Avoid needing 2to3 nonzero fixer by defining __bool__

By defining both __nonzero__ (for Python 2) and __bool__
(for Python 3) we avoid needing the 2to3 nonzero fixer,
and a runtime choice of method name.

The redundant method seems harmless.

Bio/Phylo/BaseTree.py

@@ -1017,14 +1017,17 @@ def __len__(self):
         """Number of clades directy under the root."""
         return len(self.clades)
 
-    def __nonzero__(self):
-        """Boolean value of an instance of this class.
+    #Python 3:
+    def __bool__(self):
+        """Boolean value of an instance of this class (True).
 
         NB: If this method is not defined, but ``__len__``  is, then the object
         is considered true if the result of ``__len__()`` is nonzero. We want
         Clade instances to always be considered True.
         """
         return True
+    #Python 2:
+    __nonzero__ = __bool__
 
     def __str__(self):
         if self.name:

Bio/SearchIO/_model/hit.py

@@ -149,9 +149,13 @@ def __iter__(self):
     def __len__(self):
         return len(self.hsps)
 
-    def __nonzero__(self):
+    #Python 3:
+    def __bool__(self):
         return bool(self.hsps)
 
+    #Python 2:
+    __nonzero__= __bool__
+
     def __contains__(self, hsp):
         return hsp in self._items
 

Bio/SearchIO/_model/hsp.py

@@ -289,9 +289,13 @@ def __contains__(self, fragment):
     def __len__(self):
         return len(self._items)
 
-    def __nonzero__(self):
+    #Python 3:
+    def __bool__(self):
         return bool(self._items)
 
+    #Python 2:
+    __nonzero__= __bool__
+
     def __str__(self):
 
         lines = []

Bio/SearchIO/_model/query.py

@@ -289,9 +289,13 @@ def __contains__(self, hit_key):
     def __len__(self):
         return len(self._items)
 
-    def __nonzero__(self):
+    #Python 3:
+    def __bool__(self):
         return bool(self._items)
 
+    #Python 2:
+    __nonzero__= __bool__
+
     def __repr__(self):
         return "QueryResult(id=%r, %r hits)" % (self.id, len(self))
 

Bio/SeqFeature.py

@@ -338,8 +338,9 @@ def extract(self, parent_sequence):
         """
         return self.location.extract(parent_sequence)
 
-    def __nonzero__(self):
-        """Returns True regardless of the length of the feature.
+    #Python 3:
+    def __bool__(self):
+        """Boolean value of an instance of this class (True).
 
         This behaviour is for backwards compatibility, since until the
         __len__ method was added, a SeqFeature always evaluated as True.
@@ -352,6 +353,9 @@ def __nonzero__(self):
         """
         return True
 
+    #Python 2:
+    __nonzero__= __bool__
+
     def __len__(self):
         """Returns the length of the region described by a feature.
 

Bio/SeqRecord.py

@@ -711,8 +711,9 @@ def __len__(self):
         """
         return len(self.seq)
 
-    def __nonzero__(self):
-        """Returns True regardless of the length of the sequence.
+    #Python 3:
+    def __bool__(self):
+        """Boolean value of an instance of this class (True).
 
         This behaviour is for backwards compatibility, since until the
         __len__ method was added, a SeqRecord always evaluated as True.
@@ -726,6 +727,9 @@ def __nonzero__(self):
         """
         return True
 
+    #Python 2:
+    __nonzero__= __bool__
+
     def __add__(self, other):
         """Add another sequence or string to this sequence.
 

do2to3.py

@@ -34,13 +34,11 @@
 import lib2to3.main
 from io import StringIO
 
+#Dictionary of troublesome files needing 2to3,
+#keys are filenames (with leading ./ prefix),
+#values are a list of 2to3 fixer names (strings):
 troublesome = {
-    "./Bio/SeqFeature.py": ["nonzero"],
-    "./Bio/SeqRecord.py": ["nonzero"],
-    "./Bio/Phylo/BaseTree.py": ["nonzero", "unicode"],
-    "./Bio/SearchIO/_model/hit.py": ["nonzero"],
-    "./Bio/SearchIO/_model/hsp.py": ["nonzero"],
-    "./Bio/SearchIO/_model/query.py": ["nonzero"],
+    "./Bio/Phylo/BaseTree.py": ["unicode"],
     "./Bio/Entrez/Parser.py": ["unicode"],
     "./Bio/Phylo/PhyloXMLIO.py": ["unicode"],
     "./Bio/SearchIO/BlastIO/blast_xml.py": ["unicode"],