Avoid cElementTree on Python 3.1 due to http://bugs.python.org/issue9257

Bio/Phylo/PhyloXMLIO.py

@@ -22,16 +22,16 @@
 
 from Bio.Phylo import PhyloXML as PX
 
-if (3, 0, 0) <= sys.version_info[:3] <= (3, 1, 3):
-    # Workaround for cElementTree regression in python 3.0--3.1.3
-    # See http://bugs.python.org/issue9257
-    from xml.etree import ElementTree
-else:
-    try:
-        from xml.etree import cElementTree as ElementTree
-    except ImportError:
-        # Alternative Python implementation, perhaps?
+#For speed try to use cElementTree rather than ElementTree
+try:
+    if (3, 0) <= sys.version_info[:2] <= (3, 1):
+        # Workaround for bug in python 3.0 and 3.1,
+        # see http://bugs.python.org/issue9257
         from xml.etree import ElementTree as ElementTree
+    else:
+        from xml.etree import cElementTree as ElementTree
+except ImportError:
+    from xml.etree import ElementTree as ElementTree
 
 # Recognize the phyloXML namespace when parsing
 # See http://effbot.org/zone/element-namespaces.htm

Bio/SearchIO/BlastIO/blast_xml.py

@@ -6,13 +6,23 @@
 """Bio.SearchIO parser for BLAST+ XML output formats."""
 # for more info: http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.mod.dtd
 
+import sys
 import re
 from itertools import chain
 from xml.sax.saxutils import XMLGenerator, escape
+
+
+#For speed try to use cElementTree rather than ElementTree
 try:
-    from xml.etree import cElementTree as ET
+    if (3, 0) <= sys.version_info[:2] <= (3, 1):
+        # Workaround for bug in python 3.0 and 3.1,
+        # see http://bugs.python.org/issue9257
+        from xml.etree import ElementTree as ElementTree
+    else:
+        from xml.etree import cElementTree as ElementTree
 except ImportError:
-    from xml.etree import ElementTree as ET
+    from xml.etree import ElementTree as ElementTree
+
 
 from Bio._py3k import _as_bytes, _bytes_to_string
 _empty_bytes_string = _as_bytes("")
@@ -176,7 +186,7 @@ class BlastXmlParser(object):
     """Parser for the BLAST XML format"""
 
     def __init__(self, handle):
-        self.xml_iter = iter(ET.iterparse(handle, events=('start', 'end')))
+        self.xml_iter = iter(ElementTree.iterparse(handle, events=('start', 'end')))
         self._meta, self._fallback = self._parse_preamble()
 
     def __iter__(self):

Bio/SeqIO/UniprotIO.py

@@ -26,10 +26,11 @@
 except ImportError:
     from StringIO import StringIO
 
-#For speed try to use cElementTree rather than ElemenTree
+#For speed try to use cElementTree rather than ElementTree
 try:
-    if (3, 0, 0) <= sys.version_info[:3] <= (3, 1, 3):
-        #workaround for bug in python 3 to 3.1.3  see http://bugs.python.org/issue9257
+    if (3, 0) <= sys.version_info[:2] <= (3, 1):
+        # Workaround for bug in python 3.0 and 3.1,
+        # see http://bugs.python.org/issue9257
         from xml.etree import ElementTree as ElementTree
     else:
         from xml.etree import cElementTree as ElementTree