py3: first stage of xrange to range

- range import from six.moves
- No conversion of range to list

boost/rational.py

@@ -1,5 +1,6 @@
 from __future__ import absolute_import, division, print_function
 import boost.python
+from six.moves import range
 ext = boost.python.import_ext("boost_rational_ext")
 from boost_rational_ext import *
 

boost_adaptbx/graph/tests/tst_graph_clustering_algorithm.py

@@ -4,6 +4,7 @@
 from boost_adaptbx.graph import clustering_algorithm
 
 import unittest
+from six.moves import range
 
 
 class TestBetweennessCentralityClustering(unittest.TestCase):

boost_adaptbx/graph/tests/tst_graph_metric.py

@@ -4,6 +4,7 @@
 from boost_adaptbx.graph import metric
 
 import unittest
+from six.moves import range
 
 
 class TestBrandesBetweennessCentrality(unittest.TestCase):

boost_adaptbx/hybrid_times.py

@@ -2,6 +2,7 @@
 
 from boost_python_hybrid_times_ext import run_c_plus_plus
 import sys, os
+from six.moves import range
 
 if (not hasattr(sys, "gettickeraccumulation")):
   print("***************************************************")

boost_adaptbx/tests/tst_python_streambuf.py

@@ -2,6 +2,7 @@
 
 import boost.python
 from boost.python import streambuf, ostream
+from six.moves import range
 ext = boost.python.import_ext("boost_adaptbx_python_streambuf_test_ext")
 import StringIO
 import cStringIO

boost_adaptbx/tests/tst_rational.py

@@ -2,6 +2,7 @@
 
 from boost import rational
 from libtbx.test_utils import Exception_expected, approx_equal, show_diff
+from six.moves import range
 try:
   import cPickle as pickle
 except ImportError:

boost_adaptbx/tests/tst_string_representation.py

@@ -1,4 +1,5 @@
 from __future__ import absolute_import, division, print_function
+from six.moves import range
 
 def exercise():
   import boost.python

cma_es/cma_es_interface.py

@@ -1,6 +1,7 @@
 from __future__ import absolute_import, division, print_function
 from scitbx.array_family import flex
 from cma_es import cma_es
+from six.moves import range
 
 class cma_es_driver(object):
   """
@@ -22,7 +23,7 @@ def __init__(self, N, mean, sigma, evaluator, l=0):
       pop_size = p.accessor().all()[0]
       # update objective function
       v = flex.double(pop_size)
-      for i in xrange(pop_size):
+      for i in range(pop_size):
         vector = p[(i*N):(i*N + N)]
         v[i] = self.evaluator( vector )
       self.optimizer.update_distribution(v)

cma_es/tst_cma_es.py

@@ -2,22 +2,23 @@
 from libtbx.test_utils import approx_equal
 from scitbx.array_family import flex
 from cma_es import cma_es
+from six.moves import range
 
 # =============================================================================
 center = flex.double([8.0,-13.0,0.5])
 
 def obj_fun(x):
   assert(len(x) == 3)
   fun = 0.0
-  for i in xrange(len(x)):
+  for i in range(len(x)):
     xi = x[i] - center[i]
     fun += xi*xi
   return fun
 
 # from example1.c
 def fitfun(x,N):
   isum = 1e4*x[0]*x[0] + 1e-4*x[1]*x[1]
-  for i in xrange(2,N):
+  for i in range(2,N):
     isum += x[i]*x[i]
   return isum
 
@@ -34,7 +35,7 @@ def test_cma_es():
 
     # update objective function
     v = flex.double(pop_size)
-    for i in xrange(pop_size):
+    for i in range(pop_size):
       v[i] = obj_fun(p[(i*N):(i*N + N)])
     m.update_distribution(v)
 
@@ -88,7 +89,7 @@ def test_cma_es_lambda():
 
     # update objective function
     v = flex.double(pop_size)
-    for i in xrange(pop_size):
+    for i in range(pop_size):
       v[i] = obj_fun(p[(i*N):(i*N + N)])
     m.update_distribution(v)
 
@@ -107,7 +108,7 @@ def test_cma_es_file():
 
     # update objective function
     v = flex.double(pop_size)
-    for i in xrange(pop_size):
+    for i in range(pop_size):
       v[i] = fitfun(p[(i*N):(i*N + N)],N)
     m.update_distribution(v)
 

cootbx/ligand_checklist.py

@@ -5,6 +5,7 @@
 import sys
 
 from libtbx.utils import to_str
+from six.moves import range
 
 t_wait = 250
 

cootbx/validation_lists.py

@@ -1,6 +1,7 @@
 
 from __future__ import absolute_import, division, print_function
 import cPickle
+from six.moves import range
 try :
   import gobject
 except ImportError :

crys3d/command_line/multiplicity_viewer.py

@@ -11,6 +11,7 @@
 from cctbx import crystal
 import wx
 import sys
+from six.moves import range
 
 
 master_phil = iotbx.phil.parse("""

crys3d/hklview/jsview_3d.py

@@ -12,6 +12,7 @@
 import os.path, time
 import libtbx
 import webbrowser, tempfile
+from six.moves import range
 
 
 

crys3d/model.py

@@ -1,4 +1,5 @@
 from __future__ import absolute_import, division, print_function
+from six.moves import range
 
 # TODO: clean up handling of changes in atom count
 
@@ -257,7 +258,7 @@ def color_mono (self) :
     else :
       from scitbx.array_family import flex
       self.atom_colors = flex.vec3_double(
-        [ self.base_color for i in xrange(0, self.atoms.size()) ]
+        [ self.base_color for i in range(0, self.atoms.size()) ]
       )
       self._color_cache["mono"] = self.atom_colors
 

crys3d/qttbx/xray_structure_viewer.py

@@ -12,6 +12,7 @@
 from scitbx import matrix as mat
 import itertools
 import six
+from six.moves import range
 
 
 def display(**kwds):
@@ -180,7 +181,7 @@ def draw_object_in_cartesian_coordinates(self):
     self.principal_ellipses_tex.unbind()
 
     self.bond_material.execute()
-    for i in xrange(0, len(self.bonds), 2):
+    for i in range(0, len(self.bonds), 2):
       start, end = self.bonds[i], self.bonds[i+1]
       self.cylindre_proto.draw(start, end, base_radius=0.05)
 

crys3d/reverse_selection.py

@@ -5,6 +5,7 @@
 from libtbx import adopt_init_args
 import re
 import six
+from six.moves import range
 
 single_quote = re.compile(r"'")
 

crys3d/ribbon.py

@@ -6,6 +6,7 @@
 import scitbx.matrix
 import time
 import sys
+from six.moves import range
 
 class cartoon (object) :
   def __init__ (self, pdb_hierarchy, sec_str, selection_cache=None) :

crys3d/wx_extra.py

@@ -2,6 +2,7 @@
 import wx
 
 import libtbx.object_oriented_patterns as oop
+from six.moves import range
 
 class copy_init_args(object):
   def __init__(self, args, exclude=()):
@@ -34,8 +35,8 @@ def FillWith3DGradient(self, rect, colour, direction, step=1):
     slopes = [ x*step/d for x in step_adjustements ]
     red_green_slopes = [ x*58 for x in slopes ]
     blue_slopes      = [ x*44 for x in slopes ]
-    ranges = [ xrange(slope_breaks[i], slope_breaks[i+1])
-               for i in xrange(len(slope_breaks)-1) ]
+    ranges = [ range(slope_breaks[i], slope_breaks[i+1])
+               for i in range(len(slope_breaks)-1) ]
     for range, red_green_slope, blue_slope in zip(
       ranges, red_green_slopes, blue_slopes):
       for i in range:

cudatbx/cufft/tst_ext.py

@@ -1,4 +1,5 @@
 from __future__ import absolute_import, division, print_function
+from six.moves import range
 
 def exercise_real_to_complex_3d(benchmark=True):
   sizes_1 = [((32,32,32), 16, 0.0000001),
@@ -97,7 +98,7 @@ def exercise_complex_to_complex_3d():
     d0.reshape(flex.grid(n_complex))
     #
     t0 = time.time()
-    for i_trial in xrange(n_repeats):
+    for i_trial in range(n_repeats):
       d = d0.deep_copy()
     overhead = time.time()-t0
     print("    overhead: %.2f seconds" % overhead)
@@ -108,15 +109,15 @@ def exercise_complex_to_complex_3d():
     cufft.complex_to_complex_3d(n_complex).backward(d)
     # benchmarking run
     t0 = time.time()
-    for i_trial in xrange(n_repeats):
+    for i_trial in range(n_repeats):
       d = d0.deep_copy()
       cufft.complex_to_complex_3d(n_complex).forward(d)
       cufft.complex_to_complex_3d(n_complex).backward(d)
     print("    cufft:    %6.2f seconds" % ((time.time()-t0-overhead)/n_repeats))
     rw = d / np
     #
     t0 = time.time()
-    for i_trial in xrange(n_repeats):
+    for i_trial in range(n_repeats):
       d = d0.deep_copy()
       fftpack.complex_to_complex_3d(n_complex).forward(d)
       fftpack.complex_to_complex_3d(n_complex).backward(d)

cudatbx/math/special_functions/tst_spherical_bessel_jn.py

@@ -3,6 +3,7 @@
 
 from libtbx.test_utils import approx_equal
 from scitbx.array_family import flex
+from six.moves import range
 
 # =============================================================================
 def spherical_bessel_jn_test(write_output = False):
@@ -13,7 +14,7 @@ def spherical_bessel_jn_test(write_output = False):
   z_max = 200.0
   order = 50
   z = flex.double(z_size)
-  for i in xrange(z_size):
+  for i in range(z_size):
     z[i] = z_max * (i+1)/z_size
 
   dt = [0.0,0.0]
@@ -25,37 +26,37 @@ def spherical_bessel_jn_test(write_output = False):
   dt[0] = t1 - t0
   if write_output:
     f = open('jn_gpu.dat','w')
-    for i in xrange(order+1):
-      for j in xrange(z_size):
+    for i in range(order+1):
+      for j in range(z_size):
         f.write('%f %f\n'%(z[j],jn_gpu[i*z_size + j]))
       f.write('&\n')
     f.close()
 
   # CPU
-  jn_cpu = [ None for i in xrange(order+1) ]
+  jn_cpu = [ None for i in range(order+1) ]
   t0 = time.time()
-  for n in xrange(order+1):
+  for n in range(order+1):
     jn_cpu[n] = spherical_bessel_array(n,z)
   t1 = time.time()
   dt[1] = t1 - t0
   if write_output:
     f = open('jn_cpu.dat','w')
-    for i in xrange(order+1):
-      for j in xrange(z_size):
+    for i in range(order+1):
+      for j in range(z_size):
         f.write('%f %f\n'%(z[j],jn_cpu[i][j]))
       f.write('&\n')
     f.close()
 
   # difference
-  d_jn = [ None for i in xrange(order+1) ]
-  for n in xrange(order+1):
+  d_jn = [ None for i in range(order+1) ]
+  for n in range(order+1):
     d_jn[n] = jn_cpu[n] - jn_gpu[n*z_size:n*z_size + z_size]
-    for i in xrange(z_size):
+    for i in range(z_size):
       assert( approx_equal(d_jn[n][i]*d_jn[n][i],0.0,eps=1.0e-6) )
   if write_output:
     f = open('d_jn.dat','w')
-    for i in xrange(order+1):
-      for j in xrange(z_size):
+    for i in range(order+1):
+      for j in range(z_size):
         f.write('%f %f\n'%(z[j],d_jn[i][j]))
       f.write('&\n')
     f.close()

cudatbx/scattering/tst_direct_summation.py

@@ -5,6 +5,7 @@
 from scitbx.array_family import flex
 from scitbx import matrix
 from scitbx.math.des_3_240_21 import t_x,t_y,t_z
+from six.moves import range
 
 test_pdb = "\
 CRYST1  127.692  225.403  306.106  90.00  90.00  90.00 P 21 21 21    4\n\
@@ -39,15 +40,15 @@ def test_direct_summation():
   h = flex.vec3_double(len(indices))
   fm = matrix.sqr(p.crystal_symmetry().unit_cell().fractionalization_matrix())
   om = matrix.sqr(p.crystal_symmetry().unit_cell().orthogonalization_matrix())
-  for i in xrange(len(indices)):
+  for i in range(len(indices)):
     h[i] = fm * indices[i]
   sr = x.scattering_type_registry()
   st = x.scattering_types()
 
   sg = p.crystal_symmetry().space_group()
   r = flex.double()
   t = flex.vec3_double(len(sg))
-  for i in xrange(len(sg)):
+  for i in range(len(sg)):
     r_i = om * matrix.sqr(sg[i].r().as_double())
     for a in r_i:
       r.append(a)
@@ -62,7 +63,7 @@ def test_direct_summation():
   gpu_i = flex.norm(amplitudes)
 
   mean = 0.0
-  for i in xrange(len(cpu_i)):
+  for i in range(len(cpu_i)):
     e = math.fabs(cpu_i[i] - gpu_i[i])/cpu_i[i]
     mean += e
   mean = mean/(len(cpu_i))
@@ -77,7 +78,7 @@ def test_saxs():
   blsf = flex.double(len(xyz),0.0)
   sr = x.scattering_type_registry()
   st = x.scattering_types()
-  q = flex.double(range(101))/200.0
+  q = flex.double(list(range(101)))/200.0
 
   t_w = flex.double(len(t_x),1.0)
 

dox.sphinx/conf.py

@@ -14,6 +14,7 @@
 
 #from __future__ import absolute_import, division, print_function
 import sys, os, re
+from six.moves import range
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the