Preparing for refactor...

copycat/workspace.py

@@ -40,6 +40,16 @@ class Workspace(object):
         self.modified = WorkspaceString(self.ctx, self.modifiedString)
         self.target = WorkspaceString(self.ctx, self.targetString)
 
+    '''
+    # TODO: Initial part of refactoring in this method
+    def getAssessedUnhappiness(self, unhappiness):
+        o.Unhappiness = __adjustUnhappiness(
+            o.relativeImportance * o.Unhappiness
+            for o in self.objects)
+        pass
+    '''
+
+    # TODO: Extract method?
     def assessUnhappiness(self):
         self.intraStringUnhappiness = __adjustUnhappiness(
             o.relativeImportance * o.intraStringUnhappiness
@@ -51,6 +61,7 @@ class Workspace(object):
             o.relativeImportance * o.totalUnhappiness
             for o in self.objects)
 
+    # TODO: these 3 methods seem to be the same... are they?  If so, Extract method.
     def calculateIntraStringUnhappiness(self):
         value = sum(
             o.relativeImportance * o.intraStringUnhappiness
@@ -98,7 +109,7 @@ class Workspace(object):
         ))
 
     def numberOfUnrelatedObjects(self):
-        """A list of all objects in the workspace with >= 1 open bond slots"""
+        """Computes the number of all objects in the workspace with >= 1 open bond slots."""
         objects = [o for o in self.objects
                    if o.string == self.initial or o.string == self.target]
         objects = [o for o in objects if not o.spansString()]
@@ -116,21 +127,21 @@ class Workspace(object):
         return len(objects)
 
     def numberOfUnreplacedObjects(self):
-        """A list of all unreplaced objects in the initial string"""
+        """A list of all unreplaced objects in the initial string."""
         objects = [o for o in self.objects
                    if o.string == self.initial and isinstance(o, Letter)]
         objects = [o for o in objects if not o.replacement]
         return len(objects)
 
     def numberOfUncorrespondingObjects(self):
-        """A list of all uncorresponded objects in the initial string"""
+        """A list of all uncorresponded objects in the initial string."""
         objects = [o for o in self.objects
                    if o.string == self.initial or o.string == self.target]
         objects = [o for o in objects if not o.correspondence]
         return len(objects)
 
     def numberOfBonds(self):
-        """The number of bonds in the workspace"""
+        """The number of bonds in the workspace."""
         return sum(1 for o in self.structures if isinstance(o, Bond))
 
     def correspondences(self):

copycat/workspaceString.py

@@ -38,7 +38,7 @@ class WorkspaceString(object):
         return self.string[i]
 
     def updateRelativeImportance(self):
-        """Update the normalised importance of all objects in the string"""
+        """Update the normalised importance of all objects in the string."""
         total = sum(o.rawImportance for o in self.objects)
         if not total:
             for o in self.objects:

main.py

@@ -1,4 +1,27 @@
 #!/usr/bin/env python3
+"""
+Main Copycat program.
+
+To run it, type at the terminal:
+
+    > python main.py abc abd ppqqrr --interations 10
+
+The script takes three to five arguments. The first two are a pair of strings
+with some change, for example "abc" and "abd". The third is a string which the
+script should try to change analogously. The fourth (which defaults to "1") is
+a number of iterations. One can also specify a defined seed falue for the
+random number generator.
+
+The above might produce output such as
+
+    ppqqss: 6 (avg time 869.0, avg temp 23.4)
+    ppqqrs: 4 (avg time 439.0, avg temp 37.3)
+
+The first number indicates how many times Copycat chose that string as its
+answer; higher means "more obvious". The last number indicates the average
+final temperature of the workspace; lower means "more elegant".
+"""
+
 import argparse
 import logging