fix timeout in FSM. Improve logs

Multithreading needs pickling to work.
Pickling/unpickling didn't work in some situations, like when the
environment_agents parameter was left blank.
This was due to two reasons:

1) agents and history didn't have a setstate method, and some of their
attributes cannot be pickled (generators, sqlite connection)
2) the environment was adding generators (agents) to its state.

This fixes the situation by restricting the keys that the environment exports
when it pickles, and by adding the set/getstate methods in agents.

The resulting pickles should contain enough information to inspect
them (history, state values, etc), but very limited.

.dockerignore

@@ -0,0 +1,2 @@
+**/soil_output
+.*

.gitignore

@@ -1,5 +1,10 @@
 __pycache__/
 .idea/
 .ipynb_checkpoints/
-*.png
 *.gexf
+.*
+results
+soil_output
+docs/_build*
+build/*
+dist/*

.gitlab-ci.yml

@@ -0,0 +1,28 @@
+stages:
+  - test
+  - build
+
+build:
+  stage: build
+  image:
+    name: gcr.io/kaniko-project/executor:debug
+    entrypoint: [""]
+  tags:
+    - docker
+  script:
+    - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
+    # The skip-tls-verify flag is there because our registry certificate is self signed
+    - /kaniko/executor --context $CI_PROJECT_DIR --skip-tls-verify --dockerfile $CI_PROJECT_DIR/Dockerfile --destination $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG
+  only:
+    - tags
+
+
+test:
+  except:
+    - tags  # Avoid running tests for tags, because they are already run for the branch
+  tags:
+    - docker
+  image: python:3.7
+  stage: test
+  script:
+    - python setup.py test

CHANGELOG.md

@@ -0,0 +1,19 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+### Changed
+### Added
+### Fixed
+
+## [0.13.7]
+### Changed
+* History now defaults to not backing up! This makes it more intuitive to load the history for examination, at the expense of rewriting something. That should not happen because History is only created in the Environment, and that has `backup=True`.
+### Added
+* Agent names are assigned based on their agent types
+* Agent logging uses the agent name.
+* FSM agents can now return a timeout in addition to a new state. e.g. `return self.idle, self.env.timeout(2)` will execute the *different_state* in 2 *units of time* (`t_step=now+2`).
+* Example of using timeouts in FSM (custom_timeouts)
+* `network_agents` entries may include an `ids` entry. If set, it should be a list of node ids that should be assigned that agent type. This complements the previous behavior of setting agent type with `weights`.

Dockerfile

@@ -0,0 +1,12 @@
+FROM python:3.7
+
+WORKDIR /usr/src/app
+
+COPY test-requirements.txt requirements.txt /usr/src/app/
+RUN pip install --no-cache-dir -r test-requirements.txt -r requirements.txt
+
+COPY ./ /usr/src/app
+
+RUN pip install '.[web]'
+
+ENTRYPOINT ["python", "-m", "soil"]

MANIFEST.in

@@ -0,0 +1,4 @@
+include requirements.txt
+include test-requirements.txt
+include README.rst
+graft soil

Makefile

@@ -0,0 +1,4 @@
+test:
+	docker-compose exec dev python -m pytest -s -v
+
+.PHONY: test

README.md

@@ -1,12 +1,34 @@
-#[Soil](https://github.com/gsi-upm/soil)
+# [SOIL](https://github.com/gsi-upm/soil)
 
-The purpose of Soil (SOcial network sImuLator) is provding an Agent-based Social Simulator written in Python for Social Networks.
-
-
-In order to see quickly how to use Soil, you can follow the following [tutorial](https://github.com/gsi-upm/soil/blob/master/soil_tutorial.ipynb).
+Soil is an extensible and user-friendly Agent-based Social Simulator for Social Networks.
+Learn how to run your own simulations with our [documentation](http://soilsim.readthedocs.io).
 
+Follow our [tutorial](examples/tutorial/soil_tutorial.ipynb) to develop your own agent models.
 
+If you use Soil in your research, don't forget to cite this paper:
 
+```bibtex
+@inbook{soil-gsi-conference-2017,
+    author = "S{\'a}nchez, Jes{\'u}s M. and Iglesias, Carlos A. and S{\'a}nchez-Rada, J. Fernando",
+    booktitle = "Advances in Practical Applications of Cyber-Physical Multi-Agent Systems: The PAAMS Collection",
+    doi = "10.1007/978-3-319-59930-4_19",
+    editor = "Demazeau Y., Davidsson P., Bajo J., Vale Z.",
+    isbn = "978-3-319-59929-8",
+    keywords = "soil;social networks;agent based social simulation;python",
+    month = "June",
+    organization = "PAAMS 2017",
+    pages = "234-245",
+    publisher = "Springer Verlag",
+    series = "LNAI",
+    title = "{S}oil: {A}n {A}gent-{B}ased {S}ocial {S}imulator in {P}ython for {M}odelling and {S}imulation of {S}ocial {N}etworks",
+    url = "https://link.springer.com/chapter/10.1007/978-3-319-59930-4_19",
+    volume = "10349",
+    year = "2017",
+}
 
+```
 
 @Copyright GSI - Universidad Politécnica de Madrid 2017
+
+[![SOIL](logo_gsi.png)](https://www.gsi.dit.upm.es)
+

debug.py

@@ -0,0 +1,3 @@
+import soil
+soil.main()
+import pdb

docker-compose.yml

@@ -0,0 +1,12 @@
+version: '3'
+services:
+  dev:
+    build: .
+    environment:
+      PYTHONDONTWRITEBYTECODE: 1
+    volumes:
+      - .:/usr/src/app
+    tty: true
+    entrypoint: /bin/bash
+    ports:
+      - '8001:8001'

docs/_build/html/.buildinfo

@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: d241ad8149638a17f61def88be87f400
-tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/index.rst.txt

@@ -1,25 +0,0 @@
-.. Soil documentation master file, created by
-   sphinx-quickstart on Tue Apr 25 12:48:56 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to Soil's documentation!
-================================
-
-Soil is an Agent-based Social Simulator in Python for modelling and simulation of Social Networks.
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Learn more about soil:
-
-   installation
-   usage
-   models
-
-
-
-.. Indices and tables
-   ==================
-   * :ref:`genindex`
-   * :ref:`modindex`
-   * :ref:`search`

docs/_build/html/_sources/installation.rst.txt

@@ -1,7 +0,0 @@
-Installation
-------------
-The latest version can be installed through GitLab.
-
-.. code:: bash
-
-   git clone https://lab.cluster.gsi.dit.upm.es/soil/soil.git

docs/_build/html/_sources/models.rst.txt

@@ -1,112 +0,0 @@
-Developing new models
----------------------
-This document describes how to develop a new analysis model.
-
-What is a model?
-================
-
-A model defines the behaviour of the agents with a view to assessing their effects on the system as a whole.
-In practice, a model consists of at least two parts:
-
-* Python module: the actual code that describes the behaviour.
-* Setting up the variables in the Settings JSON file.
-
-This separation allows us to run the simulation with different agents.
-
-Models Code
-===========
-
-All the models are imported to the main file. The initialization look like this:
-
-.. code:: python
-
-    import settings
-
-    networkStatus = {}  # Dict that will contain the status of every agent in the network
-
-    sentimentCorrelationNodeArray = []
-    for x in range(0, settings.network_params["number_of_nodes"]):
-        sentimentCorrelationNodeArray.append({'id': x})
-    # Initialize agent states. Let's assume everyone is normal.
-    init_states = [{'id': 0, } for _ in range(settings.network_params["number_of_nodes"])]
-        # add keys as as necessary, but "id" must always refer to that state category
-
-A new model have to inherit the BaseBehaviour class which is in the same module.
-There are two basics methods:
-
-* __init__
-* step: used to define the behaviour over time.
-
-Variable Initialization
-=======================
-
-The different parameters of the model have to be initialize in the Simulation Settings JSON file which will be
-passed as a parameter to the simulation.
-
-.. code:: json
-
-    {
-        "agent": ["SISaModel","ControlModelM2"],
-
-        "neutral_discontent_spon_prob": 0.04,
-        "neutral_discontent_infected_prob": 0.04,
-        "neutral_content_spon_prob": 0.18,
-        "neutral_content_infected_prob": 0.02,
-
-        "discontent_neutral": 0.13,
-        "discontent_content": 0.07,
-        "variance_d_c": 0.02,
-
-        "content_discontent": 0.009,
-        "variance_c_d": 0.003,
-        "content_neutral": 0.088,
-
-        "standard_variance": 0.055,
-
-
-        "prob_neutral_making_denier": 0.035,
-
-        "prob_infect": 0.075,
-
-        "prob_cured_healing_infected": 0.035,
-        "prob_cured_vaccinate_neutral": 0.035,
-
-        "prob_vaccinated_healing_infected": 0.035,
-        "prob_vaccinated_vaccinate_neutral": 0.035,
-        "prob_generate_anti_rumor": 0.035
-    }
-
-In this file you will also define the models you are going to simulate. You can simulate as many models as you want.
-The simulation returns one result for each model, executing each model separately. For the usage, see :doc:`usage`.
-
-Example Model
-=============
-
-In this section, we will implement a Sentiment Correlation Model.
-
-The class would look like this:
-
-.. code:: python
-
-    from ..BaseBehaviour import *
-    from .. import sentimentCorrelationNodeArray
-
-    class SentimentCorrelationModel(BaseBehaviour):
-
-        def __init__(self, environment=None, agent_id=0, state=()):
-            super().__init__(environment=environment, agent_id=agent_id, state=state)
-            self.outside_effects_prob = environment.environment_params['outside_effects_prob']
-            self.anger_prob = environment.environment_params['anger_prob']
-            self.joy_prob = environment.environment_params['joy_prob']
-            self.sadness_prob = environment.environment_params['sadness_prob']
-            self.disgust_prob = environment.environment_params['disgust_prob']
-            self.time_awareness = []
-            for i in range(4):  # In this model we have 4 sentiments
-                self.time_awareness.append(0)  # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
-            sentimentCorrelationNodeArray[self.id][self.env.now] = 0
-
-        def step(self, now):
-            self.behaviour()  # Method which define the behaviour
-            super().step(now)
-
-The variables will be modified by the user, so you have to include them in the Simulation Settings JSON file.

docs/_build/html/_sources/usage.rst.txt

@@ -1,99 +0,0 @@
-Usage
------
-
-First of all, you need to install the package. See :doc:`installation` for installation instructions.
-
-Simulation Settings
-===================
-
-Once installed, before running a simulation, you need to configure it.
-
-* In the Settings JSON file you will find the configuration of the network.
-
-  .. code:: python
-
-    {
-        "network_type": 1,
-        "number_of_nodes": 1000,
-        "max_time": 50,
-        "num_trials": 1,
-        "timeout": 2
-    }
-
-* In the Settings JSON file, you will also find the configuration of the models.
-
-Network Types
-=============
-
-There are three types of network implemented, but you could add more.
-
-.. code:: python
-
-    if settings.network_type == 0:
-        G = nx.complete_graph(settings.number_of_nodes)
-    if settings.network_type == 1:
-        G = nx.barabasi_albert_graph(settings.number_of_nodes, 10)
-    if settings.network_type == 2:
-        G = nx.margulis_gabber_galil_graph(settings.number_of_nodes, None)
-    # More types of networks can be added here
-
-Models Settings
-===============
-
-After having configured the simulation, the next step is setting up the variables of the models.
-For this, you will need to modify the Settings JSON file again.
-
-.. code:: json
-
-    {
-        "agent": ["SISaModel","ControlModelM2"],
-
-        "neutral_discontent_spon_prob": 0.04,
-        "neutral_discontent_infected_prob": 0.04,
-        "neutral_content_spon_prob": 0.18,
-        "neutral_content_infected_prob": 0.02,
-
-        "discontent_neutral": 0.13,
-        "discontent_content": 0.07,
-        "variance_d_c": 0.02,
-
-        "content_discontent": 0.009,
-        "variance_c_d": 0.003,
-        "content_neutral": 0.088,
-
-        "standard_variance": 0.055,
-
-
-        "prob_neutral_making_denier": 0.035,
-
-        "prob_infect": 0.075,
-
-        "prob_cured_healing_infected": 0.035,
-        "prob_cured_vaccinate_neutral": 0.035,
-
-        "prob_vaccinated_healing_infected": 0.035,
-        "prob_vaccinated_vaccinate_neutral": 0.035,
-        "prob_generate_anti_rumor": 0.035
-    }
-
-In this file you will define the different models you are going to simulate. You can simulate as many models
-as you want. Each model will be simulated separately.
-
-After setting up the models, you have to initialize the parameters of each one. You will find the parameters needed
-in the documentation of each model.
-
-Parameter validation will fail if a required parameter without a default has not been provided.
-
-Running the Simulation
-======================
-
-After setting all the configuration, you will be able to run the simulation. All you need to do is execute:
-
-.. code:: bash
-
-    python3 soil.py
-
-The simulation will return a dynamic graph .gexf file which could be visualized with
-`Gephi <https://gephi.org/users/download/>`__.
-
-It will also return one .png picture for each model simulated.

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docs/_build/html/_static/custom.css

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docs/_build/html/_static/doctools.js

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- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
-  jQuery.uaMatch = function(ua) {
-    ua = ua.toLowerCase();
-
-    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
-      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
-      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
-      /(msie) ([\w.]+)/.exec(ua) ||
-      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
-      [];
-
-    return {
-      browser: match[ 1 ] || "",
-      version: match[ 2 ] || "0"
-    };
-  };
-  jQuery.browser = {};
-  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
-}
-
-/**
- * Small JavaScript module for the documentation.
- */
-var Documentation = {
-
-  init : function() {
-    this.fixFirefoxAnchorBug();
-    this.highlightSearchWords();
-    this.initIndexTable();
-    
-  },
-
-  /**
-   * i18n support
-   */
-  TRANSLATIONS : {},
-  PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
-  LOCALE : 'unknown',
-
-  // gettext and ngettext don't access this so that the functions
-  // can safely bound to a different name (_ = Documentation.gettext)
-  gettext : function(string) {
-    var translated = Documentation.TRANSLATIONS[string];
-    if (typeof translated == 'undefined')
-      return string;
-    return (typeof translated == 'string') ? translated : translated[0];
-  },
-
-  ngettext : function(singular, plural, n) {
-    var translated = Documentation.TRANSLATIONS[singular];
-    if (typeof translated == 'undefined')
-      return (n == 1) ? singular : plural;
-    return translated[Documentation.PLURALEXPR(n)];
-  },
-
-  addTranslations : function(catalog) {
-    for (var key in catalog.messages)
-      this.TRANSLATIONS[key] = catalog.messages[key];
-    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
-    this.LOCALE = catalog.locale;
-  },
-
-  /**
-   * add context elements like header anchor links
-   */
-  addContextElements : function() {
-    $('div[id] > :header:first').each(function() {
-      $('<a class="headerlink">\u00B6</a>').
-      attr('href', '#' + this.id).
-      attr('title', _('Permalink to this headline')).
-      appendTo(this);
-    });
-    $('dt[id]').each(function() {
-      $('<a class="headerlink">\u00B6</a>').
-      attr('href', '#' + this.id).
-      attr('title', _('Permalink to this definition')).
-      appendTo(this);
-    });
-  },
-
-  /**
-   * workaround a firefox stupidity
-   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
-   */
-  fixFirefoxAnchorBug : function() {
-    if (document.location.hash)
-      window.setTimeout(function() {
-        document.location.href += '';
-      }, 10);
-  },
-
-  /**
-   * highlight the search words provided in the url in the text
-   */
-  highlightSearchWords : function() {
-    var params = $.getQueryParameters();
-    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
-    if (terms.length) {
-      var body = $('div.body');
-      if (!body.length) {
-        body = $('body');
-      }
-      window.setTimeout(function() {
-        $.each(terms, function() {
-          body.highlightText(this.toLowerCase(), 'highlighted');
-        });
-      }, 10);
-      $('<p class="highlight-link"><a href="javascript:Documentation.' +
-        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
-          .appendTo($('#searchbox'));
-    }
-  },
-
-  /**
-   * init the domain index toggle buttons
-   */
-  initIndexTable : function() {
-    var togglers = $('img.toggler').click(function() {
-      var src = $(this).attr('src');
-      var idnum = $(this).attr('id').substr(7);
-      $('tr.cg-' + idnum).toggle();
-      if (src.substr(-9) == 'minus.png')
-        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
-      else
-        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
-    }).css('display', '');
-    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
-        togglers.click();
-    }
-  },
-
-  /**
-   * helper function to hide the search marks again
-   */
-  hideSearchWords : function() {
-    $('#searchbox .highlight-link').fadeOut(300);
-    $('span.highlighted').removeClass('highlighted');
-  },
-
-  /**
-   * make the url absolute
-   */
-  makeURL : function(relativeURL) {
-    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
-  },
-
-  /**
-   * get the current relative url
-   */
-  getCurrentURL : function() {
-    var path = document.location.pathname;
-    var parts = path.split(/\//);
-    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
-      if (this == '..')
-        parts.pop();
-    });
-    var url = parts.join('/');
-    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
-  },
-
-  initOnKeyListeners: function() {
-    $(document).keyup(function(event) {
-      var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box or textarea
-      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
-        switch (event.keyCode) {
-          case 37: // left
-            var prevHref = $('link[rel="prev"]').prop('href');
-            if (prevHref) {
-              window.location.href = prevHref;
-              return false;
-            }
-          case 39: // right
-            var nextHref = $('link[rel="next"]').prop('href');
-            if (nextHref) {
-              window.location.href = nextHref;
-              return false;
-            }
-        }
-      }
-    });
-  }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
-  Documentation.init();
-});

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docs/_build/html/_static/searchtools.js

@@ -1,758 +0,0 @@
-/*
- * searchtools.js_t
- * ~~~~~~~~~~~~~~~~
- *
- * Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-
-/* Non-minified version JS is _stemmer.js if file is provided */ 
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
-  var step2list = {
-    ational: 'ate',
-    tional: 'tion',
-    enci: 'ence',
-    anci: 'ance',
-    izer: 'ize',
-    bli: 'ble',
-    alli: 'al',
-    entli: 'ent',
-    eli: 'e',
-    ousli: 'ous',
-    ization: 'ize',
-    ation: 'ate',
-    ator: 'ate',
-    alism: 'al',
-    iveness: 'ive',
-    fulness: 'ful',
-    ousness: 'ous',
-    aliti: 'al',
-    iviti: 'ive',
-    biliti: 'ble',
-    logi: 'log'
-  };
-
-  var step3list = {
-    icate: 'ic',
-    ative: '',
-    alize: 'al',
-    iciti: 'ic',
-    ical: 'ic',
-    ful: '',
-    ness: ''
-  };
-
-  var c = "[^aeiou]";          // consonant
-  var v = "[aeiouy]";          // vowel
-  var C = c + "[^aeiouy]*";    // consonant sequence
-  var V = v + "[aeiou]*";      // vowel sequence
-
-  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
-  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
-  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
-  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
-
-  this.stemWord = function (w) {
-    var stem;
-    var suffix;
-    var firstch;
-    var origword = w;
-
-    if (w.length < 3)
-      return w;
-
-    var re;
-    var re2;
-    var re3;
-    var re4;
-
-    firstch = w.substr(0,1);
-    if (firstch == "y")
-      w = firstch.toUpperCase() + w.substr(1);
-
-    // Step 1a
-    re = /^(.+?)(ss|i)es$/;
-    re2 = /^(.+?)([^s])s$/;
-
-    if (re.test(w))
-      w = w.replace(re,"$1$2");
-    else if (re2.test(w))
-      w = w.replace(re2,"$1$2");
-
-    // Step 1b
-    re = /^(.+?)eed$/;
-    re2 = /^(.+?)(ed|ing)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      re = new RegExp(mgr0);
-      if (re.test(fp[1])) {
-        re = /.$/;
-        w = w.replace(re,"");
-      }
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1];
-      re2 = new RegExp(s_v);
-      if (re2.test(stem)) {
-        w = stem;
-        re2 = /(at|bl|iz)$/;
-        re3 = new RegExp("([^aeiouylsz])\\1$");
-        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-        if (re2.test(w))
-          w = w + "e";
-        else if (re3.test(w)) {
-          re = /.$/;
-          w = w.replace(re,"");
-        }
-        else if (re4.test(w))
-          w = w + "e";
-      }
-    }
-
-    // Step 1c
-    re = /^(.+?)y$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(s_v);
-      if (re.test(stem))
-        w = stem + "i";
-    }
-
-    // Step 2
-    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step2list[suffix];
-    }
-
-    // Step 3
-    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step3list[suffix];
-    }
-
-    // Step 4
-    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
-    re2 = /^(.+?)(s|t)(ion)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      if (re.test(stem))
-        w = stem;
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1] + fp[2];
-      re2 = new RegExp(mgr1);
-      if (re2.test(stem))
-        w = stem;
-    }
-
-    // Step 5
-    re = /^(.+?)e$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      re2 = new RegExp(meq1);
-      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
-        w = stem;
-    }
-    re = /ll$/;
-    re2 = new RegExp(mgr1);
-    if (re.test(w) && re2.test(w)) {
-      re = /.$/;
-      w = w.replace(re,"");
-    }
-
-    // and turn initial Y back to y
-    if (firstch == "y")
-      w = firstch.toLowerCase() + w.substr(1);
-    return w;
-  }
-}
-
-
-
-/**
- * Simple result scoring code.
- */
-var Scorer = {
-  // Implement the following function to further tweak the score for each result
-  // The function takes a result array [filename, title, anchor, descr, score]
-  // and returns the new score.
-  /*
-  score: function(result) {
-    return result[4];
-  },
-  */
-
-  // query matches the full name of an object
-  objNameMatch: 11,
-  // or matches in the last dotted part of the object name
-  objPartialMatch: 6,
-  // Additive scores depending on the priority of the object
-  objPrio: {0:  15,   // used to be importantResults
-            1:  5,   // used to be objectResults
-            2: -5},  // used to be unimportantResults
-  //  Used when the priority is not in the mapping.
-  objPrioDefault: 0,
-
-  // query found in title
-  title: 15,
-  // query found in terms
-  term: 5
-};
-
-
-
-
-
-var splitChars = (function() {
-    var result = {};
-    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
-         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
-         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
-         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
-         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
-         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
-         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
-         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
-         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
-         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
-    var i, j, start, end;
-    for (i = 0; i < singles.length; i++) {
-        result[singles[i]] = true;
-    }
-    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
-         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
-         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
-         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
-         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
-         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
-         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
-         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
-         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
-         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
-         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
-         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
-         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
-         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
-         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
-         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
-         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
-         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
-         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
-         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
-         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
-         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
-         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
-         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
-         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
-         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
-         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
-         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
-         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
-         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
-         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
-         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
-         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
-         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
-         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
-         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
-         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
-         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
-         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
-         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
-         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
-         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
-         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
-         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
-         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
-         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
-         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
-         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
-         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
-    for (i = 0; i < ranges.length; i++) {
-        start = ranges[i][0];
-        end = ranges[i][1];
-        for (j = start; j <= end; j++) {
-            result[j] = true;
-        }
-    }
-    return result;
-})();
-
-function splitQuery(query) {
-    var result = [];
-    var start = -1;
-    for (var i = 0; i < query.length; i++) {
-        if (splitChars[query.charCodeAt(i)]) {
-            if (start !== -1) {
-                result.push(query.slice(start, i));
-                start = -1;
-            }
-        } else if (start === -1) {
-            start = i;
-        }
-    }
-    if (start !== -1) {
-        result.push(query.slice(start));
-    }
-    return result;
-}
-
-
-
-
-/**
- * Search Module
- */
-var Search = {
-
-  _index : null,
-  _queued_query : null,
-  _pulse_status : -1,
-
-  init : function() {
-      var params = $.getQueryParameters();
-      if (params.q) {
-          var query = params.q[0];
-          $('input[name="q"]')[0].value = query;
-          this.performSearch(query);
-      }
-  },
-
-  loadIndex : function(url) {
-    $.ajax({type: "GET", url: url, data: null,
-            dataType: "script", cache: true,
-            complete: function(jqxhr, textstatus) {
-              if (textstatus != "success") {
-                document.getElementById("searchindexloader").src = url;
-              }
-            }});
-  },
-
-  setIndex : function(index) {
-    var q;
-    this._index = index;
-    if ((q = this._queued_query) !== null) {
-      this._queued_query = null;
-      Search.query(q);
-    }
-  },
-
-  hasIndex : function() {
-      return this._index !== null;
-  },
-
-  deferQuery : function(query) {
-      this._queued_query = query;
-  },
-
-  stopPulse : function() {
-      this._pulse_status = 0;
-  },
-
-  startPulse : function() {
-    if (this._pulse_status >= 0)
-        return;
-    function pulse() {
-      var i;
-      Search._pulse_status = (Search._pulse_status + 1) % 4;
-      var dotString = '';
-      for (i = 0; i < Search._pulse_status; i++)
-        dotString += '.';
-      Search.dots.text(dotString);
-      if (Search._pulse_status > -1)
-        window.setTimeout(pulse, 500);
-    }
-    pulse();
-  },
-
-  /**
-   * perform a search for something (or wait until index is loaded)
-   */
-  performSearch : function(query) {
-    // create the required interface elements
-    this.out = $('#search-results');
-    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
-    this.dots = $('<span></span>').appendTo(this.title);
-    this.status = $('<p style="display: none"></p>').appendTo(this.out);
-    this.output = $('<ul class="search"/>').appendTo(this.out);
-
-    $('#search-progress').text(_('Preparing search...'));
-    this.startPulse();
-
-    // index already loaded, the browser was quick!
-    if (this.hasIndex())
-      this.query(query);
-    else
-      this.deferQuery(query);
-  },
-
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  query : function(query) {
-    var i;
-    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
-
-    // stem the searchterms and add them to the correct list
-    var stemmer = new Stemmer();
-    var searchterms = [];
-    var excluded = [];
-    var hlterms = [];
-    var tmp = splitQuery(query);
-    var objectterms = [];
-    for (i = 0; i < tmp.length; i++) {
-      if (tmp[i] !== "") {
-          objectterms.push(tmp[i].toLowerCase());
-      }
-
-      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] === "") {
-        // skip this "word"
-        continue;
-      }
-      // stem the word
-      var word = stemmer.stemWord(tmp[i].toLowerCase());
-      // prevent stemmer from cutting word smaller than two chars
-      if(word.length < 3 && tmp[i].length >= 3) {
-        word = tmp[i];
-      }
-      var toAppend;
-      // select the correct list
-      if (word[0] == '-') {
-        toAppend = excluded;
-        word = word.substr(1);
-      }
-      else {
-        toAppend = searchterms;
-        hlterms.push(tmp[i].toLowerCase());
-      }
-      // only add if not already in the list
-      if (!$u.contains(toAppend, word))
-        toAppend.push(word);
-    }
-    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
-    // console.debug('SEARCH: searching for:');
-    // console.info('required: ', searchterms);
-    // console.info('excluded: ', excluded);
-
-    // prepare search
-    var terms = this._index.terms;
-    var titleterms = this._index.titleterms;
-
-    // array of [filename, title, anchor, descr, score]
-    var results = [];
-    $('#search-progress').empty();
-
-    // lookup as object
-    for (i = 0; i < objectterms.length; i++) {
-      var others = [].concat(objectterms.slice(0, i),
-                             objectterms.slice(i+1, objectterms.length));
-      results = results.concat(this.performObjectSearch(objectterms[i], others));
-    }
-
-    // lookup as search terms in fulltext
-    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
-
-    // let the scorer override scores with a custom scoring function
-    if (Scorer.score) {
-      for (i = 0; i < results.length; i++)
-        results[i][4] = Scorer.score(results[i]);
-    }
-
-    // now sort the results by score (in opposite order of appearance, since the
-    // display function below uses pop() to retrieve items) and then
-    // alphabetically
-    results.sort(function(a, b) {
-      var left = a[4];
-      var right = b[4];
-      if (left > right) {
-        return 1;
-      } else if (left < right) {
-        return -1;
-      } else {
-        // same score: sort alphabetically
-        left = a[1].toLowerCase();
-        right = b[1].toLowerCase();
-        return (left > right) ? -1 : ((left < right) ? 1 : 0);
-      }
-    });
-
-    // for debugging
-    //Search.lastresults = results.slice();  // a copy
-    //console.info('search results:', Search.lastresults);
-
-    // print the results
-    var resultCount = results.length;
-    function displayNextItem() {
-      // results left, load the summary and display it
-      if (results.length) {
-        var item = results.pop();
-        var listItem = $('<li style="display:none"></li>');
-        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
-          // dirhtml builder
-          var dirname = item[0] + '/';
-          if (dirname.match(/\/index\/$/)) {
-            dirname = dirname.substring(0, dirname.length-6);
-          } else if (dirname == 'index/') {
-            dirname = '';
-          }
-          listItem.append($('<a/>').attr('href',
-            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
-            highlightstring + item[2]).html(item[1]));
-        } else {
-          // normal html builders
-          listItem.append($('<a/>').attr('href',
-            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
-            highlightstring + item[2]).html(item[1]));
-        }
-        if (item[3]) {
-          listItem.append($('<span> (' + item[3] + ')</span>'));
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
-                  dataType: "text",
-                  complete: function(jqxhr, textstatus) {
-                    var data = jqxhr.responseText;
-                    if (data !== '' && data !== undefined) {
-                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
-                    }
-                    Search.output.append(listItem);
-                    listItem.slideDown(5, function() {
-                      displayNextItem();
-                    });
-                  }});
-        } else {
-          // no source available, just display title
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        }
-      }
-      // search finished, update title and status message
-      else {
-        Search.stopPulse();
-        Search.title.text(_('Search Results'));
-        if (!resultCount)
-          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
-        else
-            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
-        Search.status.fadeIn(500);
-      }
-    }
-    displayNextItem();
-  },
-
-  /**
-   * search for object names
-   */
-  performObjectSearch : function(object, otherterms) {
-    var filenames = this._index.filenames;
-    var docnames = this._index.docnames;
-    var objects = this._index.objects;
-    var objnames = this._index.objnames;
-    var titles = this._index.titles;
-
-    var i;
-    var results = [];
-
-    for (var prefix in objects) {
-      for (var name in objects[prefix]) {
-        var fullname = (prefix ? prefix + '.' : '') + name;
-        if (fullname.toLowerCase().indexOf(object) > -1) {
-          var score = 0;
-          var parts = fullname.split('.');
-          // check for different match types: exact matches of full name or
-          // "last name" (i.e. last dotted part)
-          if (fullname == object || parts[parts.length - 1] == object) {
-            score += Scorer.objNameMatch;
-          // matches in last name
-          } else if (parts[parts.length - 1].indexOf(object) > -1) {
-            score += Scorer.objPartialMatch;
-          }
-          var match = objects[prefix][name];
-          var objname = objnames[match[1]][2];
-          var title = titles[match[0]];
-          // If more than one term searched for, we require other words to be
-          // found in the name/title/description
-          if (otherterms.length > 0) {
-            var haystack = (prefix + ' ' + name + ' ' +
-                            objname + ' ' + title).toLowerCase();
-            var allfound = true;
-            for (i = 0; i < otherterms.length; i++) {
-              if (haystack.indexOf(otherterms[i]) == -1) {
-                allfound = false;
-                break;
-              }
-            }
-            if (!allfound) {
-              continue;
-            }
-          }
-          var descr = objname + _(', in ') + title;
-
-          var anchor = match[3];
-          if (anchor === '')
-            anchor = fullname;
-          else if (anchor == '-')
-            anchor = objnames[match[1]][1] + '-' + fullname;
-          // add custom score for some objects according to scorer
-          if (Scorer.objPrio.hasOwnProperty(match[2])) {
-            score += Scorer.objPrio[match[2]];
-          } else {
-            score += Scorer.objPrioDefault;
-          }
-          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
-        }
-      }
-    }
-
-    return results;
-  },
-
-  /**
-   * search for full-text terms in the index
-   */
-  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
-    var docnames = this._index.docnames;
-    var filenames = this._index.filenames;
-    var titles = this._index.titles;
-
-    var i, j, file;
-    var fileMap = {};
-    var scoreMap = {};
-    var results = [];
-
-    // perform the search on the required terms
-    for (i = 0; i < searchterms.length; i++) {
-      var word = searchterms[i];
-      var files = [];
-      var _o = [
-        {files: terms[word], score: Scorer.term},
-        {files: titleterms[word], score: Scorer.title}
-      ];
-
-      // no match but word was a required one
-      if ($u.every(_o, function(o){return o.files === undefined;})) {
-        break;
-      }
-      // found search word in contents
-      $u.each(_o, function(o) {
-        var _files = o.files;
-        if (_files === undefined)
-          return
-
-        if (_files.length === undefined)
-          _files = [_files];
-        files = files.concat(_files);
-
-        // set score for the word in each file to Scorer.term
-        for (j = 0; j < _files.length; j++) {
-          file = _files[j];
-          if (!(file in scoreMap))
-            scoreMap[file] = {}
-          scoreMap[file][word] = o.score;
-        }
-      });
-
-      // create the mapping
-      for (j = 0; j < files.length; j++) {
-        file = files[j];
-        if (file in fileMap)
-          fileMap[file].push(word);
-        else
-          fileMap[file] = [word];
-      }
-    }
-
-    // now check if the files don't contain excluded terms
-    for (file in fileMap) {
-      var valid = true;
-
-      // check if all requirements are matched
-      if (fileMap[file].length != searchterms.length)
-          continue;
-
-      // ensure that none of the excluded terms is in the search result
-      for (i = 0; i < excluded.length; i++) {
-        if (terms[excluded[i]] == file ||
-            titleterms[excluded[i]] == file ||
-            $u.contains(terms[excluded[i]] || [], file) ||
-            $u.contains(titleterms[excluded[i]] || [], file)) {
-          valid = false;
-          break;
-        }
-      }
-
-      // if we have still a valid result we can add it to the result list
-      if (valid) {
-        // select one (max) score for the file.
-        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
-        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
-        results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
-      }
-    }
-    return results;
-  },
-
-  /**
-   * helper function to return a node containing the
-   * search summary for a given text. keywords is a list
-   * of stemmed words, hlwords is the list of normal, unstemmed
-   * words. the first one is used to find the occurrence, the
-   * latter for highlighting it.
-   */
-  makeSearchSummary : function(text, keywords, hlwords) {
-    var textLower = text.toLowerCase();
-    var start = 0;
-    $.each(keywords, function() {
-      var i = textLower.indexOf(this.toLowerCase());
-      if (i > -1)
-        start = i;
-    });
-    start = Math.max(start - 120, 0);
-    var excerpt = ((start > 0) ? '...' : '') +
-      $.trim(text.substr(start, 240)) +
-      ((start + 240 - text.length) ? '...' : '');
-    var rv = $('<div class="context"></div>').text(excerpt);
-    $.each(hlwords, function() {
-      rv = rv.highlightText(this, 'highlighted');
-    });
-    return rv;
-  }
-};
-
-$(document).ready(function() {
-  Search.init();
-});

docs/_build/html/_static/underscore-1.3.1.js

@@ -1,999 +0,0 @@
-//     Underscore.js 1.3.1
-//     (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-//     Underscore is freely distributable under the MIT license.
-//     Portions of Underscore are inspired or borrowed from Prototype,
-//     Oliver Steele's Functional, and John Resig's Micro-Templating.
-//     For all details and documentation:
-//     http://documentcloud.github.com/underscore
-
-(function() {
-
-  // Baseline setup
-  // --------------
-
-  // Establish the root object, `window` in the browser, or `global` on the server.
-  var root = this;
-
-  // Save the previous value of the `_` variable.
-  var previousUnderscore = root._;
-
-  // Establish the object that gets returned to break out of a loop iteration.
-  var breaker = {};
-
-  // Save bytes in the minified (but not gzipped) version:
-  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
-
-  // Create quick reference variables for speed access to core prototypes.
-  var slice            = ArrayProto.slice,
-      unshift          = ArrayProto.unshift,
-      toString         = ObjProto.toString,
-      hasOwnProperty   = ObjProto.hasOwnProperty;
-
-  // All **ECMAScript 5** native function implementations that we hope to use
-  // are declared here.
-  var
-    nativeForEach      = ArrayProto.forEach,
-    nativeMap          = ArrayProto.map,
-    nativeReduce       = ArrayProto.reduce,
-    nativeReduceRight  = ArrayProto.reduceRight,
-    nativeFilter       = ArrayProto.filter,
-    nativeEvery        = ArrayProto.every,
-    nativeSome         = ArrayProto.some,
-    nativeIndexOf      = ArrayProto.indexOf,
-    nativeLastIndexOf  = ArrayProto.lastIndexOf,
-    nativeIsArray      = Array.isArray,
-    nativeKeys         = Object.keys,
-    nativeBind         = FuncProto.bind;
-
-  // Create a safe reference to the Underscore object for use below.
-  var _ = function(obj) { return new wrapper(obj); };
-
-  // Export the Underscore object for **Node.js**, with
-  // backwards-compatibility for the old `require()` API. If we're in
-  // the browser, add `_` as a global object via a string identifier,
-  // for Closure Compiler "advanced" mode.
-  if (typeof exports !== 'undefined') {
-    if (typeof module !== 'undefined' && module.exports) {
-      exports = module.exports = _;
-    }
-    exports._ = _;
-  } else {
-    root['_'] = _;
-  }
-
-  // Current version.
-  _.VERSION = '1.3.1';
-
-  // Collection Functions
-  // --------------------
-
-  // The cornerstone, an `each` implementation, aka `forEach`.
-  // Handles objects with the built-in `forEach`, arrays, and raw objects.
-  // Delegates to **ECMAScript 5**'s native `forEach` if available.
-  var each = _.each = _.forEach = function(obj, iterator, context) {
-    if (obj == null) return;
-    if (nativeForEach && obj.forEach === nativeForEach) {
-      obj.forEach(iterator, context);
-    } else if (obj.length === +obj.length) {
-      for (var i = 0, l = obj.length; i < l; i++) {
-        if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
-      }
-    } else {
-      for (var key in obj) {
-        if (_.has(obj, key)) {
-          if (iterator.call(context, obj[key], key, obj) === breaker) return;
-        }
-      }
-    }
-  };
-
-  // Return the results of applying the iterator to each element.
-  // Delegates to **ECMAScript 5**'s native `map` if available.
-  _.map = _.collect = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
-    each(obj, function(value, index, list) {
-      results[results.length] = iterator.call(context, value, index, list);
-    });
-    if (obj.length === +obj.length) results.length = obj.length;
-    return results;
-  };
-
-  // **Reduce** builds up a single result from a list of values, aka `inject`,
-  // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
-  _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
-    var initial = arguments.length > 2;
-    if (obj == null) obj = [];
-    if (nativeReduce && obj.reduce === nativeReduce) {
-      if (context) iterator = _.bind(iterator, context);
-      return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
-    }
-    each(obj, function(value, index, list) {
-      if (!initial) {
-        memo = value;
-        initial = true;
-      } else {
-        memo = iterator.call(context, memo, value, index, list);
-      }
-    });
-    if (!initial) throw new TypeError('Reduce of empty array with no initial value');
-    return memo;
-  };
-
-  // The right-associative version of reduce, also known as `foldr`.
-  // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
-  _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
-    var initial = arguments.length > 2;
-    if (obj == null) obj = [];
-    if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
-      if (context) iterator = _.bind(iterator, context);
-      return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
-    }
-    var reversed = _.toArray(obj).reverse();
-    if (context && !initial) iterator = _.bind(iterator, context);
-    return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
-  };
-
-  // Return the first value which passes a truth test. Aliased as `detect`.
-  _.find = _.detect = function(obj, iterator, context) {
-    var result;
-    any(obj, function(value, index, list) {
-      if (iterator.call(context, value, index, list)) {
-        result = value;
-        return true;
-      }
-    });
-    return result;
-  };
-
-  // Return all the elements that pass a truth test.
-  // Delegates to **ECMAScript 5**'s native `filter` if available.
-  // Aliased as `select`.
-  _.filter = _.select = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
-    each(obj, function(value, index, list) {
-      if (iterator.call(context, value, index, list)) results[results.length] = value;
-    });
-    return results;
-  };
-
-  // Return all the elements for which a truth test fails.
-  _.reject = function(obj, iterator, context) {
-    var results = [];
-    if (obj == null) return results;
-    each(obj, function(value, index, list) {
-      if (!iterator.call(context, value, index, list)) results[results.length] = value;
-    });
-    return results;
-  };
-
-  // Determine whether all of the elements match a truth test.
-  // Delegates to **ECMAScript 5**'s native `every` if available.
-  // Aliased as `all`.
-  _.every = _.all = function(obj, iterator, context) {
-    var result = true;
-    if (obj == null) return result;
-    if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
-    each(obj, function(value, index, list) {
-      if (!(result = result && iterator.call(context, value, index, list))) return breaker;
-    });
-    return result;
-  };
-
-  // Determine if at least one element in the object matches a truth test.
-  // Delegates to **ECMAScript 5**'s native `some` if available.
-  // Aliased as `any`.
-  var any = _.some = _.any = function(obj, iterator, context) {
-    iterator || (iterator = _.identity);
-    var result = false;
-    if (obj == null) return result;
-    if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
-    each(obj, function(value, index, list) {
-      if (result || (result = iterator.call(context, value, index, list))) return breaker;
-    });
-    return !!result;
-  };
-
-  // Determine if a given value is included in the array or object using `===`.
-  // Aliased as `contains`.
-  _.include = _.contains = function(obj, target) {
-    var found = false;
-    if (obj == null) return found;
-    if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
-    found = any(obj, function(value) {
-      return value === target;
-    });
-    return found;
-  };
-
-  // Invoke a method (with arguments) on every item in a collection.
-  _.invoke = function(obj, method) {
-    var args = slice.call(arguments, 2);
-    return _.map(obj, function(value) {
-      return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
-    });
-  };
-
-  // Convenience version of a common use case of `map`: fetching a property.
-  _.pluck = function(obj, key) {
-    return _.map(obj, function(value){ return value[key]; });
-  };
-
-  // Return the maximum element or (element-based computation).
-  _.max = function(obj, iterator, context) {
-    if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
-    if (!iterator && _.isEmpty(obj)) return -Infinity;
-    var result = {computed : -Infinity};
-    each(obj, function(value, index, list) {
-      var computed = iterator ? iterator.call(context, value, index, list) : value;
-      computed >= result.computed && (result = {value : value, computed : computed});
-    });
-    return result.value;
-  };
-
-  // Return the minimum element (or element-based computation).
-  _.min = function(obj, iterator, context) {
-    if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
-    if (!iterator && _.isEmpty(obj)) return Infinity;
-    var result = {computed : Infinity};
-    each(obj, function(value, index, list) {
-      var computed = iterator ? iterator.call(context, value, index, list) : value;
-      computed < result.computed && (result = {value : value, computed : computed});
-    });
-    return result.value;
-  };
-
-  // Shuffle an array.
-  _.shuffle = function(obj) {
-    var shuffled = [], rand;
-    each(obj, function(value, index, list) {
-      if (index == 0) {
-        shuffled[0] = value;
-      } else {
-        rand = Math.floor(Math.random() * (index + 1));
-        shuffled[index] = shuffled[rand];
-        shuffled[rand] = value;
-      }
-    });
-    return shuffled;
-  };
-
-  // Sort the object's values by a criterion produced by an iterator.
-  _.sortBy = function(obj, iterator, context) {
-    return _.pluck(_.map(obj, function(value, index, list) {
-      return {
-        value : value,
-        criteria : iterator.call(context, value, index, list)
-      };
-    }).sort(function(left, right) {
-      var a = left.criteria, b = right.criteria;
-      return a < b ? -1 : a > b ? 1 : 0;
-    }), 'value');
-  };
-
-  // Groups the object's values by a criterion. Pass either a string attribute
-  // to group by, or a function that returns the criterion.
-  _.groupBy = function(obj, val) {
-    var result = {};
-    var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
-    each(obj, function(value, index) {
-      var key = iterator(value, index);
-      (result[key] || (result[key] = [])).push(value);
-    });
-    return result;
-  };
-
-  // Use a comparator function to figure out at what index an object should
-  // be inserted so as to maintain order. Uses binary search.
-  _.sortedIndex = function(array, obj, iterator) {
-    iterator || (iterator = _.identity);
-    var low = 0, high = array.length;
-    while (low < high) {
-      var mid = (low + high) >> 1;
-      iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
-    }
-    return low;
-  };
-
-  // Safely convert anything iterable into a real, live array.
-  _.toArray = function(iterable) {
-    if (!iterable)                return [];
-    if (iterable.toArray)         return iterable.toArray();
-    if (_.isArray(iterable))      return slice.call(iterable);
-    if (_.isArguments(iterable))  return slice.call(iterable);
-    return _.values(iterable);
-  };
-
-  // Return the number of elements in an object.
-  _.size = function(obj) {
-    return _.toArray(obj).length;
-  };
-
-  // Array Functions
-  // ---------------
-
-  // Get the first element of an array. Passing **n** will return the first N
-  // values in the array. Aliased as `head`. The **guard** check allows it to work
-  // with `_.map`.
-  _.first = _.head = function(array, n, guard) {
-    return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
-  };
-
-  // Returns everything but the last entry of the array. Especcialy useful on
-  // the arguments object. Passing **n** will return all the values in
-  // the array, excluding the last N. The **guard** check allows it to work with
-  // `_.map`.
-  _.initial = function(array, n, guard) {
-    return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
-  };
-
-  // Get the last element of an array. Passing **n** will return the last N
-  // values in the array. The **guard** check allows it to work with `_.map`.
-  _.last = function(array, n, guard) {
-    if ((n != null) && !guard) {
-      return slice.call(array, Math.max(array.length - n, 0));
-    } else {
-      return array[array.length - 1];
-    }
-  };
-
-  // Returns everything but the first entry of the array. Aliased as `tail`.
-  // Especially useful on the arguments object. Passing an **index** will return
-  // the rest of the values in the array from that index onward. The **guard**
-  // check allows it to work with `_.map`.
-  _.rest = _.tail = function(array, index, guard) {
-    return slice.call(array, (index == null) || guard ? 1 : index);
-  };
-
-  // Trim out all falsy values from an array.
-  _.compact = function(array) {
-    return _.filter(array, function(value){ return !!value; });
-  };
-
-  // Return a completely flattened version of an array.
-  _.flatten = function(array, shallow) {
-    return _.reduce(array, function(memo, value) {
-      if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
-      memo[memo.length] = value;
-      return memo;
-    }, []);
-  };
-
-  // Return a version of the array that does not contain the specified value(s).
-  _.without = function(array) {
-    return _.difference(array, slice.call(arguments, 1));
-  };
-
-  // Produce a duplicate-free version of the array. If the array has already
-  // been sorted, you have the option of using a faster algorithm.
-  // Aliased as `unique`.
-  _.uniq = _.unique = function(array, isSorted, iterator) {
-    var initial = iterator ? _.map(array, iterator) : array;
-    var result = [];
-    _.reduce(initial, function(memo, el, i) {
-      if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
-        memo[memo.length] = el;
-        result[result.length] = array[i];
-      }
-      return memo;
-    }, []);
-    return result;
-  };
-
-  // Produce an array that contains the union: each distinct element from all of
-  // the passed-in arrays.
-  _.union = function() {
-    return _.uniq(_.flatten(arguments, true));
-  };
-
-  // Produce an array that contains every item shared between all the
-  // passed-in arrays. (Aliased as "intersect" for back-compat.)
-  _.intersection = _.intersect = function(array) {
-    var rest = slice.call(arguments, 1);
-    return _.filter(_.uniq(array), function(item) {
-      return _.every(rest, function(other) {
-        return _.indexOf(other, item) >= 0;
-      });
-    });
-  };
-
-  // Take the difference between one array and a number of other arrays.
-  // Only the elements present in just the first array will remain.
-  _.difference = function(array) {
-    var rest = _.flatten(slice.call(arguments, 1));
-    return _.filter(array, function(value){ return !_.include(rest, value); });
-  };
-
-  // Zip together multiple lists into a single array -- elements that share
-  // an index go together.
-  _.zip = function() {
-    var args = slice.call(arguments);
-    var length = _.max(_.pluck(args, 'length'));
-    var results = new Array(length);
-    for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
-    return results;
-  };
-
-  // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
-  // we need this function. Return the position of the first occurrence of an
-  // item in an array, or -1 if the item is not included in the array.
-  // Delegates to **ECMAScript 5**'s native `indexOf` if available.
-  // If the array is large and already in sort order, pass `true`
-  // for **isSorted** to use binary search.
-  _.indexOf = function(array, item, isSorted) {
-    if (array == null) return -1;
-    var i, l;
-    if (isSorted) {
-      i = _.sortedIndex(array, item);
-      return array[i] === item ? i : -1;
-    }
-    if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
-    for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
-    return -1;
-  };
-
-  // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
-  _.lastIndexOf = function(array, item) {
-    if (array == null) return -1;
-    if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
-    var i = array.length;
-    while (i--) if (i in array && array[i] === item) return i;
-    return -1;
-  };
-
-  // Generate an integer Array containing an arithmetic progression. A port of
-  // the native Python `range()` function. See
-  // [the Python documentation](http://docs.python.org/library/functions.html#range).
-  _.range = function(start, stop, step) {
-    if (arguments.length <= 1) {
-      stop = start || 0;
-      start = 0;
-    }
-    step = arguments[2] || 1;
-
-    var len = Math.max(Math.ceil((stop - start) / step), 0);
-    var idx = 0;
-    var range = new Array(len);
-
-    while(idx < len) {
-      range[idx++] = start;
-      start += step;
-    }
-
-    return range;
-  };
-
-  // Function (ahem) Functions
-  // ------------------
-
-  // Reusable constructor function for prototype setting.
-  var ctor = function(){};
-
-  // Create a function bound to a given object (assigning `this`, and arguments,
-  // optionally). Binding with arguments is also known as `curry`.
-  // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
-  // We check for `func.bind` first, to fail fast when `func` is undefined.
-  _.bind = function bind(func, context) {
-    var bound, args;
-    if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
-    if (!_.isFunction(func)) throw new TypeError;
-    args = slice.call(arguments, 2);
-    return bound = function() {
-      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
-      ctor.prototype = func.prototype;
-      var self = new ctor;
-      var result = func.apply(self, args.concat(slice.call(arguments)));
-      if (Object(result) === result) return result;
-      return self;
-    };
-  };
-
-  // Bind all of an object's methods to that object. Useful for ensuring that
-  // all callbacks defined on an object belong to it.
-  _.bindAll = function(obj) {
-    var funcs = slice.call(arguments, 1);
-    if (funcs.length == 0) funcs = _.functions(obj);
-    each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
-    return obj;
-  };
-
-  // Memoize an expensive function by storing its results.
-  _.memoize = function(func, hasher) {
-    var memo = {};
-    hasher || (hasher = _.identity);
-    return function() {
-      var key = hasher.apply(this, arguments);
-      return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
-    };
-  };
-
-  // Delays a function for the given number of milliseconds, and then calls
-  // it with the arguments supplied.
-  _.delay = function(func, wait) {
-    var args = slice.call(arguments, 2);
-    return setTimeout(function(){ return func.apply(func, args); }, wait);
-  };
-
-  // Defers a function, scheduling it to run after the current call stack has
-  // cleared.
-  _.defer = function(func) {
-    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
-  };
-
-  // Returns a function, that, when invoked, will only be triggered at most once
-  // during a given window of time.
-  _.throttle = function(func, wait) {
-    var context, args, timeout, throttling, more;
-    var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
-    return function() {
-      context = this; args = arguments;
-      var later = function() {
-        timeout = null;
-        if (more) func.apply(context, args);
-        whenDone();
-      };
-      if (!timeout) timeout = setTimeout(later, wait);
-      if (throttling) {
-        more = true;
-      } else {
-        func.apply(context, args);
-      }
-      whenDone();
-      throttling = true;
-    };
-  };
-
-  // Returns a function, that, as long as it continues to be invoked, will not
-  // be triggered. The function will be called after it stops being called for
-  // N milliseconds.
-  _.debounce = function(func, wait) {
-    var timeout;
-    return function() {
-      var context = this, args = arguments;
-      var later = function() {
-        timeout = null;
-        func.apply(context, args);
-      };
-      clearTimeout(timeout);
-      timeout = setTimeout(later, wait);
-    };
-  };
-
-  // Returns a function that will be executed at most one time, no matter how
-  // often you call it. Useful for lazy initialization.
-  _.once = function(func) {
-    var ran = false, memo;
-    return function() {
-      if (ran) return memo;
-      ran = true;
-      return memo = func.apply(this, arguments);
-    };
-  };
-
-  // Returns the first function passed as an argument to the second,
-  // allowing you to adjust arguments, run code before and after, and
-  // conditionally execute the original function.
-  _.wrap = function(func, wrapper) {
-    return function() {
-      var args = [func].concat(slice.call(arguments, 0));
-      return wrapper.apply(this, args);
-    };
-  };
-
-  // Returns a function that is the composition of a list of functions, each
-  // consuming the return value of the function that follows.
-  _.compose = function() {
-    var funcs = arguments;
-    return function() {
-      var args = arguments;
-      for (var i = funcs.length - 1; i >= 0; i--) {
-        args = [funcs[i].apply(this, args)];
-      }
-      return args[0];
-    };
-  };
-
-  // Returns a function that will only be executed after being called N times.
-  _.after = function(times, func) {
-    if (times <= 0) return func();
-    return function() {
-      if (--times < 1) { return func.apply(this, arguments); }
-    };
-  };
-
-  // Object Functions
-  // ----------------
-
-  // Retrieve the names of an object's properties.
-  // Delegates to **ECMAScript 5**'s native `Object.keys`
-  _.keys = nativeKeys || function(obj) {
-    if (obj !== Object(obj)) throw new TypeError('Invalid object');
-    var keys = [];
-    for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
-    return keys;
-  };
-
-  // Retrieve the values of an object's properties.
-  _.values = function(obj) {
-    return _.map(obj, _.identity);
-  };
-
-  // Return a sorted list of the function names available on the object.
-  // Aliased as `methods`
-  _.functions = _.methods = function(obj) {
-    var names = [];
-    for (var key in obj) {
-      if (_.isFunction(obj[key])) names.push(key);
-    }
-    return names.sort();
-  };
-
-  // Extend a given object with all the properties in passed-in object(s).
-  _.extend = function(obj) {
-    each(slice.call(arguments, 1), function(source) {
-      for (var prop in source) {
-        obj[prop] = source[prop];
-      }
-    });
-    return obj;
-  };
-
-  // Fill in a given object with default properties.
-  _.defaults = function(obj) {
-    each(slice.call(arguments, 1), function(source) {
-      for (var prop in source) {
-        if (obj[prop] == null) obj[prop] = source[prop];
-      }
-    });
-    return obj;
-  };
-
-  // Create a (shallow-cloned) duplicate of an object.
-  _.clone = function(obj) {
-    if (!_.isObject(obj)) return obj;
-    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
-  };
-
-  // Invokes interceptor with the obj, and then returns obj.
-  // The primary purpose of this method is to "tap into" a method chain, in
-  // order to perform operations on intermediate results within the chain.
-  _.tap = function(obj, interceptor) {
-    interceptor(obj);
-    return obj;
-  };
-
-  // Internal recursive comparison function.
-  function eq(a, b, stack) {
-    // Identical objects are equal. `0 === -0`, but they aren't identical.
-    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
-    if (a === b) return a !== 0 || 1 / a == 1 / b;
-    // A strict comparison is necessary because `null == undefined`.
-    if (a == null || b == null) return a === b;
-    // Unwrap any wrapped objects.
-    if (a._chain) a = a._wrapped;
-    if (b._chain) b = b._wrapped;
-    // Invoke a custom `isEqual` method if one is provided.
-    if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
-    if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
-    // Compare `[[Class]]` names.
-    var className = toString.call(a);
-    if (className != toString.call(b)) return false;
-    switch (className) {
-      // Strings, numbers, dates, and booleans are compared by value.
-      case '[object String]':
-        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
-        // equivalent to `new String("5")`.
-        return a == String(b);
-      case '[object Number]':
-        // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
-        // other numeric values.
-        return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
-      case '[object Date]':
-      case '[object Boolean]':
-        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
-        // millisecond representations. Note that invalid dates with millisecond representations
-        // of `NaN` are not equivalent.
-        return +a == +b;
-      // RegExps are compared by their source patterns and flags.
-      case '[object RegExp]':
-        return a.source == b.source &&
-               a.global == b.global &&
-               a.multiline == b.multiline &&
-               a.ignoreCase == b.ignoreCase;
-    }
-    if (typeof a != 'object' || typeof b != 'object') return false;
-    // Assume equality for cyclic structures. The algorithm for detecting cyclic
-    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
-    var length = stack.length;
-    while (length--) {
-      // Linear search. Performance is inversely proportional to the number of
-      // unique nested structures.
-      if (stack[length] == a) return true;
-    }
-    // Add the first object to the stack of traversed objects.
-    stack.push(a);
-    var size = 0, result = true;
-    // Recursively compare objects and arrays.
-    if (className == '[object Array]') {
-      // Compare array lengths to determine if a deep comparison is necessary.
-      size = a.length;
-      result = size == b.length;
-      if (result) {
-        // Deep compare the contents, ignoring non-numeric properties.
-        while (size--) {
-          // Ensure commutative equality for sparse arrays.
-          if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
-        }
-      }
-    } else {
-      // Objects with different constructors are not equivalent.
-      if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
-      // Deep compare objects.
-      for (var key in a) {
-        if (_.has(a, key)) {
-          // Count the expected number of properties.
-          size++;
-          // Deep compare each member.
-          if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
-        }
-      }
-      // Ensure that both objects contain the same number of properties.
-      if (result) {
-        for (key in b) {
-          if (_.has(b, key) && !(size--)) break;
-        }
-        result = !size;
-      }
-    }
-    // Remove the first object from the stack of traversed objects.
-    stack.pop();
-    return result;
-  }
-
-  // Perform a deep comparison to check if two objects are equal.
-  _.isEqual = function(a, b) {
-    return eq(a, b, []);
-  };
-
-  // Is a given array, string, or object empty?
-  // An "empty" object has no enumerable own-properties.
-  _.isEmpty = function(obj) {
-    if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
-    for (var key in obj) if (_.has(obj, key)) return false;
-    return true;
-  };
-
-  // Is a given value a DOM element?
-  _.isElement = function(obj) {
-    return !!(obj && obj.nodeType == 1);
-  };
-
-  // Is a given value an array?
-  // Delegates to ECMA5's native Array.isArray
-  _.isArray = nativeIsArray || function(obj) {
-    return toString.call(obj) == '[object Array]';
-  };
-
-  // Is a given variable an object?
-  _.isObject = function(obj) {
-    return obj === Object(obj);
-  };
-
-  // Is a given variable an arguments object?
-  _.isArguments = function(obj) {
-    return toString.call(obj) == '[object Arguments]';
-  };
-  if (!_.isArguments(arguments)) {
-    _.isArguments = function(obj) {
-      return !!(obj && _.has(obj, 'callee'));
-    };
-  }
-
-  // Is a given value a function?
-  _.isFunction = function(obj) {
-    return toString.call(obj) == '[object Function]';
-  };
-
-  // Is a given value a string?
-  _.isString = function(obj) {
-    return toString.call(obj) == '[object String]';
-  };
-
-  // Is a given value a number?
-  _.isNumber = function(obj) {
-    return toString.call(obj) == '[object Number]';
-  };
-
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docs/_build/html/_static/underscore.js

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docs/_build/html/_static/websupport.js

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-  $.fn.autogrow.resize = function(textarea) {
-    var lineHeight = parseInt($(textarea).css('line-height'), 10);
-    var lines = textarea.value.split('\n');
-    var columns = textarea.cols;
-    var lineCount = 0;
-    $.each(lines, function() {
-      lineCount += Math.ceil(this.length / columns) || 1;
-    });
-    var height = lineHeight * (lineCount + 1);
-    $(textarea).css('height', height);
-  };
-})(jQuery);
-
-(function($) {
-  var comp, by;
-
-  function init() {
-    initEvents();
-    initComparator();
-  }
-
-  function initEvents() {
-    $(document).on("click", 'a.comment-close', function(event) {
-      event.preventDefault();
-      hide($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.vote', function(event) {
-      event.preventDefault();
-      handleVote($(this));
-    });
-    $(document).on("click", 'a.reply', function(event) {
-      event.preventDefault();
-      openReply($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.close-reply', function(event) {
-      event.preventDefault();
-      closeReply($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.sort-option', function(event) {
-      event.preventDefault();
-      handleReSort($(this));
-    });
-    $(document).on("click", 'a.show-proposal', function(event) {
-      event.preventDefault();
-      showProposal($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.hide-proposal', function(event) {
-      event.preventDefault();
-      hideProposal($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.show-propose-change', function(event) {
-      event.preventDefault();
-      showProposeChange($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.hide-propose-change', function(event) {
-      event.preventDefault();
-      hideProposeChange($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.accept-comment', function(event) {
-      event.preventDefault();
-      acceptComment($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.delete-comment', function(event) {
-      event.preventDefault();
-      deleteComment($(this).attr('id').substring(2));
-    });
-    $(document).on("click", 'a.comment-markup', function(event) {
-      event.preventDefault();
-      toggleCommentMarkupBox($(this).attr('id').substring(2));
-    });
-  }
-
-  /**
-   * Set comp, which is a comparator function used for sorting and
-   * inserting comments into the list.
-   */
-  function setComparator() {
-    // If the first three letters are "asc", sort in ascending order
-    // and remove the prefix.
-    if (by.substring(0,3) == 'asc') {
-      var i = by.substring(3);
-      comp = function(a, b) { return a[i] - b[i]; };
-    } else {
-      // Otherwise sort in descending order.
-      comp = function(a, b) { return b[by] - a[by]; };
-    }
-
-    // Reset link styles and format the selected sort option.
-    $('a.sel').attr('href', '#').removeClass('sel');
-    $('a.by' + by).removeAttr('href').addClass('sel');
-  }
-
-  /**
-   * Create a comp function. If the user has preferences stored in
-   * the sortBy cookie, use those, otherwise use the default.
-   */
-  function initComparator() {
-    by = 'rating'; // Default to sort by rating.
-    // If the sortBy cookie is set, use that instead.
-    if (document.cookie.length > 0) {
-      var start = document.cookie.indexOf('sortBy=');
-      if (start != -1) {
-        start = start + 7;
-        var end = document.cookie.indexOf(";", start);
-        if (end == -1) {
-          end = document.cookie.length;
-          by = unescape(document.cookie.substring(start, end));
-        }
-      }
-    }
-    setComparator();
-  }
-
-  /**
-   * Show a comment div.
-   */
-  function show(id) {
-    $('#ao' + id).hide();
-    $('#ah' + id).show();
-    var context = $.extend({id: id}, opts);
-    var popup = $(renderTemplate(popupTemplate, context)).hide();
-    popup.find('textarea[name="proposal"]').hide();
-    popup.find('a.by' + by).addClass('sel');
-    var form = popup.find('#cf' + id);
-    form.submit(function(event) {
-      event.preventDefault();
-      addComment(form);
-    });
-    $('#s' + id).after(popup);
-    popup.slideDown('fast', function() {
-      getComments(id);
-    });
-  }
-
-  /**
-   * Hide a comment div.
-   */
-  function hide(id) {
-    $('#ah' + id).hide();
-    $('#ao' + id).show();
-    var div = $('#sc' + id);
-    div.slideUp('fast', function() {
-      div.remove();
-    });
-  }
-
-  /**
-   * Perform an ajax request to get comments for a node
-   * and insert the comments into the comments tree.
-   */
-  function getComments(id) {
-    $.ajax({
-     type: 'GET',
-     url: opts.getCommentsURL,
-     data: {node: id},
-     success: function(data, textStatus, request) {
-       var ul = $('#cl' + id);
-       var speed = 100;
-       $('#cf' + id)
-         .find('textarea[name="proposal"]')
-         .data('source', data.source);
-
-       if (data.comments.length === 0) {
-         ul.html('<li>No comments yet.</li>');
-         ul.data('empty', true);
-       } else {
-         // If there are comments, sort them and put them in the list.
-         var comments = sortComments(data.comments);
-         speed = data.comments.length * 100;
-         appendComments(comments, ul);
-         ul.data('empty', false);
-       }
-       $('#cn' + id).slideUp(speed + 200);
-       ul.slideDown(speed);
-     },
-     error: function(request, textStatus, error) {
-       showError('Oops, there was a problem retrieving the comments.');
-     },
-     dataType: 'json'
-    });
-  }
-
-  /**
-   * Add a comment via ajax and insert the comment into the comment tree.
-   */
-  function addComment(form) {
-    var node_id = form.find('input[name="node"]').val();
-    var parent_id = form.find('input[name="parent"]').val();
-    var text = form.find('textarea[name="comment"]').val();
-    var proposal = form.find('textarea[name="proposal"]').val();
-
-    if (text == '') {
-      showError('Please enter a comment.');
-      return;
-    }
-
-    // Disable the form that is being submitted.
-    form.find('textarea,input').attr('disabled', 'disabled');
-
-    // Send the comment to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.addCommentURL,
-      dataType: 'json',
-      data: {
-        node: node_id,
-        parent: parent_id,
-        text: text,
-        proposal: proposal
-      },
-      success: function(data, textStatus, error) {
-        // Reset the form.
-        if (node_id) {
-          hideProposeChange(node_id);
-        }
-        form.find('textarea')
-          .val('')
-          .add(form.find('input'))
-          .removeAttr('disabled');
-	var ul = $('#cl' + (node_id || parent_id));
-        if (ul.data('empty')) {
-          $(ul).empty();
-          ul.data('empty', false);
-        }
-        insertComment(data.comment);
-        var ao = $('#ao' + node_id);
-        ao.find('img').attr({'src': opts.commentBrightImage});
-        if (node_id) {
-          // if this was a "root" comment, remove the commenting box
-          // (the user can get it back by reopening the comment popup)
-          $('#ca' + node_id).slideUp();
-        }
-      },
-      error: function(request, textStatus, error) {
-        form.find('textarea,input').removeAttr('disabled');
-        showError('Oops, there was a problem adding the comment.');
-      }
-    });
-  }
-
-  /**
-   * Recursively append comments to the main comment list and children
-   * lists, creating the comment tree.
-   */
-  function appendComments(comments, ul) {
-    $.each(comments, function() {
-      var div = createCommentDiv(this);
-      ul.append($(document.createElement('li')).html(div));
-      appendComments(this.children, div.find('ul.comment-children'));
-      // To avoid stagnating data, don't store the comments children in data.
-      this.children = null;
-      div.data('comment', this);
-    });
-  }
-
-  /**
-   * After adding a new comment, it must be inserted in the correct
-   * location in the comment tree.
-   */
-  function insertComment(comment) {
-    var div = createCommentDiv(comment);
-
-    // To avoid stagnating data, don't store the comments children in data.
-    comment.children = null;
-    div.data('comment', comment);
-
-    var ul = $('#cl' + (comment.node || comment.parent));
-    var siblings = getChildren(ul);
-
-    var li = $(document.createElement('li'));
-    li.hide();
-
-    // Determine where in the parents children list to insert this comment.
-    for(i=0; i < siblings.length; i++) {
-      if (comp(comment, siblings[i]) <= 0) {
-        $('#cd' + siblings[i].id)
-          .parent()
-          .before(li.html(div));
-        li.slideDown('fast');
-        return;
-      }
-    }
-
-    // If we get here, this comment rates lower than all the others,
-    // or it is the only comment in the list.
-    ul.append(li.html(div));
-    li.slideDown('fast');
-  }
-
-  function acceptComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.acceptCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        $('#cm' + id).fadeOut('fast');
-        $('#cd' + id).removeClass('moderate');
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem accepting the comment.');
-      }
-    });
-  }
-
-  function deleteComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.deleteCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        var div = $('#cd' + id);
-        if (data == 'delete') {
-          // Moderator mode: remove the comment and all children immediately
-          div.slideUp('fast', function() {
-            div.remove();
-          });
-          return;
-        }
-        // User mode: only mark the comment as deleted
-        div
-          .find('span.user-id:first')
-          .text('[deleted]').end()
-          .find('div.comment-text:first')
-          .text('[deleted]').end()
-          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
-                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
-          .remove();
-        var comment = div.data('comment');
-        comment.username = '[deleted]';
-        comment.text = '[deleted]';
-        div.data('comment', comment);
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem deleting the comment.');
-      }
-    });
-  }
-
-  function showProposal(id) {
-    $('#sp' + id).hide();
-    $('#hp' + id).show();
-    $('#pr' + id).slideDown('fast');
-  }
-
-  function hideProposal(id) {
-    $('#hp' + id).hide();
-    $('#sp' + id).show();
-    $('#pr' + id).slideUp('fast');
-  }
-
-  function showProposeChange(id) {
-    $('#pc' + id).hide();
-    $('#hc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val(textarea.data('source'));
-    $.fn.autogrow.resize(textarea[0]);
-    textarea.slideDown('fast');
-  }
-
-  function hideProposeChange(id) {
-    $('#hc' + id).hide();
-    $('#pc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val('').removeAttr('disabled');
-    textarea.slideUp('fast');
-  }
-
-  function toggleCommentMarkupBox(id) {
-    $('#mb' + id).toggle();
-  }
-
-  /** Handle when the user clicks on a sort by link. */
-  function handleReSort(link) {
-    var classes = link.attr('class').split(/\s+/);
-    for (var i=0; i<classes.length; i++) {
-      if (classes[i] != 'sort-option') {
-	by = classes[i].substring(2);
-      }
-    }
-    setComparator();
-    // Save/update the sortBy cookie.
-    var expiration = new Date();
-    expiration.setDate(expiration.getDate() + 365);
-    document.cookie= 'sortBy=' + escape(by) +
-                     ';expires=' + expiration.toUTCString();
-    $('ul.comment-ul').each(function(index, ul) {
-      var comments = getChildren($(ul), true);
-      comments = sortComments(comments);
-      appendComments(comments, $(ul).empty());
-    });
-  }
-
-  /**
-   * Function to process a vote when a user clicks an arrow.
-   */
-  function handleVote(link) {
-    if (!opts.voting) {
-      showError("You'll need to login to vote.");
-      return;
-    }
-
-    var id = link.attr('id');
-    if (!id) {
-      // Didn't click on one of the voting arrows.
-      return;
-    }
-    // If it is an unvote, the new vote value is 0,
-    // Otherwise it's 1 for an upvote, or -1 for a downvote.
-    var value = 0;
-    if (id.charAt(1) != 'u') {
-      value = id.charAt(0) == 'u' ? 1 : -1;
-    }
-    // The data to be sent to the server.
-    var d = {
-      comment_id: id.substring(2),
-      value: value
-    };
-
-    // Swap the vote and unvote links.
-    link.hide();
-    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
-      .show();
-
-    // The div the comment is displayed in.
-    var div = $('div#cd' + d.comment_id);
-    var data = div.data('comment');
-
-    // If this is not an unvote, and the other vote arrow has
-    // already been pressed, unpress it.
-    if ((d.value !== 0) && (data.vote === d.value * -1)) {
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
-    }
-
-    // Update the comments rating in the local data.
-    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
-    data.vote = d.value;
-    div.data('comment', data);
-
-    // Change the rating text.
-    div.find('.rating:first')
-      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
-    // Send the vote information to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.processVoteURL,
-      data: d,
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem casting that vote.');
-      }
-    });
-  }
-
-  /**
-   * Open a reply form used to reply to an existing comment.
-   */
-  function openReply(id) {
-    // Swap out the reply link for the hide link
-    $('#rl' + id).hide();
-    $('#cr' + id).show();
-
-    // Add the reply li to the children ul.
-    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
-    $('#cl' + id)
-      .prepend(div)
-      // Setup the submit handler for the reply form.
-      .find('#rf' + id)
-      .submit(function(event) {
-        event.preventDefault();
-        addComment($('#rf' + id));
-        closeReply(id);
-      })
-      .find('input[type=button]')
-      .click(function() {
-        closeReply(id);
-      });
-    div.slideDown('fast', function() {
-      $('#rf' + id).find('textarea').focus();
-    });
-  }
-
-  /**
-   * Close the reply form opened with openReply.
-   */
-  function closeReply(id) {
-    // Remove the reply div from the DOM.
-    $('#rd' + id).slideUp('fast', function() {
-      $(this).remove();
-    });
-
-    // Swap out the hide link for the reply link
-    $('#cr' + id).hide();
-    $('#rl' + id).show();
-  }
-
-  /**
-   * Recursively sort a tree of comments using the comp comparator.
-   */
-  function sortComments(comments) {
-    comments.sort(comp);
-    $.each(comments, function() {
-      this.children = sortComments(this.children);
-    });
-    return comments;
-  }
-
-  /**
-   * Get the children comments from a ul. If recursive is true,
-   * recursively include childrens' children.
-   */
-  function getChildren(ul, recursive) {
-    var children = [];
-    ul.children().children("[id^='cd']")
-      .each(function() {
-        var comment = $(this).data('comment');
-        if (recursive)
-          comment.children = getChildren($(this).find('#cl' + comment.id), true);
-        children.push(comment);
-      });
-    return children;
-  }
-
-  /** Create a div to display a comment in. */
-  function createCommentDiv(comment) {
-    if (!comment.displayed && !opts.moderator) {
-      return $('<div class="moderate">Thank you!  Your comment will show up '
-               + 'once it is has been approved by a moderator.</div>');
-    }
-    // Prettify the comment rating.
-    comment.pretty_rating = comment.rating + ' point' +
-      (comment.rating == 1 ? '' : 's');
-    // Make a class (for displaying not yet moderated comments differently)
-    comment.css_class = comment.displayed ? '' : ' moderate';
-    // Create a div for this comment.
-    var context = $.extend({}, opts, comment);
-    var div = $(renderTemplate(commentTemplate, context));
-
-    // If the user has voted on this comment, highlight the correct arrow.
-    if (comment.vote) {
-      var direction = (comment.vote == 1) ? 'u' : 'd';
-      div.find('#' + direction + 'v' + comment.id).hide();
-      div.find('#' + direction + 'u' + comment.id).show();
-    }
-
-    if (opts.moderator || comment.text != '[deleted]') {
-      div.find('a.reply').show();
-      if (comment.proposal_diff)
-        div.find('#sp' + comment.id).show();
-      if (opts.moderator && !comment.displayed)
-        div.find('#cm' + comment.id).show();
-      if (opts.moderator || (opts.username == comment.username))
-        div.find('#dc' + comment.id).show();
-    }
-    return div;
-  }
-
-  /**
-   * A simple template renderer. Placeholders such as <%id%> are replaced
-   * by context['id'] with items being escaped. Placeholders such as <#id#>
-   * are not escaped.
-   */
-  function renderTemplate(template, context) {
-    var esc = $(document.createElement('div'));
-
-    function handle(ph, escape) {
-      var cur = context;
-      $.each(ph.split('.'), function() {
-        cur = cur[this];
-      });
-      return escape ? esc.text(cur || "").html() : cur;
-    }
-
-    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
-      return handle(arguments[2], arguments[1] == '%' ? true : false);
-    });
-  }
-
-  /** Flash an error message briefly. */
-  function showError(message) {
-    $(document.createElement('div')).attr({'class': 'popup-error'})
-      .append($(document.createElement('div'))
-               .attr({'class': 'error-message'}).text(message))
-      .appendTo('body')
-      .fadeIn("slow")
-      .delay(2000)
-      .fadeOut("slow");
-  }
-
-  /** Add a link the user uses to open the comments popup. */
-  $.fn.comment = function() {
-    return this.each(function() {
-      var id = $(this).attr('id').substring(1);
-      var count = COMMENT_METADATA[id];
-      var title = count + ' comment' + (count == 1 ? '' : 's');
-      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
-      var addcls = count == 0 ? ' nocomment' : '';
-      $(this)
-        .append(
-          $(document.createElement('a')).attr({
-            href: '#',
-            'class': 'sphinx-comment-open' + addcls,
-            id: 'ao' + id
-          })
-            .append($(document.createElement('img')).attr({
-              src: image,
-              alt: 'comment',
-              title: title
-            }))
-            .click(function(event) {
-              event.preventDefault();
-              show($(this).attr('id').substring(2));
-            })
-        )
-        .append(
-          $(document.createElement('a')).attr({
-            href: '#',
-            'class': 'sphinx-comment-close hidden',
-            id: 'ah' + id
-          })
-            .append($(document.createElement('img')).attr({
-              src: opts.closeCommentImage,
-              alt: 'close',
-              title: 'close'
-            }))
-            .click(function(event) {
-              event.preventDefault();
-              hide($(this).attr('id').substring(2));
-            })
-        );
-    });
-  };
-
-  var opts = {
-    processVoteURL: '/_process_vote',
-    addCommentURL: '/_add_comment',
-    getCommentsURL: '/_get_comments',
-    acceptCommentURL: '/_accept_comment',
-    deleteCommentURL: '/_delete_comment',
-    commentImage: '/static/_static/comment.png',
-    closeCommentImage: '/static/_static/comment-close.png',
-    loadingImage: '/static/_static/ajax-loader.gif',
-    commentBrightImage: '/static/_static/comment-bright.png',
-    upArrow: '/static/_static/up.png',
-    downArrow: '/static/_static/down.png',
-    upArrowPressed: '/static/_static/up-pressed.png',
-    downArrowPressed: '/static/_static/down-pressed.png',
-    voting: false,
-    moderator: false
-  };
-
-  if (typeof COMMENT_OPTIONS != "undefined") {
-    opts = jQuery.extend(opts, COMMENT_OPTIONS);
-  }
-
-  var popupTemplate = '\
-    <div class="sphinx-comments" id="sc<%id%>">\
-      <p class="sort-options">\
-        Sort by:\
-        <a href="#" class="sort-option byrating">best rated</a>\
-        <a href="#" class="sort-option byascage">newest</a>\
-        <a href="#" class="sort-option byage">oldest</a>\
-      </p>\
-      <div class="comment-header">Comments</div>\
-      <div class="comment-loading" id="cn<%id%>">\
-        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
-      <ul id="cl<%id%>" class="comment-ul"></ul>\
-      <div id="ca<%id%>">\
-      <p class="add-a-comment">Add a comment\
-        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
-      <div class="comment-markup-box" id="mb<%id%>">\
-        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
-        <code>``code``</code>, \
-        code blocks: <code>::</code> and an indented block after blank line</div>\
-      <form method="post" id="cf<%id%>" class="comment-form" action="">\
-        <textarea name="comment" cols="80"></textarea>\
-        <p class="propose-button">\
-          <a href="#" id="pc<%id%>" class="show-propose-change">\
-            Propose a change &#9657;\
-          </a>\
-          <a href="#" id="hc<%id%>" class="hide-propose-change">\
-            Propose a change &#9663;\
-          </a>\
-        </p>\
-        <textarea name="proposal" id="pt<%id%>" cols="80"\
-                  spellcheck="false"></textarea>\
-        <input type="submit" value="Add comment" />\
-        <input type="hidden" name="node" value="<%id%>" />\
-        <input type="hidden" name="parent" value="" />\
-      </form>\
-      </div>\
-    </div>';
-
-  var commentTemplate = '\
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-<p>Soil is an Agent-based Social Simulator in Python for modelling and simulation of Social Networks.</p>
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-<p>This document describes how to develop a new analysis model.</p>
-<div class="section" id="what-is-a-model">
-<h2>What is a model?<a class="headerlink" href="#what-is-a-model" title="Permalink to this headline">¶</a></h2>
-<p>A model defines the behaviour of the agents with a view to assessing their effects on the system as a whole.
-In practice, a model consists of at least two parts:</p>
-<ul class="simple">
-<li>Python module: the actual code that describes the behaviour.</li>
-<li>Setting up the variables in the Settings JSON file.</li>
-</ul>
-<p>This separation allows us to run the simulation with different agents.</p>
-</div>
-<div class="section" id="models-code">
-<h2>Models Code<a class="headerlink" href="#models-code" title="Permalink to this headline">¶</a></h2>
-<p>All the models are imported to the main file. The initialization look like this:</p>
-<div class="code python highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">settings</span>
-
-<span class="n">networkStatus</span> <span class="o">=</span> <span class="p">{}</span>  <span class="c1"># Dict that will contain the status of every agent in the network</span>
-
-<span class="n">sentimentCorrelationNodeArray</span> <span class="o">=</span> <span class="p">[]</span>
-<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">settings</span><span class="o">.</span><span class="n">network_params</span><span class="p">[</span><span class="s2">&quot;number_of_nodes&quot;</span><span class="p">]):</span>
-    <span class="n">sentimentCorrelationNodeArray</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="n">x</span><span class="p">})</span>
-<span class="c1"># Initialize agent states. Let&#39;s assume everyone is normal.</span>
-<span class="n">init_states</span> <span class="o">=</span> <span class="p">[{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="mi">0</span><span class="p">,</span> <span class="p">}</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">network_params</span><span class="p">[</span><span class="s2">&quot;number_of_nodes&quot;</span><span class="p">])]</span>
-    <span class="c1"># add keys as as necessary, but &quot;id&quot; must always refer to that state category</span>
-</pre></div>
-</div>
-<p>A new model have to inherit the BaseBehaviour class which is in the same module.
-There are two basics methods:</p>
-<ul class="simple">
-<li>__init__</li>
-<li>step: used to define the behaviour over time.</li>
-</ul>
-</div>
-<div class="section" id="variable-initialization">
-<h2>Variable Initialization<a class="headerlink" href="#variable-initialization" title="Permalink to this headline">¶</a></h2>
-<p>The different parameters of the model have to be initialize in the Simulation Settings JSON file which will be
-passed as a parameter to the simulation.</p>
-<div class="code json highlight-default"><div class="highlight"><pre><span></span><span class="p">{</span>
-    <span class="s2">&quot;agent&quot;</span><span class="p">:</span> <span class="p">[</span><span class="s2">&quot;SISaModel&quot;</span><span class="p">,</span><span class="s2">&quot;ControlModelM2&quot;</span><span class="p">],</span>
-
-    <span class="s2">&quot;neutral_discontent_spon_prob&quot;</span><span class="p">:</span> <span class="mf">0.04</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_discontent_infected_prob&quot;</span><span class="p">:</span> <span class="mf">0.04</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_content_spon_prob&quot;</span><span class="p">:</span> <span class="mf">0.18</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_content_infected_prob&quot;</span><span class="p">:</span> <span class="mf">0.02</span><span class="p">,</span>
-
-    <span class="s2">&quot;discontent_neutral&quot;</span><span class="p">:</span> <span class="mf">0.13</span><span class="p">,</span>
-    <span class="s2">&quot;discontent_content&quot;</span><span class="p">:</span> <span class="mf">0.07</span><span class="p">,</span>
-    <span class="s2">&quot;variance_d_c&quot;</span><span class="p">:</span> <span class="mf">0.02</span><span class="p">,</span>
-
-    <span class="s2">&quot;content_discontent&quot;</span><span class="p">:</span> <span class="mf">0.009</span><span class="p">,</span>
-    <span class="s2">&quot;variance_c_d&quot;</span><span class="p">:</span> <span class="mf">0.003</span><span class="p">,</span>
-    <span class="s2">&quot;content_neutral&quot;</span><span class="p">:</span> <span class="mf">0.088</span><span class="p">,</span>
-
-    <span class="s2">&quot;standard_variance&quot;</span><span class="p">:</span> <span class="mf">0.055</span><span class="p">,</span>
-
-
-    <span class="s2">&quot;prob_neutral_making_denier&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_infect&quot;</span><span class="p">:</span> <span class="mf">0.075</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_cured_healing_infected&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_cured_vaccinate_neutral&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_vaccinated_healing_infected&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_vaccinated_vaccinate_neutral&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_generate_anti_rumor&quot;</span><span class="p">:</span> <span class="mf">0.035</span>
-<span class="p">}</span>
-</pre></div>
-</div>
-<p>In this file you will also define the models you are going to simulate. You can simulate as many models as you want.
-The simulation returns one result for each model, executing each model separately. For the usage, see <a class="reference internal" href="usage.html"><span class="doc">Usage</span></a>.</p>
-</div>
-<div class="section" id="example-model">
-<h2>Example Model<a class="headerlink" href="#example-model" title="Permalink to this headline">¶</a></h2>
-<p>In this section, we will implement a Sentiment Correlation Model.</p>
-<p>The class would look like this:</p>
-<div class="code python highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">..BaseBehaviour</span> <span class="k">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">..</span> <span class="k">import</span> <span class="n">sentimentCorrelationNodeArray</span>
-
-<span class="k">class</span> <span class="nc">SentimentCorrelationModel</span><span class="p">(</span><span class="n">BaseBehaviour</span><span class="p">):</span>
-
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">environment</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">agent_id</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">state</span><span class="o">=</span><span class="p">()):</span>
-        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="n">environment</span><span class="o">=</span><span class="n">environment</span><span class="p">,</span> <span class="n">agent_id</span><span class="o">=</span><span class="n">agent_id</span><span class="p">,</span> <span class="n">state</span><span class="o">=</span><span class="n">state</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">outside_effects_prob</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">environment_params</span><span class="p">[</span><span class="s1">&#39;outside_effects_prob&#39;</span><span class="p">]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">anger_prob</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">environment_params</span><span class="p">[</span><span class="s1">&#39;anger_prob&#39;</span><span class="p">]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">joy_prob</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">environment_params</span><span class="p">[</span><span class="s1">&#39;joy_prob&#39;</span><span class="p">]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">sadness_prob</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">environment_params</span><span class="p">[</span><span class="s1">&#39;sadness_prob&#39;</span><span class="p">]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">disgust_prob</span> <span class="o">=</span> <span class="n">environment</span><span class="o">.</span><span class="n">environment_params</span><span class="p">[</span><span class="s1">&#39;disgust_prob&#39;</span><span class="p">]</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">time_awareness</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">4</span><span class="p">):</span>  <span class="c1"># In this model we have 4 sentiments</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">time_awareness</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>  <span class="c1"># 0-&gt; Anger, 1-&gt; joy, 2-&gt;sadness, 3 -&gt; disgust</span>
-        <span class="n">sentimentCorrelationNodeArray</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">id</span><span class="p">][</span><span class="bp">self</span><span class="o">.</span><span class="n">env</span><span class="o">.</span><span class="n">now</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
-
-    <span class="k">def</span> <span class="nf">step</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">now</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">behaviour</span><span class="p">()</span>  <span class="c1"># Method which define the behaviour</span>
-        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">step</span><span class="p">(</span><span class="n">now</span><span class="p">)</span>
-</pre></div>
-</div>
-<p>The variables will be modified by the user, so you have to include them in the Simulation Settings JSON file.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Developing new models</a><ul>
-<li><a class="reference internal" href="#what-is-a-model">What is a model?</a></li>
-<li><a class="reference internal" href="#models-code">Models Code</a></li>
-<li><a class="reference internal" href="#variable-initialization">Variable Initialization</a></li>
-<li><a class="reference internal" href="#example-model">Example Model</a></li>
-</ul>
-</li>
-</ul>
-<div class="relations">
-<h3>Related Topics</h3>
-<ul>
-  <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="usage.html" title="previous chapter">Usage</a></li>
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-          <div class="body" role="main">
-            
-  <div class="section" id="usage">
-<h1>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h1>
-<p>First of all, you need to install the package. See <a class="reference internal" href="installation.html"><span class="doc">Installation</span></a> for installation instructions.</p>
-<div class="section" id="simulation-settings">
-<h2>Simulation Settings<a class="headerlink" href="#simulation-settings" title="Permalink to this headline">¶</a></h2>
-<p>Once installed, before running a simulation, you need to configure it.</p>
-<ul>
-<li><p class="first">In the Settings JSON file you will find the configuration of the network.</p>
-<div class="code python highlight-default"><div class="highlight"><pre><span></span><span class="p">{</span>
-    <span class="s2">&quot;network_type&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
-    <span class="s2">&quot;number_of_nodes&quot;</span><span class="p">:</span> <span class="mi">1000</span><span class="p">,</span>
-    <span class="s2">&quot;max_time&quot;</span><span class="p">:</span> <span class="mi">50</span><span class="p">,</span>
-    <span class="s2">&quot;num_trials&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
-    <span class="s2">&quot;timeout&quot;</span><span class="p">:</span> <span class="mi">2</span>
-<span class="p">}</span>
-</pre></div>
-</div>
-</li>
-<li><p class="first">In the Settings JSON file, you will also find the configuration of the models.</p>
-</li>
-</ul>
-</div>
-<div class="section" id="network-types">
-<h2>Network Types<a class="headerlink" href="#network-types" title="Permalink to this headline">¶</a></h2>
-<p>There are three types of network implemented, but you could add more.</p>
-<div class="code python highlight-default"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="n">settings</span><span class="o">.</span><span class="n">network_type</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-    <span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">complete_graph</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">)</span>
-<span class="k">if</span> <span class="n">settings</span><span class="o">.</span><span class="n">network_type</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
-    <span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">barabasi_albert_graph</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
-<span class="k">if</span> <span class="n">settings</span><span class="o">.</span><span class="n">network_type</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
-    <span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">margulis_gabber_galil_graph</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
-<span class="c1"># More types of networks can be added here</span>
-</pre></div>
-</div>
-</div>
-<div class="section" id="models-settings">
-<h2>Models Settings<a class="headerlink" href="#models-settings" title="Permalink to this headline">¶</a></h2>
-<p>After having configured the simulation, the next step is setting up the variables of the models.
-For this, you will need to modify the Settings JSON file again.</p>
-<div class="code json highlight-default"><div class="highlight"><pre><span></span><span class="p">{</span>
-    <span class="s2">&quot;agent&quot;</span><span class="p">:</span> <span class="p">[</span><span class="s2">&quot;SISaModel&quot;</span><span class="p">,</span><span class="s2">&quot;ControlModelM2&quot;</span><span class="p">],</span>
-
-    <span class="s2">&quot;neutral_discontent_spon_prob&quot;</span><span class="p">:</span> <span class="mf">0.04</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_discontent_infected_prob&quot;</span><span class="p">:</span> <span class="mf">0.04</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_content_spon_prob&quot;</span><span class="p">:</span> <span class="mf">0.18</span><span class="p">,</span>
-    <span class="s2">&quot;neutral_content_infected_prob&quot;</span><span class="p">:</span> <span class="mf">0.02</span><span class="p">,</span>
-
-    <span class="s2">&quot;discontent_neutral&quot;</span><span class="p">:</span> <span class="mf">0.13</span><span class="p">,</span>
-    <span class="s2">&quot;discontent_content&quot;</span><span class="p">:</span> <span class="mf">0.07</span><span class="p">,</span>
-    <span class="s2">&quot;variance_d_c&quot;</span><span class="p">:</span> <span class="mf">0.02</span><span class="p">,</span>
-
-    <span class="s2">&quot;content_discontent&quot;</span><span class="p">:</span> <span class="mf">0.009</span><span class="p">,</span>
-    <span class="s2">&quot;variance_c_d&quot;</span><span class="p">:</span> <span class="mf">0.003</span><span class="p">,</span>
-    <span class="s2">&quot;content_neutral&quot;</span><span class="p">:</span> <span class="mf">0.088</span><span class="p">,</span>
-
-    <span class="s2">&quot;standard_variance&quot;</span><span class="p">:</span> <span class="mf">0.055</span><span class="p">,</span>
-
-
-    <span class="s2">&quot;prob_neutral_making_denier&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_infect&quot;</span><span class="p">:</span> <span class="mf">0.075</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_cured_healing_infected&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_cured_vaccinate_neutral&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-
-    <span class="s2">&quot;prob_vaccinated_healing_infected&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_vaccinated_vaccinate_neutral&quot;</span><span class="p">:</span> <span class="mf">0.035</span><span class="p">,</span>
-    <span class="s2">&quot;prob_generate_anti_rumor&quot;</span><span class="p">:</span> <span class="mf">0.035</span>
-<span class="p">}</span>
-</pre></div>
-</div>
-<p>In this file you will define the different models you are going to simulate. You can simulate as many models
-as you want. Each model will be simulated separately.</p>
-<p>After setting up the models, you have to initialize the parameters of each one. You will find the parameters needed
-in the documentation of each model.</p>
-<p>Parameter validation will fail if a required parameter without a default has not been provided.</p>
-</div>
-<div class="section" id="running-the-simulation">
-<h2>Running the Simulation<a class="headerlink" href="#running-the-simulation" title="Permalink to this headline">¶</a></h2>
-<p>After setting all the configuration, you will be able to run the simulation. All you need to do is execute:</p>
-<div class="code bash highlight-default"><div class="highlight"><pre><span></span><span class="n">python3</span> <span class="n">soil</span><span class="o">.</span><span class="n">py</span>
-</pre></div>
-</div>
-<p>The simulation will return a dynamic graph .gexf file which could be visualized with
-<a class="reference external" href="https://gephi.org/users/download/">Gephi</a>.</p>
-<p>It will also return one .png picture for each model simulated.</p>
-</div>
-</div>
-
-
-          </div>
-        </div>
-      </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="index.html">Table Of Contents</a></h3>
-  <ul>
-<li><a class="reference internal" href="#">Usage</a><ul>
-<li><a class="reference internal" href="#simulation-settings">Simulation Settings</a></li>
-<li><a class="reference internal" href="#network-types">Network Types</a></li>
-<li><a class="reference internal" href="#models-settings">Models Settings</a></li>
-<li><a class="reference internal" href="#running-the-simulation">Running the Simulation</a></li>
-</ul>
-</li>
-</ul>
-<div class="relations">
-<h3>Related Topics</h3>
-<ul>
-  <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="installation.html" title="previous chapter">Installation</a></li>
-      <li>Next: <a href="models.html" title="next chapter">Developing new models</a></li>
-  </ul></li>
-</ul>
-</div>
-  <div role="note" aria-label="source link">
-    <h3>This Page</h3>
-    <ul class="this-page-menu">
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-            rel="nofollow">Show Source</a></li>
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docs/configuration.rst

@@ -0,0 +1,244 @@
+Configuring a simulation
+------------------------
+
+There are two ways to configure a simulation: programmatically and with a configuration file.
+In both cases, the parameters used are the same.
+The advantage of a configuration file is that it is a clean declarative description, and it makes it easier to reproduce.
+
+Simulation configuration files can be formatted in ``json`` or ``yaml`` and they define all the parameters of a simulation.
+Here's an example (``example.yml``).
+
+.. code:: yaml
+          
+    ---
+    name: MyExampleSimulation
+    max_time: 50
+    num_trials: 3
+    interval: 2
+    network_params:
+        generator: barabasi_albert_graph
+        n: 100
+        m: 2
+    network_agents:
+        - agent_type: SISaModel
+           weight: 1
+            state:
+            id: content
+        - agent_type: SISaModel
+            weight: 1
+            state:
+            id: discontent
+        - agent_type: SISaModel
+            weight: 8
+            state:
+            id: neutral
+    environment_params:
+        prob_infect: 0.075
+
+
+This example configuration will run three trials (``num_trials``) of a simulation containing a randomly generated network (``network_params``).
+The 100 nodes in the network will be SISaModel agents (``network_agents.agent_type``), which is an agent behavior that is included in Soil.
+10% of the agents (``weight=1``) will start in the content state, 10% in the discontent state, and the remaining 80% (``weight=8``) in the neutral state.
+All agents will have access to the environment (``environment_params``), which only contains one variable, ``prob_infected``.
+The state of the agents will be updated every 2 seconds (``interval``).
+
+Now run the simulation with the command line tool:
+
+.. code:: bash
+
+   soil example.yml
+
+Once the simulation finishes, its results will be stored in a folder named ``MyExampleSimulation``.
+Three types of objects are saved by default: a pickle of the simulation; a ``YAML`` representation of the simulation (which can be used to re-launch it); and for every trial, a ``sqlite`` file with the content of the state of every network node and the environment parameters at every step of the simulation.
+
+
+.. code::
+
+    soil_output
+    └── MyExampleSimulation
+        ├── MyExampleSimulation.dumped.yml
+        ├── MyExampleSimulation.simulation.pickle
+        ├── MyExampleSimulation_trial_0.db.sqlite
+        ├── MyExampleSimulation_trial_1.db.sqlite
+        └── MyExampleSimulation_trial_2.db.sqlite
+
+
+You may also ask soil to export the states in a ``csv`` file, and the network in gephi format (``gexf``).
+
+Network
+=======
+
+The network topology for the simulation can be loaded from an existing network file or generated with one of the random network generation methods from networkx.
+
+Loading a network
+#################
+
+To load an existing network, specify its path in the configuration:
+
+.. code:: yaml
+
+   ---
+   network_params:
+      path: /tmp/mynetwork.gexf
+
+Soil will try to guess what networkx method to use to read the file based on its extension.
+However, we only test using ``gexf`` files.
+
+For simple networks, you may also include them in the configuration itself using , using the ``topology`` parameter like so:
+
+.. code:: yaml
+
+   ---
+   topology:
+       nodes:
+          - id: First
+          - id: Second
+       links:
+          - source: First
+            target: Second
+
+
+Generating a random network
+###########################
+
+To generate a random network using one of networkx's built-in methods, specify the `graph generation algorithm <https://networkx.github.io/documentation/development/reference/generators.html>`_ and other parameters.
+For example, the following configuration is equivalent to :code:`nx.complete_graph(n=100)`:
+
+.. code:: yaml
+
+    network_params:
+        generator: complete_graph
+        n: 100
+
+Environment
+============
+The environment is the place where the shared state of the simulation is stored.
+For instance, the probability of disease outbreak.
+The configuration file may specify the initial value of the environment parameters:
+
+.. code:: yaml
+
+    environment_params:
+        daily_probability_of_earthquake: 0.001
+        number_of_earthquakes: 0
+
+All agents have access to the environment parameters.
+
+In some scenarios, it is useful to have a custom environment, to provide additional methods or to control the way agents update environment state.
+For example, if our agents play the lottery, the environment could provide a method to decide whether the agent wins, instead of leaving it to the agent.
+
+
+Agents
+======
+Agents are a way of modelling behavior.
+Agents can be characterized with two variables: agent type (``agent_type``) and state.
+Only one agent is executed at a time (generally, every ``interval`` seconds), and it has access to its state and the environment parameters.
+Through the environment, it can access the network topology and the state of other agents.
+
+There are three three types of agents according to how they are added to the simulation: network agents and environment agent.
+
+Network Agents
+##############
+Network agents are attached to a node in the topology.
+The configuration file allows you to specify how agents will be mapped to topology nodes.
+
+The simplest way is to specify a single type of agent.
+Hence, every node in the network will be associated to an agent of that type.
+
+.. code:: yaml
+
+   agent_type: SISaModel
+
+It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (using the ``weight`` property).
+For instance, with following configuration, it is five times more likely for a node to be assigned a CounterModel type than a SISaModel type.
+
+.. code:: yaml
+
+    network_agents:
+          - agent_type: SISaModel
+            weight: 1
+          - agent_type: CounterModel
+            weight: 5
+
+The third option is to specify the type of agent on the node itself, e.g.:
+
+
+.. code:: yaml
+
+   topology:
+       nodes:
+           - id: first
+   agent_type: BaseAgent
+   states:
+       first:
+         agent_type: SISaModel
+          
+
+This would also work with a randomly generated network:
+
+
+.. code:: yaml
+
+   network:
+       generator: complete
+       n: 5
+   agent_type: BaseAgent
+   states:
+       - agent_type: SISaModel
+
+              
+
+In addition to agent type, you may add a custom initial state to the distribution.
+This is very useful to add the same agent type with different states.
+e.g., to populate the network with SISaModel, roughly 10% of them with a discontent state:
+
+.. code:: yaml
+
+    network_agents:
+        - agent_type: SISaModel
+            weight: 9
+            state:
+            id: neutral
+        - agent_type: SISaModel
+            weight: 1
+            state:
+            id: discontent
+
+Lastly, the configuration may include initial state for one or more nodes.
+For instance, to add a state for the two nodes in this configuration:
+
+.. code:: yaml
+
+   agent_type: SISaModel
+   network:
+      generator: complete_graph
+      n: 2
+   states:
+     - id: content
+     - id: discontent
+
+
+Or to add state only to specific nodes (by ``id``).
+For example, to apply special skills to Linux Torvalds in a simulation:
+
+.. literalinclude:: ../examples/torvalds.yml
+   :language: yaml
+
+
+Environment Agents
+##################
+In addition to network agents, more agents can be added to the simulation.
+These agents are programmed in much the same way as network agents, the only difference is that they will not be assigned to network nodes.
+
+
+.. code::
+
+   environment_agents:
+       - agent_type: MyAgent
+         state:
+           mood: happy
+       - agent_type: DummyAgent
+
+
+You may use environment agents to model events that a normal agent cannot control, such as natural disasters or chance.
+They are also useful to add behavior that has little to do with the network and the interactions within that network.

docs/index.rst

@@ -6,16 +6,43 @@
 Welcome to Soil's documentation!
 ================================
 
-Soil is an Agent-based Social Simulator in Python for modelling and simulation of Social Networks.
+Soil is an Agent-based Social Simulator in Python focused on Social Networks.
+
+If you use Soil in your research, do not forget to cite this paper:
+
+.. code:: bibtex
+
+    @inbook{soil-gsi-conference-2017,
+        author = "S{\'a}nchez, Jes{\'u}s M. and Iglesias, Carlos A. and S{\'a}nchez-Rada, J. Fernando",
+        booktitle = "Advances in Practical Applications of Cyber-Physical Multi-Agent Systems: The PAAMS Collection",
+        doi = "10.1007/978-3-319-59930-4_19",
+        editor = "Demazeau Y., Davidsson P., Bajo J., Vale Z.",
+        isbn = "978-3-319-59929-8",
+        keywords = "soil;social networks;agent based social simulation;python",
+        month = "June",
+        organization = "PAAMS 2017",
+        pages = "234-245",
+        publisher = "Springer Verlag",
+        series = "LNAI",
+        title = "{S}oil: {A}n {A}gent-{B}ased {S}ocial {S}imulator in {P}ython for {M}odelling and {S}imulation of {S}ocial {N}etworks",
+        url = "https://link.springer.com/chapter/10.1007/978-3-319-59930-4_19",
+        volume = "10349",
+        year = "2017",
+    }
+
+
+
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 0
    :caption: Learn more about soil:
 
    installation
-   usage
-   models
+   quickstart
+   configuration
+   Tutorial <soil_tutorial>
 
+..
 
 
 .. Indices and tables

docs/installation.rst

@@ -1,7 +1,24 @@
 Installation
 ------------
-The latest version can be installed through GitLab.
+
+The easiest way to install Soil is through pip, with Python >= 3.4:
 
 .. code:: bash
 
-   git clone https://lab.cluster.gsi.dit.upm.es/soil/soil.git
+   pip install soil
+
+
+Now test that it worked by running the command line tool
+
+.. code:: bash
+
+   soil --help
+
+Or using soil programmatically:
+
+.. code:: python
+
+   import soil
+   print(soil.__version__)
+
+The latest version can be installed through `GitLab <https://lab.cluster.gsi.dit.upm.es/soil/soil.git>`_.

docs/models.rst

@@ -1,112 +0,0 @@
-Developing new models
----------------------
-This document describes how to develop a new analysis model.
-
-What is a model?
-================
-
-A model defines the behaviour of the agents with a view to assessing their effects on the system as a whole.
-In practice, a model consists of at least two parts:
-
-* Python module: the actual code that describes the behaviour.
-* Setting up the variables in the Settings JSON file.
-
-This separation allows us to run the simulation with different agents.
-
-Models Code
-===========
-
-All the models are imported to the main file. The initialization look like this:
-
-.. code:: python
-
-    import settings
-
-    networkStatus = {}  # Dict that will contain the status of every agent in the network
-
-    sentimentCorrelationNodeArray = []
-    for x in range(0, settings.network_params["number_of_nodes"]):
-        sentimentCorrelationNodeArray.append({'id': x})
-    # Initialize agent states. Let's assume everyone is normal.
-    init_states = [{'id': 0, } for _ in range(settings.network_params["number_of_nodes"])]
-        # add keys as as necessary, but "id" must always refer to that state category
-
-A new model have to inherit the BaseBehaviour class which is in the same module.
-There are two basics methods:
-
-* __init__
-* step: used to define the behaviour over time.
-
-Variable Initialization
-=======================
-
-The different parameters of the model have to be initialize in the Simulation Settings JSON file which will be
-passed as a parameter to the simulation.
-
-.. code:: json
-
-    {
-        "agent": ["SISaModel","ControlModelM2"],
-
-        "neutral_discontent_spon_prob": 0.04,
-        "neutral_discontent_infected_prob": 0.04,
-        "neutral_content_spon_prob": 0.18,
-        "neutral_content_infected_prob": 0.02,
-
-        "discontent_neutral": 0.13,
-        "discontent_content": 0.07,
-        "variance_d_c": 0.02,
-
-        "content_discontent": 0.009,
-        "variance_c_d": 0.003,
-        "content_neutral": 0.088,
-
-        "standard_variance": 0.055,
-
-
-        "prob_neutral_making_denier": 0.035,
-
-        "prob_infect": 0.075,
-
-        "prob_cured_healing_infected": 0.035,
-        "prob_cured_vaccinate_neutral": 0.035,
-
-        "prob_vaccinated_healing_infected": 0.035,
-        "prob_vaccinated_vaccinate_neutral": 0.035,
-        "prob_generate_anti_rumor": 0.035
-    }
-
-In this file you will also define the models you are going to simulate. You can simulate as many models as you want.
-The simulation returns one result for each model, executing each model separately. For the usage, see :doc:`usage`.
-
-Example Model
-=============
-
-In this section, we will implement a Sentiment Correlation Model.
-
-The class would look like this:
-
-.. code:: python
-
-    from ..BaseBehaviour import *
-    from .. import sentimentCorrelationNodeArray
-
-    class SentimentCorrelationModel(BaseBehaviour):
-
-        def __init__(self, environment=None, agent_id=0, state=()):
-            super().__init__(environment=environment, agent_id=agent_id, state=state)
-            self.outside_effects_prob = environment.environment_params['outside_effects_prob']
-            self.anger_prob = environment.environment_params['anger_prob']
-            self.joy_prob = environment.environment_params['joy_prob']
-            self.sadness_prob = environment.environment_params['sadness_prob']
-            self.disgust_prob = environment.environment_params['disgust_prob']
-            self.time_awareness = []
-            for i in range(4):  # In this model we have 4 sentiments
-                self.time_awareness.append(0)  # 0-> Anger, 1-> joy, 2->sadness, 3 -> disgust
-            sentimentCorrelationNodeArray[self.id][self.env.now] = 0
-
-        def step(self, now):
-            self.behaviour()  # Method which define the behaviour
-            super().step(now)
-
-The variables will be modified by the user, so you have to include them in the Simulation Settings JSON file.

docs/quickstart.rst

@@ -0,0 +1,93 @@
+Quickstart
+----------
+
+This section shows how to run your first simulation with Soil.
+For installation instructions, see :doc:`installation`.
+
+There are mainly two parts in a simulation: agent classes and simulation configuration.
+An agent class defines how the agent will behave throughout the simulation.
+The configuration includes things such as number of agents to use and their type, network topology to use, etc.
+
+
+.. image:: soil.png
+  :width: 80%
+  :align: center
+
+
+Soil includes several agent classes in the ``soil.agents`` module, and we will use them in this quickstart.
+If you are interested in developing your own agents classes, see :doc:`soil_tutorial`.
+
+Configuration
+=============
+To get you started, we will use this configuration (:download:`download the file <quickstart.yml>` directly):
+
+.. literalinclude:: quickstart.yml
+   :language: yaml
+
+The agent type used, SISa, is a very simple model.
+It only has three states (neutral, content and discontent),
+Its parameters are the probabilities to change from one state to another, either spontaneously or because of contagion from neighboring agents.
+
+Running the simulation
+======================
+
+To see the simulation in action, simply point soil to the configuration, and tell it to store the graph and the history of agent states and environment parameters at every point.
+
+.. code::
+
+    ❯ soil --graph --csv quickstart.yml                                                          [13:35:29]
+    INFO:soil:Using config(s): quickstart
+    INFO:soil:Dumping results to soil_output/quickstart : ['csv', 'gexf']
+    INFO:soil:Starting simulation quickstart at 13:35:30.
+    INFO:soil:Starting Simulation quickstart trial 0 at 13:35:30.
+    INFO:soil:Finished Simulation quickstart trial 0 at 13:35:49 in 19.43677067756653 seconds
+    INFO:soil:Starting Dumping simulation quickstart trial 0 at 13:35:49.
+    INFO:soil:Finished Dumping simulation quickstart trial 0 at 13:35:51 in 1.7733407020568848 seconds
+    INFO:soil:Dumping results to soil_output/quickstart
+    INFO:soil:Finished simulation quickstart at 13:35:51 in 21.29862952232361 seconds
+
+
+The ``CSV`` file should look like this:
+
+.. code::
+
+   agent_id,t_step,key,value
+   env,0,neutral_discontent_spon_prob,0.05
+   env,0,neutral_discontent_infected_prob,0.1
+   env,0,neutral_content_spon_prob,0.2
+   env,0,neutral_content_infected_prob,0.4
+   env,0,discontent_neutral,0.2
+   env,0,discontent_content,0.05
+   env,0,content_discontent,0.05
+   env,0,variance_d_c,0.05
+   env,0,variance_c_d,0.1
+
+Results and visualization
+=========================
+
+The environment variables are marked as ``agent_id`` env.
+Th exported values are only stored when they change.
+To find out how to get every key and value at every point in the simulation, check out the :doc:`soil_tutorial`.
+
+The dynamic graph is exported as a .gexf file which could be visualized with
+`Gephi <https://gephi.org/users/download/>`__.
+Now it is your turn to experiment with the simulation.
+Change some of the parameters, such as the number of agents, the probability of becoming content, or the type of network, and see how the results change.
+
+
+Soil also includes a web server that allows you to upload your simulations, change parameters, and visualize the results, including a timeline of the network.
+To make it work, you have to install soil like this:
+
+.. code::
+
+  pip install soil[web]
+
+Once installed, the soil web UI can be run in two ways:
+
+.. code::
+
+  soil-web
+
+  # OR
+
+  python -m soil.web

docs/quickstart.yml

@@ -0,0 +1,30 @@
+---
+name: quickstart
+num_trials: 1
+max_time: 1000
+network_agents:
+  - agent_type: SISaModel
+    state:
+      id: neutral
+    weight: 1
+  - agent_type: SISaModel
+    state:
+      id: content
+    weight: 2
+network_params:
+  n: 100
+  k: 5
+  p: 0.2
+  generator: newman_watts_strogatz_graph
+environment_params:
+    neutral_discontent_spon_prob: 0.05
+    neutral_discontent_infected_prob: 0.1
+    neutral_content_spon_prob: 0.2
+    neutral_content_infected_prob: 0.4
+    discontent_neutral: 0.2
+    discontent_content: 0.05
+    content_discontent: 0.05
+    variance_d_c: 0.05
+    variance_c_d: 0.1
+    content_neutral: 0.1
+    standard_variance: 0.1

docs/usage.rst

@@ -1,99 +0,0 @@
-Usage
------
-
-First of all, you need to install the package. See :doc:`installation` for installation instructions.
-
-Simulation Settings
-===================
-
-Once installed, before running a simulation, you need to configure it.
-
-* In the Settings JSON file you will find the configuration of the network.
-
-  .. code:: python
-
-    {
-        "network_type": 1,
-        "number_of_nodes": 1000,
-        "max_time": 50,
-        "num_trials": 1,
-        "timeout": 2
-    }
-
-* In the Settings JSON file, you will also find the configuration of the models.
-
-Network Types
-=============
-
-There are three types of network implemented, but you could add more.
-
-.. code:: python
-
-    if settings.network_type == 0:
-        G = nx.complete_graph(settings.number_of_nodes)
-    if settings.network_type == 1:
-        G = nx.barabasi_albert_graph(settings.number_of_nodes, 10)
-    if settings.network_type == 2:
-        G = nx.margulis_gabber_galil_graph(settings.number_of_nodes, None)
-    # More types of networks can be added here
-
-Models Settings
-===============
-
-After having configured the simulation, the next step is setting up the variables of the models.
-For this, you will need to modify the Settings JSON file again.
-
-.. code:: json
-
-    {
-        "agent": ["SISaModel","ControlModelM2"],
-
-        "neutral_discontent_spon_prob": 0.04,
-        "neutral_discontent_infected_prob": 0.04,
-        "neutral_content_spon_prob": 0.18,
-        "neutral_content_infected_prob": 0.02,
-
-        "discontent_neutral": 0.13,
-        "discontent_content": 0.07,
-        "variance_d_c": 0.02,
-
-        "content_discontent": 0.009,
-        "variance_c_d": 0.003,
-        "content_neutral": 0.088,
-
-        "standard_variance": 0.055,
-
-
-        "prob_neutral_making_denier": 0.035,
-
-        "prob_infect": 0.075,
-
-        "prob_cured_healing_infected": 0.035,
-        "prob_cured_vaccinate_neutral": 0.035,
-
-        "prob_vaccinated_healing_infected": 0.035,
-        "prob_vaccinated_vaccinate_neutral": 0.035,
-        "prob_generate_anti_rumor": 0.035
-    }
-
-In this file you will define the different models you are going to simulate. You can simulate as many models
-as you want. Each model will be simulated separately.
-
-After setting up the models, you have to initialize the parameters of each one. You will find the parameters needed
-in the documentation of each model.
-
-Parameter validation will fail if a required parameter without a default has not been provided.
-
-Running the Simulation
-======================
-
-After setting all the configuration, you will be able to run the simulation. All you need to do is execute:
-
-.. code:: bash
-
-    python3 soil.py
-
-The simulation will return a dynamic graph .gexf file which could be visualized with
-`Gephi <https://gephi.org/users/download/>`__.
-
-It will also return one .png picture for each model simulated.

examples/complete.yml

@@ -0,0 +1,28 @@
+---
+name: simple
+dir_path: "/tmp/"
+num_trials: 3
+dry_run: True
+max_time: 100
+interval: 1
+seed: "CompleteSeed!"
+dump: false
+network_params:
+  generator: complete_graph
+  n: 10
+network_agents:
+  - agent_type: CounterModel
+    weight: 1
+    state:
+      id: 0
+  - agent_type: AggregatedCounter
+    weight: 0.2
+environment_agents: []
+environment_class: Environment
+environment_params:
+  am_i_complete: true
+default_state:
+  incidents: 0
+states:
+  - name: 'The first node'
+  - name: 'The second node'

examples/custom_generator/custom_generator.yml

@@ -0,0 +1,17 @@
+---
+name: custom-generator
+description: Using a custom generator for the network
+num_trials: 3
+dry_run: True
+max_time: 100
+interval: 1
+network_params:
+  generator: mymodule.mygenerator
+# These are custom parameters
+  n: 10
+  n_edges: 5  
+network_agents:
+  - agent_type: CounterModel
+    weight: 1
+    state:
+      id: 0