Edit of documentation

Closes #675

This also lays some early work for #225 by putting a bibliography.rst
file in place and adding sources to a handful of strategies (TitForTat,
Grudger, Joss and WSLS).
- add minor modifications to landing page.
- remove incorrect statement about installation.
- tweak match docs.
- fix PEP8 in simple tournament docs.
- make minor adj to results + add bibliography
- add a bibliography and adds some references to some of the strategies.
- tidy of syntax for interactions.
- remove digits (skipping doctest anyway).
- tiny change to noisy tournament docs.
- apply minor changes to spatial tournament.
- add relevant bibliographic items.
- add reference for morality docs.
- import axl in strategy docs.
- import as axl in transformers docs.
- set a seed with axl in making tourn docs.
- make minor stylistic tweaks to read and write docs
- remove unclear part of contrib guidelines: perhaps I just misunderstood what this was saying?
- add a word to index for strategy contrib
- simplify and correct strategy contrib instructions.
- add instructions about references to contrib docs.
- improve rst syntax in add strategy docs.
- minor fixes to class contrib.
- minor tweaks to writing tests.
- grammar in running tests.
- grammar in contributing to the library.
- simplify the tournament overview section.
- sources for some strategies.

axelrod/strategies/axelrod_first.py

@@ -210,6 +210,11 @@ class Joss(MemoryOnePlayer):
     """
     Cooperates with probability 0.9 when the opponent cooperates, otherwise
     emulates Tit-For-Tat.
+
+    Names:
+
+    - Joss [Axelrod1980]_
+    - Hard Joss [Stewart2012]_
     """
 
     name = "Joss"

axelrod/strategies/grudger.py

@@ -3,7 +3,17 @@
 C, D = Actions.C, Actions.D
 
 class Grudger(Player):
-    """A player starts by cooperating however will defect if at any point the opponent has defected."""
+    """
+    A player starts by cooperating however will defect if at any point the
+    opponent has defected.
+
+    Names:
+
+    - Friedman's strategy: [Axelrod1980]_
+    - Grudger: [Li2011]_
+    - Grim: [Berg2015]_
+    - Grim Trigger: [Banks1980]_
+    """
 
     name = 'Grudger'
     classifier = {

axelrod/strategies/memoryone.py

@@ -68,7 +68,15 @@ def strategy(self, opponent):
 
 
 class WinStayLoseShift(MemoryOnePlayer):
-    """Win-Stay Lose-Shift, also called Pavlov."""
+    """
+    Win-Stay Lose-Shift, also called Pavlov.
+
+    Names:
+
+    - WSLS: [Stewart2012]_
+    - Win Stay Lose Shift: [Nowak1993]_
+    - Pavlov: [Kraines1989]_
+    """
 
     name = 'Win-Stay Lose-Shift'
     classifier = {

axelrod/strategies/titfortat.py

@@ -12,6 +12,11 @@ class TitForTat(Player):
     Note that the code for this strategy is written in a fairly verbose
     way. This is done so that it can serve as an example strategy for
     those who might be new to Python.
+
+    Names
+
+    - Rapoport's strategy: [Axelrod1980]_
+    - TitForTat: [Axelrod1980]_
     """
 
     # These are various properties for the strategy

docs/community.rst

@@ -1,3 +1,5 @@
+.. _community:
+
 Community
 =========
 

docs/index.rst

@@ -83,10 +83,12 @@ Study the evolutionary process using a Moran process::
 As well as this, the library has a growing collection of strategies. The
 :ref:`strategies-index` gives a description of them.
 
-For further details there is a library of tutorials available:
+For further details there is a library of :ref:`tutorials` available and a
+:ref:`community` page with information about how to get support and/or make
+contributions.
 
-Tutorials
----------
+Table of Contents
+-----------------
 
 .. toctree::
    :maxdepth: 3

docs/reference/bibliography.rst

@@ -0,0 +1,19 @@
+.. _bibliography:
+
+Bibliography
+============
+
+This is a collection of various bibliographic items referenced in the
+documentation.
+
+.. [Axelrod1980] Axelrod, R. (1980). Effective Choice in the Prisoner’s Dilemma. Journal of Conflict Resolution, 24(1), 3–25.
+.. [Banks1980] Banks, J. S., & Sundaram, R. K. (1990). Repeated games, finite automata, and complexity. Games and Economic Behavior, 2(2), 97–117.  http://doi.org/10.1016/0899-8256(90)90024-O
+.. [Berg2015] Berg, P. Van Den, & Weissing, F. J. (2015). The importance of mechanisms for the evolution of cooperation. Proceedings of the Royal Society B-Biological Sciences, 282.
+.. [Kraines1989] Kraines, D. & Kraines, V. Theor Decis (1989) 26: 47.  doi:10.1007/BF00134056
+.. [Li2011] Li, J., Hingston, P., Member, S., & Kendall, G. (2011). Engineering Design of Strategies for Winning Iterated Prisoner ’ s Dilemma Competitions, 3(4), 348–360.
+.. [Nowak1992] Nowak, M. a., & May, R. M. (1992). Evolutionary games and spatial chaos. Nature. http://doi.org/10.1038/359826a0
+.. [Nowak1993] Nowak, M., & Sigmund, K. (1993). A strategy of win-stay, lose-shift that outperforms tit-for-tat in the Prisoner’s Dilemma game. Nature, 364(6432), 56–58. http://doi.org/10.1038/364056a0
+.. [Press2012] Press, W. H., & Dyson, F. J. (2012). Iterated Prisoner’s Dilemma contains strategies that dominate any evolutionary opponent. Proceedings of the National Academy of Sciences, 109(26), 10409–10413.  http://doi.org/10.1073/pnas.1206569109
+.. [Singer-Clark2014] Singer-Clark, T. (2014). Morality Metrics On Iterated Prisoner’s Dilemma Players.
+.. [Stewart2012] Stewart, a. J., & Plotkin, J. B. (2012). Extortion and cooperation in the Prisoner’s Dilemma. Proceedings of the National Academy of Sciences, 109(26), 10134–10135. http://doi.org/10.1073/pnas.1208087109
+.. [Szabó1992] Szabó, G., & Fáth, G. (2007). Evolutionary games on graphs. Physics Reports, 446(4-6), 97–216. http://doi.org/10.1016/j.physrep.2007.04.004

docs/reference/index.rst

@@ -12,4 +12,5 @@ Contents:
    play_contexts.rst
    overview_of_strategies.rst
    all_strategies.rst
+   bibliography.rst
    glossary.rst