Merge pull request #15 from BD2KGenomics/issues/14python3

Futurize (resolves #14)

Author: ejacox

setup.py

@@ -15,12 +15,12 @@
 
     package_dir={ '': 'src' },
     packages=find_packages( 'src' ),
-    install_requires=[ ],
+    install_requires=[ 'future' ],
     tests_require=[
         'pytest==2.7.2',
         'mock==1.0.1',
         'lockfile==0.11.0',
-        'boto==2.38.0' ],
+        'boto==2.38.0'],
     namespace_packages=[ 'bd2k' ] )
 
 from setuptools.command.test import test as TestCommand

src/bd2k/util/collections.py

@@ -1,5 +1,6 @@
 from __future__ import absolute_import
 
+from builtins import next
 import collections
 from itertools import dropwhile
 
@@ -155,7 +156,7 @@ def rindex( l, v ):
     2
     """
     try:
-        n = next( dropwhile( lambda (i, x): v != x, enumerate( reversed( l ), 1 ) ) )[ 0 ]
+        n = next( dropwhile( lambda i_x: v != i_x[1], enumerate( reversed( l ), 1 ) ) )[ 0 ]
     except StopIteration:
         raise ValueError( v )
     else:

src/bd2k/util/d32.py

@@ -1,3 +1,4 @@
+from __future__ import division
 # Copyright (c) 2015 Hannes Schmidt
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy of this software
@@ -17,6 +18,10 @@
 
 # Inspired by Dominic Tarr's JavaScript at https://github.com/dominictarr/d64
 
+from builtins import str
+from builtins import range
+from builtins import object
+from past.utils import old_div
 class D32( object ):
     """
     Base32 encoding and decoding without padding, and using an arbitrary alphabet.
@@ -26,7 +31,7 @@ def __init__( self, alphabet ):
         super( D32, self ).__init__( )
         self.alphabet = bytearray( alphabet )
         self.lookup = bytearray( 255 )
-        for i in xrange( 32 ):
+        for i in range( 32 ):
             self.lookup[ self.alphabet[ i ] ] = i
 
     def encode( self, d ):
@@ -44,7 +49,7 @@ def encode( self, d ):
         '222k62s62o'
         """
         m = len( d )
-        n = (m * 8 + 4) / 5
+        n = old_div((m * 8 + 4), 5)
         padding = 8 - n % 8
         e = bytearray( n + padding )
         i, j = 0, 0
@@ -83,7 +88,7 @@ def decode( self, e ):
         '\\xff'
         """
         n = len( e )
-        m = n * 5 / 8
+        m = old_div(n * 5, 8)
         padding = 5 - m % 5
         d = bytearray( m + padding )
         i, j = 0, 0
@@ -104,7 +109,7 @@ def decode( self, e ):
             d[ i + 4 ] = g[ 6 ] << 5 & 255 | g[ 7 ]
             j += 8
             i += 5
-        return str( d[ :-padding ] )
+        return bytes( d[ :-padding ] )
 
 
 # A variant of Base64 that maintains the lexicographical ordering such that for any given list of

src/bd2k/util/d64.py

@@ -1,3 +1,4 @@
+from __future__ import division
 # Copyright (c) 2014 Dominic Tarr
 # Copyright (c) 2015 Hannes Schmidt
 #
@@ -20,13 +21,17 @@
 
 
 
+from builtins import str
+from builtins import range
+from builtins import object
+from past.utils import old_div
 class D64( object ):
     def __init__( self, special_chars ):
         super( D64, self ).__init__( )
         alphabet = 'PYFGCRLAOEUIDHTNSQJKXBMWVZpyfgcrlaoeuidhtnsqjkxbmwvz1234567890'
         self.alphabet = bytearray( sorted( alphabet + special_chars ) )
         self.lookup = bytearray( 255 )
-        for i in xrange( 64 ):
+        for i in range( 64 ):
             code = self.alphabet[ i ]
             self.lookup[ code ] = i
 
@@ -45,11 +50,11 @@ def encode( self, data ):
         '..31.kF40VR'
         """
         l = len( data )
-        s = bytearray( (l * 4 + 2) / 3 )
+        s = bytearray( old_div((l * 4 + 2), 3) )
         hang = 0
         j = 0
         a = self.alphabet
-        for i in xrange( l ):
+        for i in range( l ):
             v = ord( data[ i ] )
             r = i % 3
             if r == 0:
@@ -89,11 +94,11 @@ def decode( self, e ):
         """
         n = len( e )
         j = 0
-        b = bytearray( n * 3 / 4 )
+        b = bytearray( old_div(n * 3, 4) )
         hang = 0
         l = self.lookup
 
-        for i in xrange( n ):
+        for i in range( n ):
             v = l[ ord( e[ i ] ) ]
             r = i % 4
             if r == 0:
@@ -111,7 +116,7 @@ def decode( self, e ):
                 j += 1
             else:
                 assert False
-        return str( b )
+        return bytes( b )
 
 
 standard = D64( '._' )

src/bd2k/util/ec2/credentials.py

@@ -109,7 +109,7 @@ def _populate_keys_from_metadata_server( self ):
         log.debug( 'Racing to create %s.', tmp_path )
         # Only one process, the winner, will succeed
         try:
-            fd = os.open( tmp_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0600 )
+            fd = os.open( tmp_path, os.O_CREAT | os.O_EXCL | os.O_WRONLY, 0o600 )
         except OSError as e:
             if e.errno == errno.EEXIST:
                 log.debug( 'Lost the race to create %s. Waiting on winner to remove it.', tmp_path )

src/bd2k/util/ec2/test/test_credentials.py

@@ -1,3 +1,4 @@
+from builtins import range
 import logging
 
 import errno

src/bd2k/util/exceptions.py

@@ -1,3 +1,4 @@
+from builtins import object
 from contextlib import contextmanager
 import sys
 

src/bd2k/util/hashes.py

@@ -1,3 +1,6 @@
+from builtins import str
+from builtins import next
+from past.builtins import basestring
 def hash_json( hash_obj, value ):
     """
     Compute the hash of a parsed JSON value using the given hash object. This function does not
@@ -58,7 +61,7 @@ def hash_json( hash_obj, value ):
     ValueError: Type <type 'object'> is not supported
     """
     try:
-        items = value.iteritems( )
+        items = iter(value.items( ))
     except AttributeError:
         # Must check for string before testing iterability since strings are iterable
         if isinstance( value, basestring ):
@@ -123,7 +126,8 @@ def _hash_hashable( hash_obj, items ):
     hash_obj.update( '}' )
 
 
-def _hash_hashable_item( hash_obj, (k, v) ):
+def _hash_hashable_item( hash_obj, k_v ):
+    (k, v) = k_v
     if isinstance( k, basestring ):
         hash_obj.update( k )
         hash_obj.update( ':' )

src/bd2k/util/humanize.py

@@ -8,8 +8,10 @@
 Author: Giampaolo Rodola' <g.rodola [AT] gmail [DOT] com>
 License: MIT
 """
+from __future__ import division
 
 # see: http://goo.gl/kTQMs
+from past.utils import old_div
 SYMBOLS = {
     'customary'     : ('', 'K', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y'),
     'customary_ext' : ('byte', 'kilo', 'mega', 'giga', 'tera', 'peta', 'exa',
@@ -65,7 +67,7 @@ def bytes2human(n, fmt='%(value).1f %(symbol)s', symbols='customary'):
         prefix[s] = 1 << (i+1)*10
     for symbol in reversed(symbols[1:]):
         if n >= prefix[symbol]:
-            value = float(n) / prefix[symbol]
+            value = old_div(float(n), prefix[symbol])
             return fmt % locals()
     return fmt % dict(symbol=symbols[0], value=n)
 
@@ -110,7 +112,7 @@ def human2bytes(s):
         s = s[1:]
     num = float(num)
     letter = s.strip()
-    for name, sset in SYMBOLS.items():
+    for name, sset in list(SYMBOLS.items()):
         if letter in sset:
             break
     else:

src/bd2k/util/iterables.py

@@ -1,4 +1,11 @@
-from itertools import takewhile, izip, izip_longest, dropwhile, imap, chain
+from builtins import map
+from builtins import zip
+from builtins import object
+from itertools import takewhile, dropwhile, chain
+try:
+    from itertools import zip_longest as zip_longest
+except:
+    from itertools import izip_longest as zip_longest
 
 
 def common_prefix( xs, ys ):
@@ -18,7 +25,7 @@ def common_prefix( xs, ys ):
     >>> list( common_prefix('A','B') )
     []
     """
-    return imap( lambda (x, y): x, takewhile( lambda (a, b): a == b, izip( xs, ys ) ) )
+    return map( lambda x_y: x_y[0], takewhile( lambda a_b: a_b[0] == a_b[1], zip( xs, ys ) ) )
 
 
 def disparate_suffix( xs, ys ):
@@ -38,7 +45,7 @@ def disparate_suffix( xs, ys ):
     >>> list( disparate_suffix('A','B') )
     [('A', 'B')]
     """
-    return dropwhile( lambda (a, b): a == b, izip_longest( xs, ys ) )
+    return dropwhile( lambda a_b1: a_b1[0] == a_b1[1], zip_longest( xs, ys ) )
 
 
 def flatten( iterables ):
@@ -121,7 +128,7 @@ def expand( x ):
                     i = x,
             return i
 
-        return flatten( imap( expand, self.args ) )
+        return flatten( map( expand, self.args ) )
 
 
 # noinspection PyPep8Naming
@@ -166,4 +173,4 @@ def expand( x ):
             except AttributeError:
                 return x,
 
-        return flatten( imap( expand, self.iterables ) )
+        return flatten( map( expand, self.iterables ) )