprocess.call('cd doxygen; doxygen', shell=True)
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# -- Project information -----------------------------------------------------
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project = 'kastore'
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copyright = '2018, Tskit developers'
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author = 'Tskit developers'
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# The short X.Y version
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version = ''
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# The full version, including alpha/beta/rc tags
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release = ''
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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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#
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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.intersphinx',
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'sphinx.ext.todo',
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'breathe',
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]
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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(es) of source filenames.
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# You can specify multiple suffix as a list of string:
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#
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# source_suffix = ['.rst', '.md']
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source_suffix = '.rst'
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# The master toctree document.
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master_doc = 'index'
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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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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
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language = None
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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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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
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# The name of the Pygments (syntax highlighting) style to use.
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pygments_style = None
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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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#
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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
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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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#
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# html_theme_options = {}
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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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# Custom sidebar templates, must be a dictionary that maps document names
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# to template names.
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#
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# The default sidebars (for documents that don't match any pattern) are
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# defined by theme itself. Builtin themes are using these templates by
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# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
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# 'searchbox.html']``.
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#
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# html_sidebars = {}
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# -- Options for HTMLHelp output ---------------------------------------------
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# Output file base name for HTML help builder.
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htmlhelp_basename = 'kastoredoc'
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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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#
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# 'papersize': 'letterpaper',
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# The font size ('10pt', '11pt' or '12pt').
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#
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# 'pointsize': '10pt',
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# Additional stuff for the LaTeX preamble.
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#
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# 'preamble': '',
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# Latex figure (float) alignment
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#
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# 'figure_align': 'htbp',
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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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(master_doc, 'kastore.tex', 'kastore Documentation',
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'Tskit developers', 'manual'),
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]
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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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(master_doc, 'kastore', 'kastore Documentation',
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[author], 1)
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]
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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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(master_doc, 'kastore', 'kastore Documentation',
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author, 'kastore', 'One line description of project.',
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'Miscellaneous'),
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]
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# -- Options for Epub output -------------------------------------------------
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# Bibliographic Dublin Core info.
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epub_title = project
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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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#
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# epub_identifier = ''
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# A unique identification for the text.
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#
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# epub_uid = ''
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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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# -- Extension configuration -------------------------------------------------
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# -- Options for intersphinx extension ---------------------------------------
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {'https://docs.python.org/': None}
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# -- Options for todo extension ----------------------------------------------
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# If true, `todo` and `todoList` produce output, else they produce nothing.
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todo_include_todos = True
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# Breath extension lets us include doxygen C documentation.
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breathe_projects = {"kastore": "doxygen/xml" }
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breathe_default_project = "kastore"
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breathe_domain_by_extension = {"h": "c"}
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breathe_show_define_initializer = True
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# TODO add an RST epilogue defining the version numbers of the Python
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# and C APIs. Should be simple to do the Python version. Getting C
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# will probably mean parsing the doxygen XML.

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