Merge pull request #24 from ihmeuw/feature/docs

Feature/docs

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = vivarium
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf build/*

docs/source/api_reference.rst

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+API Reference
+=============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api_reference/framework
+   api_reference/interface
+   api_reference/config_tree
+   api_reference/interpolation
+   api_reference/test_util

docs/source/api_reference/config_tree.rst

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+Config Tree
+===========
+
+.. automodule:: vivarium.config_tree

docs/source/api_reference/framework.rst

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+Framework
+=========
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   framework/components
+   framework/configuration
+   framework/engine
+   framework/event
+   framework/lookup
+   framework/metrics
+   framework/plugins
+   framework/population
+   framework/randomness
+   framework/results_writer
+   framework/state_machine
+   framework/time
+   framework/util
+   framework/values

docs/source/api_reference/framework/components.rst

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+Components
+----------
+
+.. automodule:: vivarium.framework.components
+   :imported-members:

docs/source/api_reference/framework/configuration.rst

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+Configuration
+-------------
+
+.. automodule:: vivarium.framework.configuration

docs/source/api_reference/framework/engine.rst

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+Engine
+------
+
+.. automodule:: vivarium.framework.engine

docs/source/api_reference/framework/event.rst

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+Event
+-----
+
+.. automodule:: vivarium.framework.event

docs/source/api_reference/framework/lookup.rst

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+Lookup
+------
+
+.. automodule:: vivarium.framework.lookup

docs/source/api_reference/framework/metrics.rst

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+Metrics
+-------
+
+.. automodule:: vivarium.framework.metrics

docs/source/api_reference/framework/plugins.rst

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+Plugins
+-------
+
+.. automodule:: vivarium.framework.plugins

docs/source/api_reference/framework/population.rst

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+Population
+----------
+
+.. automodule:: vivarium.framework.population

docs/source/api_reference/framework/randomness.rst

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+Randomness
+----------
+
+.. automodule:: vivarium.framework.randomness

docs/source/api_reference/framework/results_writer.rst

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+Results Writer
+--------------
+
+.. automodule:: vivarium.framework.results_writer

docs/source/api_reference/framework/state_machine.rst

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+State Machine
+-------------
+
+.. automodule:: vivarium.framework.state_machine

docs/source/api_reference/framework/time.rst

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+Time
+----
+
+.. automodule:: vivarium.framework.time

docs/source/api_reference/framework/util.rst

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+Util
+----
+
+.. automodule:: vivarium.framework.util

docs/source/api_reference/framework/values.rst

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+Values
+------
+
+.. automodule:: vivarium.framework.values

docs/source/api_reference/interface.rst

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+Interface
+=========
+
+Interactive Interface
+---------------------
+
+.. automodule:: vivarium.interface.interactive
+
+
+Command Line Interface
+----------------------
+
+.. automodule:: vivarium.interface.cli
+
+
+Utilities
+---------
+
+.. automodule:: vivarium.interface.utilities

docs/source/api_reference/interpolation.rst

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+Interpolation
+=============
+
+.. automodule:: vivarium.interpolation

docs/source/api_reference/test_util.rst

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+Test Util
+=========
+
+.. automodule:: vivarium.test_util

docs/source/conf.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# 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.
+
+# 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.
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+
+needs_sphinx = '1.5'
+
+# 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.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx_autodoc_typehints',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'vivarium'
+copyright = '2018, Alec Deason, James Collins, Michelle Park, Abraham Flaxman, Everett Mumford'
+author = 'Alec Deason, James Collins, Michelle Park, Abraham Flaxman, Everett Mumford'
+
+# 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 = '0.5'
+# The full version, including alpha/beta/rc tags.
+release = '0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- 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_path = ['_theme']
+html_theme = 'sphinx_rtd_theme'
+
+# 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 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'globaltoc.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'vivariumdoc'
+
+
+# -- 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': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# 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 = [
+    (master_doc, 'vivarium.tex', 'vivarium Documentation',
+     'Alec Deason, James Collins, Michelle Park, Abraham Flaxman, Everett Mumford', 'manual'),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'vivarium', 'vivarium Documentation',
+     [author], 1)
+]
+
+
+# -- 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 = [
+    (master_doc, 'vivarium', 'vivarium Documentation',
+     author, 'vivarium', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Example configuration for intersphinx: refer to the Python standard library.
+# intersphinx_mapping = {'https://docs.python.org/': None}
+
+
+# -- Autodoc configuration ------------------------------------------------
+
+# Sort order of members listed by autodoc
+# options are: 'alphabetical', 'groupwise', or 'bysource'
+autodoc_member_order = 'bysource'
+
+# Defaults for automodule and autoclass
+# To negate add `:no-undoc-members:` flag to a particular instance
+autodoc_default_flags = ['members', 'undoc-members' ]

docs/source/core_concepts.rst

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+Core Concepts
+=============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   core_concepts/agent_based_modelling
+   core_concepts/discrete_time_simulation
+   core_concepts/other_concepts

docs/source/core_concepts/agent_based_modelling.rst

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+Agent Based Modelling
+=====================
+

docs/source/core_concepts/discrete_time_simulation.rst

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+Discrete Time Simulation
+========================

docs/source/core_concepts/other_concepts.rst

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+Other Concepts
+==============

docs/source/getting_started.rst

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+Getting Started
+===============
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   getting_started/whats_in_the_framework
+   getting_started/agents_and_the_state_table
+   getting_started/what_is_a_components
+   getting_started/simulation_lifecycle

docs/source/getting_started/agents_and_the_state_table.rst

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+Agents and the State Table
+==========================

docs/source/getting_started/simulation_lifecycle.rst

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+Simulation Life Cycle
+=====================

docs/source/getting_started/what_is_a_components.rst

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+What is a component?
+====================

docs/source/getting_started/whats_in_the_framework.rst

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+What's in the Framework?
+========================