some progress, but needs a little more work. mostly whitespace and va…

…riable name changes to conform to pylint.

voka/metrics/cvm.py

@@ -1,25 +1,32 @@
-from math import log
-from scipy.special import binom
+'''
+Module contains a function object that calculates
+the Cramer-von-Mises test statistic between two sets.
+'''
 
-class CramerVonMises(object):
-
-    def __call__(self, v1, v2):
+class CramerVonMises:
+    '''
+    Function object that calculates
+    the Cramer-von-Mises test statistic between two sets.
+    '''
+
+    def __call__(self, vector1, vector2):
         r"""
-        Compare sequences v1, v2 with the Cramer-von-Mises test.
+        Compare sequences vector1, vector2 with the Cramer-von-Mises test.
         """
         result = 0.
-        Nu = float(sum(v1))
-        Nv = float(sum(v2))
-        if Nu == 0 and Nv == 0:
-            return 0.
+        if not sum(vector1) and not sum(vector2):
+            return result
+
+        Nu = float(sum(vector1))
+        Nv = float(sum(vector2))
 
-        for i,uv in enumerate(zip(v1, v2)):
+        for i, uv in enumerate(zip(vector1, vector2)):
             u = float(uv[0])
-            v = float(uv[1])        
+            v = float(uv[1])
             t = u + v
-            u_ecdf = sum([bn for bn in v1[:i]])/sum(v1)
-            v_ecdf = sum([bn for bn in v2[:i]])/sum(v2)        
+            u_ecdf = sum([bn for bn in vector1[:i]])/sum(vector1)
+            v_ecdf = sum([bn for bn in vector2[:i]])/sum(vector2)
             result += t*(u_ecdf - v_ecdf)**2
         factor = Nu*Nv/(Nu+Nv)**2
-        T = factor * result
-        return T
+        result = factor * result
+        return result

voka/metrics/llh.py

@@ -1,23 +1,20 @@
 from math import log
 from scipy.special import binom
 
-class LLHRatio(object):
-    
-    def __call__(self, v1, v2):
+class LLHRatio:
+
+    def __call__(self, vector1, vector2):
         r"""
-        Compare sequences v1, v2 with the log likelihood ratio test.
+        Compare sequences vector1, vector2 with the log likelihood ratio test.
         """
         result = 0.
-        Nu = float(sum(v1))
-        Nv = float(sum(v2))
-
-        if Nu == 0:
-            if Nv == 0:
-                return 1.
-            else:
-                return 0.
-
-        for u,v in zip(v1, v2):
+        if not vector1 and not vector2:
+            return result
+
+        Nu = float(sum(vector1))
+        Nv = float(sum(vector2))
+
+        for u, v in zip(vector1, vector2):
             u = float(u)
             v = float(v)
             t = u + v
@@ -26,40 +23,40 @@ def __call__(self, v1, v2):
                 continue
             if u == 0:
                 result += t*log(Nu/(Nu+Nv))
-                continue        
+                continue
             if v == 0:
                 result += t*log(Nv/(Nu+Nv))
                 continue
             term1 = t*log((1+v/u)/(1+Nv/Nu))
             term2 = v*log((Nv/Nu)*(u/v))
             result += term1 + term2
             T = -2*result
-            return T
+        return T
+
+class LLHValue:
 
-class LLHValue(object):
-
-    def __call__(self, v1, v2):
+    def __call__(self, vector1, vector2):
 
         r"""
         Compare histograms h1, h2 with the log likelihood value test.
         FIXME: This is currently returning inf on occasion.  It should
            never do that. Taking it out of the rotation.
         """
         result = 0.
-        Nu = float(sum(v1))
-        Nv = float(sum(v2))
-        if Nu == 0 and Nv == 0:
-            return 0.
-
-        for u,v in zip(v1, v2):
+        if not vector1 and not vector2:
+            return result
+
+        Nu = float(sum(vector1))
+        Nv = float(sum(vector2))
+
+        for u, v in zip(vector1, vector2):
             u = float(u)
-            v = float(v)        
+            v = float(v)
             t = u + v
-            bn = binom(t,v)
+            bn = binom(t, v)
             term1 = log(bn)
             term2 = t*log(Nu/(Nu + Nv))
             term3 = v*log(Nv/Nu)
             result += term1 + term2 + term3
             T = -result
-            return T
-
+        return T