From f78ead8938e8c55b5c5c5502ce403066eee50e67 Mon Sep 17 00:00:00 2001 From: "Billy K. Poon" Date: Tue, 14 May 2019 21:27:59 -0700 Subject: [PATCH] py3: first stage of xrange to range - range import from six.moves - No conversion of range to list --- boost/rational.py | 1 + .../tests/tst_graph_clustering_algorithm.py | 1 + boost_adaptbx/graph/tests/tst_graph_metric.py | 1 + boost_adaptbx/hybrid_times.py | 1 + boost_adaptbx/tests/tst_python_streambuf.py | 1 + boost_adaptbx/tests/tst_rational.py | 1 + .../tests/tst_string_representation.py | 1 + cma_es/cma_es_interface.py | 3 +- cma_es/tst_cma_es.py | 11 +++---- cootbx/ligand_checklist.py | 1 + cootbx/validation_lists.py | 1 + crys3d/command_line/multiplicity_viewer.py | 1 + crys3d/hklview/jsview_3d.py | 1 + crys3d/model.py | 3 +- crys3d/qttbx/xray_structure_viewer.py | 3 +- crys3d/reverse_selection.py | 1 + crys3d/ribbon.py | 1 + crys3d/wx_extra.py | 5 ++-- cudatbx/cufft/tst_ext.py | 7 +++-- .../tst_spherical_bessel_jn.py | 25 ++++++++-------- cudatbx/scattering/tst_direct_summation.py | 9 +++--- dox.sphinx/conf.py | 1 + dox/compcomm/newsletter09/sf_times_digest.py | 9 +++--- dox/siena2005/sort_merge.py | 3 +- dox/siena2005/sort_merge_initial.py | 3 +- fable/test/sf_times.py | 3 +- fftw3tbx/tst_ext.py | 29 ++++++++++--------- gltbx/generate_defines_bpl.py | 1 + gltbx/generate_fonts_ucs_cpp.py | 1 + gltbx/generate_functions_bpl.py | 1 + gltbx/images.py | 5 ++-- gltbx/tst.py | 5 ++-- gltbx/tst_ellipsoids.py | 13 +++++---- gltbx/tst_viewer_utils.py | 3 +- gltbx/wx_motion_on_tab.py | 5 ++-- gltbx/wx_scene.py | 1 + gltbx/wx_viewer.py | 3 +- libtbx/clear_paths.py | 1 + libtbx/cluster.py | 1 + libtbx/command_line/easy_qsub.py | 1 + libtbx/command_line/install.py | 1 + libtbx/command_line/parallel_simple.py | 1 + libtbx/command_line/show_dist_paths.py | 1 + .../command_line/show_python_dependencies.py | 1 + libtbx/easy_mp.py | 1 + libtbx/easy_profile.py | 1 + libtbx/easy_run.py | 1 + libtbx/math_utils.py | 1 + libtbx/option_parser.py | 1 + libtbx/path.py | 1 + libtbx/phil/tst.py | 1 + libtbx/pyframe.py | 1 + libtbx/queuing_system_utils/looping.py | 1 + libtbx/queuing_system_utils/lsf.py | 1 + libtbx/queuing_system_utils/scheduling.py | 1 + libtbx/queuing_system_utils/sge_utils.py | 1 + libtbx/queuing_system_utils/tst.py | 1 + libtbx/runtime_utils.py | 1 + libtbx/scheduling/file_queue.py | 1 + libtbx/scheduling/parallel_for.py | 3 +- libtbx/scheduling/socket_queue.py | 1 + libtbx/sphinx/pubmed.py | 1 + libtbx/table_utils.py | 1 + libtbx/test_utils/__init__.py | 1 + libtbx/tst_binary_search.py | 1 + libtbx/tst_easy_mp.py | 1 + libtbx/tst_easy_mp_state.py | 1 + libtbx/tst_easy_pickle.py | 1 + libtbx/tst_math_utils.py | 1 + libtbx/tst_object_oriented_patterns.py | 1 + libtbx/tst_path.py | 1 + libtbx/tst_representation.py | 1 + libtbx/tst_scheduling.py | 1 + libtbx/tst_str_utils.py | 1 + libtbx/tst_thread_utils.py | 1 + libtbx/tst_topological_sort.py | 1 + libtbx/tst_utils.py | 1 + libtbx/utils.py | 1 + libtbx/xmlrpc_utils.py | 1 + rstbx/bpcx/compare_mosflm_xds.py | 1 + rstbx/bpcx/detector_model/detector.py | 1 + rstbx/bpcx/ersatz_misset.py | 1 + rstbx/bpcx/uc1_2_positions.py | 1 + rstbx/bpcx/uc1_2_positions_idx.py | 1 + rstbx/bpcx/uc1_2_validate.py | 1 + rstbx/cftbx/coordinate_frame_helpers.py | 1 + rstbx/diffraction/tst_ewald_sphere.py | 1 + rstbx/slip_viewer/ring_frame.py | 1 + rstbx/slip_viewer/slip_display.py | 1 + rstbx/viewer/__init__.py | 1 + rstbx/viewer/pixels3d.py | 1 + simtbx/nanoBragg/nanoBragg_gui_frames.py | 1 + simtbx/nanoBragg/tst_gaussian_mosaicity.py | 1 + simtbx/nanoBragg/tst_nanoBragg_multipanel.py | 1 + simtbx/nanoBragg/tst_nanoBragg_pilatus.py | 1 + .../servers/mp_spotfinder_server_read_file.py | 1 + 96 files changed, 161 insertions(+), 65 deletions(-) diff --git a/boost/rational.py b/boost/rational.py index 80b367d029..8369956204 100644 --- a/boost/rational.py +++ b/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 * diff --git a/boost_adaptbx/graph/tests/tst_graph_clustering_algorithm.py b/boost_adaptbx/graph/tests/tst_graph_clustering_algorithm.py index ce0a37af91..fc1ed96abe 100644 --- a/boost_adaptbx/graph/tests/tst_graph_clustering_algorithm.py +++ b/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): diff --git a/boost_adaptbx/graph/tests/tst_graph_metric.py b/boost_adaptbx/graph/tests/tst_graph_metric.py index d5c549ddca..83e7346fe7 100644 --- a/boost_adaptbx/graph/tests/tst_graph_metric.py +++ b/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): diff --git a/boost_adaptbx/hybrid_times.py b/boost_adaptbx/hybrid_times.py index f08b545b2e..189aad3afa 100644 --- a/boost_adaptbx/hybrid_times.py +++ b/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("***************************************************") diff --git a/boost_adaptbx/tests/tst_python_streambuf.py b/boost_adaptbx/tests/tst_python_streambuf.py index 1023aa1665..b778e8221d 100644 --- a/boost_adaptbx/tests/tst_python_streambuf.py +++ b/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 diff --git a/boost_adaptbx/tests/tst_rational.py b/boost_adaptbx/tests/tst_rational.py index 03bf2b18ab..3b28a491ee 100644 --- a/boost_adaptbx/tests/tst_rational.py +++ b/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: diff --git a/boost_adaptbx/tests/tst_string_representation.py b/boost_adaptbx/tests/tst_string_representation.py index 541223d3dc..3ea113ef61 100644 --- a/boost_adaptbx/tests/tst_string_representation.py +++ b/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 diff --git a/cma_es/cma_es_interface.py b/cma_es/cma_es_interface.py index 2e1d1fecdd..e3b3a5aa6f 100644 --- a/cma_es/cma_es_interface.py +++ b/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) diff --git a/cma_es/tst_cma_es.py b/cma_es/tst_cma_es.py index 0ceea104e6..a1e84d42fc 100644 --- a/cma_es/tst_cma_es.py +++ b/cma_es/tst_cma_es.py @@ -2,6 +2,7 @@ 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]) @@ -9,7 +10,7 @@ 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 @@ -17,7 +18,7 @@ def obj_fun(x): # 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) diff --git a/cootbx/ligand_checklist.py b/cootbx/ligand_checklist.py index dec09f0baa..b24bf844b8 100644 --- a/cootbx/ligand_checklist.py +++ b/cootbx/ligand_checklist.py @@ -5,6 +5,7 @@ import sys from libtbx.utils import to_str +from six.moves import range t_wait = 250 diff --git a/cootbx/validation_lists.py b/cootbx/validation_lists.py index aa42b7c570..fae5c5a592 100644 --- a/cootbx/validation_lists.py +++ b/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 : diff --git a/crys3d/command_line/multiplicity_viewer.py b/crys3d/command_line/multiplicity_viewer.py index 514a0cd38f..deab2d394c 100644 --- a/crys3d/command_line/multiplicity_viewer.py +++ b/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(""" diff --git a/crys3d/hklview/jsview_3d.py b/crys3d/hklview/jsview_3d.py index 591d0179cd..78a9835dbb 100644 --- a/crys3d/hklview/jsview_3d.py +++ b/crys3d/hklview/jsview_3d.py @@ -12,6 +12,7 @@ import os.path, time import libtbx import webbrowser, tempfile +from six.moves import range diff --git a/crys3d/model.py b/crys3d/model.py index 146698edd8..9c4f3f4f03 100644 --- a/crys3d/model.py +++ b/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 diff --git a/crys3d/qttbx/xray_structure_viewer.py b/crys3d/qttbx/xray_structure_viewer.py index 2feea48eaf..0252da5f44 100644 --- a/crys3d/qttbx/xray_structure_viewer.py +++ b/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) diff --git a/crys3d/reverse_selection.py b/crys3d/reverse_selection.py index 17760a5add..a33eb37d50 100644 --- a/crys3d/reverse_selection.py +++ b/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"'") diff --git a/crys3d/ribbon.py b/crys3d/ribbon.py index 199b0a7cbb..433acb2b0e 100644 --- a/crys3d/ribbon.py +++ b/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) : diff --git a/crys3d/wx_extra.py b/crys3d/wx_extra.py index 7523efbd51..b41bfbbf1a 100644 --- a/crys3d/wx_extra.py +++ b/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: diff --git a/cudatbx/cufft/tst_ext.py b/cudatbx/cufft/tst_ext.py index ed1e31909a..871f2a45f3 100644 --- a/cudatbx/cufft/tst_ext.py +++ b/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) @@ -108,7 +109,7 @@ 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) @@ -116,7 +117,7 @@ def exercise_complex_to_complex_3d(): 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) diff --git a/cudatbx/math/special_functions/tst_spherical_bessel_jn.py b/cudatbx/math/special_functions/tst_spherical_bessel_jn.py index 0a7e3eff21..d90346b3ef 100644 --- a/cudatbx/math/special_functions/tst_spherical_bessel_jn.py +++ b/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() diff --git a/cudatbx/scattering/tst_direct_summation.py b/cudatbx/scattering/tst_direct_summation.py index 501fddecc4..1f323db41c 100644 --- a/cudatbx/scattering/tst_direct_summation.py +++ b/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\ @@ -39,7 +40,7 @@ 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() @@ -47,7 +48,7 @@ def test_direct_summation(): 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) diff --git a/dox.sphinx/conf.py b/dox.sphinx/conf.py index f8d38a6bea..204177f24a 100644 --- a/dox.sphinx/conf.py +++ b/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 diff --git a/dox/compcomm/newsletter09/sf_times_digest.py b/dox/compcomm/newsletter09/sf_times_digest.py index a0ff835631..3b6ee3c390 100644 --- a/dox/compcomm/newsletter09/sf_times_digest.py +++ b/dox/compcomm/newsletter09/sf_times_digest.py @@ -1,5 +1,6 @@ from __future__ import absolute_import, division, print_function import sys, os +from six.moves import range op = os.path nodes_32bit = set("""\ @@ -36,13 +37,13 @@ class table_entry(object): def __init__(O, lines): assert len(lines) == 16 - for i_line in xrange(5): + for i_line in range(5): line = lines[i_line] slot = O.__slots__[i_line] assert line.startswith(slot+": ") setattr(O, slot, line[len(slot)+2:]) O.compiler_versions = [] - for i_line in xrange(5, 10): + for i_line in range(5, 10): line = lines[i_line] assert line.startswith("compiler: ") O.compiler_versions.append(line[10:]) @@ -55,7 +56,7 @@ def __init__(O, lines): O.n_scatt = int(flds[3]) O.n_refl = int(flds[5]) O.all_utimes = [] - for i_line in xrange(11, 16): + for i_line in range(11, 16): line = lines[i_line] flds = line.split() assert len(flds) == 8 @@ -116,7 +117,7 @@ def process_time_tables(): result = [] lines = open(time_tables_path).read().splitlines() assert len(lines) == 22 * 17 - for i_line in xrange(0, len(lines), 17): + for i_line in range(0, len(lines), 17): assert lines[i_line] == "" result.append(table_entry(lines=lines[i_line+1:i_line+17])) return result diff --git a/dox/siena2005/sort_merge.py b/dox/siena2005/sort_merge.py index a4f381b6a8..f958c701ac 100644 --- a/dox/siena2005/sort_merge.py +++ b/dox/siena2005/sort_merge.py @@ -19,6 +19,7 @@ from cctbx import sgtbx from cctbx import miller import sys +from six.moves import range def run(args): assert len(args) == 1 @@ -36,7 +37,7 @@ def run(args): miller_indices = flex.miller_index() data = flex.double() sigmas = flex.double() - for i_line in xrange(3+n_symops,len(lines)): + for i_line in range(3+n_symops,len(lines)): fields = lines[i_line].split() assert len(fields) == 5 miller_indices.append([int(value) for value in fields[:3]]) diff --git a/dox/siena2005/sort_merge_initial.py b/dox/siena2005/sort_merge_initial.py index 51b5244741..77314804ab 100644 --- a/dox/siena2005/sort_merge_initial.py +++ b/dox/siena2005/sort_merge_initial.py @@ -5,6 +5,7 @@ from cctbx import sgtbx from cctbx import miller import sys +from six.moves import range def run(args): assert len(args) == 1 @@ -22,7 +23,7 @@ def run(args): miller_indices = flex.miller_index() data = flex.double() sigmas = flex.double() - for i_line in xrange(3+n_symops,len(lines)): + for i_line in range(3+n_symops,len(lines)): fields = lines[i_line].split() assert len(fields) == 5 miller_indices.append([int(value) for value in fields[:3]]) diff --git a/fable/test/sf_times.py b/fable/test/sf_times.py index 00bb35890c..ab1445c2a4 100644 --- a/fable/test/sf_times.py +++ b/fable/test/sf_times.py @@ -6,6 +6,7 @@ import platform import time import sys, os +from six.moves import range op = os.path __this_script__ = "cctbx_project/fable/test/sf_times.py" @@ -238,7 +239,7 @@ def run_once(): utimes.append(utime) print("sample utime: %.2f" % utime) sys.stdout.flush() - for _ in xrange(8): + for _ in range(8): run_once() return min(utimes) diff --git a/fftw3tbx/tst_ext.py b/fftw3tbx/tst_ext.py index 81061df93a..e4e992dd86 100644 --- a/fftw3tbx/tst_ext.py +++ b/fftw3tbx/tst_ext.py @@ -6,13 +6,14 @@ import libtbx.utils import time import sys +from six.moves import range try: from cctbx import maptbx except ImportError: maptbx = None def exercise_complex_to_complex(): print("complex_to_complex") - for n in xrange(1,256+1): + for n in range(1,256+1): dp = (flex.random_double(size=n)*2-1) * flex.polar( 1, flex.random_double(size=n)*2-1) dw = dp.deep_copy() @@ -30,20 +31,20 @@ def exercise_complex_to_complex(): 1, flex.random_double(size=n)*2-1) # 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) # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() fftw3tbx.complex_to_complex_in_place(data=d, exp_sign=-1) fftw3tbx.complex_to_complex_in_place(data=d, exp_sign=+1) print(" fftw: %.2f seconds" % (time.time()-t0-overhead)) # 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(n).forward(d) fftpack.complex_to_complex(n).backward(d) @@ -61,13 +62,13 @@ 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) # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() fftw3tbx.complex_to_complex_3d_in_place(data=d, exp_sign=-1) fftw3tbx.complex_to_complex_3d_in_place(data=d, exp_sign=+1) @@ -75,7 +76,7 @@ def exercise_complex_to_complex_3d(): 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) @@ -87,7 +88,7 @@ def exercise_complex_to_complex_3d(): def exercise_real_to_complex(): print("real_to_complex") - for n in xrange(1,256+1): + for n in range(1,256+1): fft = fftpack.real_to_complex(n) dp = flex.random_double(size=n)*2-1 dp.resize(flex.grid(fft.m_real()).set_focus(n)) @@ -106,20 +107,20 @@ def exercise_real_to_complex(): d0.resize(flex.grid(fft.m_real()).set_focus(n)) # 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) # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() c = fftw3tbx.real_to_complex_in_place(data=d) fftw3tbx.complex_to_real_in_place(data=c, n=n) print(" fftw: %.2f seconds" % (time.time()-t0-overhead)) # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() c = fftpack.real_to_complex(n).forward(d) fftpack.real_to_complex(n).backward(c) @@ -141,13 +142,13 @@ def exercise_real_to_complex_3d(): d0.reshape(flex.grid(m_real).set_focus(n_real)) # 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) # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() c = fftw3tbx.real_to_complex_3d_in_place(data=d) assert c.all() == fft.n_complex() @@ -163,7 +164,7 @@ def exercise_real_to_complex_3d(): rw = d / np # t0 = time.time() - for i_trial in xrange(n_repeats): + for i_trial in range(n_repeats): d = d0.deep_copy() c = fftpack.real_to_complex_3d(n_real).forward(d) assert c.all() == fft.n_complex() diff --git a/gltbx/generate_defines_bpl.py b/gltbx/generate_defines_bpl.py index 09ed622399..7243c0b14c 100644 --- a/gltbx/generate_defines_bpl.py +++ b/gltbx/generate_defines_bpl.py @@ -3,6 +3,7 @@ import libtbx.load_env import libtbx.path import os +from six.moves import range this = "gltbx.generate_defines_bpl" diff --git a/gltbx/generate_fonts_ucs_cpp.py b/gltbx/generate_fonts_ucs_cpp.py index 24bae35f27..5dfcae9a51 100644 --- a/gltbx/generate_fonts_ucs_cpp.py +++ b/gltbx/generate_fonts_ucs_cpp.py @@ -3,6 +3,7 @@ from libtbx.str_utils import show_string import os import sys +from six.moves import range op = os.path class font_info(object): diff --git a/gltbx/generate_functions_bpl.py b/gltbx/generate_functions_bpl.py index 736796aeae..4330199f4d 100644 --- a/gltbx/generate_functions_bpl.py +++ b/gltbx/generate_functions_bpl.py @@ -5,6 +5,7 @@ import libtbx.path import os import sys +from six.moves import range this = "gltbx.generate_functions_bpl" diff --git a/gltbx/images.py b/gltbx/images.py index f92d30df8c..3296967008 100644 --- a/gltbx/images.py +++ b/gltbx/images.py @@ -1,9 +1,10 @@ from __future__ import absolute_import, division, print_function import os.path +from six.moves import range def encode(data): edata = "" - for i in xrange(len(data)): + for i in range(len(data)): edata += "%.2x" % ord(data[i]) return edata @@ -42,7 +43,7 @@ def decode(self, edata): "8": 8, "9": 9, "a": 10, "b": 11, "c": 12, "d": 13, "e": 14, "f": 15} data = "" - for i in xrange(0, len(edata), 2): + for i in range(0, len(edata), 2): data += chr(hex_chars[edata[i]] * 16 + hex_chars[edata[i+1]]) return data diff --git a/gltbx/tst.py b/gltbx/tst.py index 5b704cd419..e3723e5d2d 100644 --- a/gltbx/tst.py +++ b/gltbx/tst.py @@ -3,16 +3,17 @@ from gltbx import glu from libtbx.test_utils import Exception_expected, show_diff import sys +from six.moves import range def exercise_converter(): textures = [] gl.glGenTextures(3, textures) assert textures == [0,0,0] - for i in xrange(10000): + for i in range(10000): textures = [] gl.glGenTextures(3, textures) assert textures == [0,0,0] - for i in xrange(10000): + for i in range(10000): textures = [9,3,5] gl.glGenTextures(3, textures) assert textures == [9,3,5] diff --git a/gltbx/tst_ellipsoids.py b/gltbx/tst_ellipsoids.py index 01e7a994d0..2758420545 100644 --- a/gltbx/tst_ellipsoids.py +++ b/gltbx/tst_ellipsoids.py @@ -5,22 +5,23 @@ import scitbx.math from scitbx import matrix from libtbx.test_utils import approx_equal +from six.moves import range def exercise_ellipsoid(n_trials=100, n_sub_trials=10): from gltbx import quadrics rnd = random.Random(0) - for i in xrange(n_trials): - centre = matrix.col([ rnd.random() for k in xrange(3) ]) - half_lengths = matrix.col([ 0.1 + rnd.random() for k in xrange(3) ]) + for i in range(n_trials): + centre = matrix.col([ rnd.random() for k in range(3) ]) + half_lengths = matrix.col([ 0.1 + rnd.random() for k in range(3) ]) r = scitbx.math.euler_angles_as_matrix( - [ rnd.uniform(0, 360) for i in xrange(3) ], deg=True) + [ rnd.uniform(0, 360) for i in range(3) ], deg=True) metrics = r * matrix.diag([ x**2 for x in half_lengths ]) * r.transpose() t = quadrics.ellipsoid_to_sphere_transform(centre, metrics.as_sym_mat3()) assert approx_equal(t.translation_part(), centre) m = matrix.sqr(t.linear_part()) assert m.determinant() > 0 - for j in xrange(n_sub_trials): - y = matrix.col([ rnd.random() for k in xrange(3) ]) + for j in range(n_sub_trials): + y = matrix.col([ rnd.random() for k in range(3) ]) c_y = y.transpose() * y x = m*y c_x = x.transpose() * metrics.inverse() * x diff --git a/gltbx/tst_viewer_utils.py b/gltbx/tst_viewer_utils.py index 636c63b064..8162a4dc51 100644 --- a/gltbx/tst_viewer_utils.py +++ b/gltbx/tst_viewer_utils.py @@ -2,6 +2,7 @@ from scitbx.array_family import flex, shared import gltbx.viewer_utils +from six.moves import range # this is the pdb file used to create the bonds table for testing ethanol_pdb = """ @@ -39,7 +40,7 @@ def exercise(): [] ]) - atoms_drawable = flex.bool([True for i in xrange(0, 10) ]) + atoms_drawable = flex.bool([True for i in range(0, 10) ]) atoms_drawable_non_h = flex.bool( [True, True, False, False, False, True, False, False, False, True] ) diff --git a/gltbx/wx_motion_on_tab.py b/gltbx/wx_motion_on_tab.py index 2ecb99a682..b7c16aab24 100644 --- a/gltbx/wx_motion_on_tab.py +++ b/gltbx/wx_motion_on_tab.py @@ -14,6 +14,7 @@ from scitbx import matrix import wx import sys +from six.moves import range class viewer(wx_viewer.show_points_and_lines_mixin): @@ -48,7 +49,7 @@ def motion_callback(self, points): wx.PostEvent(self, wx_viewer.ViewerUpdateEvent(points)) def OnUpdate(self, event): - for i in xrange(len(event.data)): + for i in range(len(event.data)): self.points[i] = event.data[i] self.labels_display_list = None self.lines_display_list = None @@ -89,7 +90,7 @@ def motion(n_steps=20, callback=None): status = callback(points) if status == False : break - for i in xrange(len(points)): + for i in range(len(points)): points[i] += shift i_step += 1 if (i_step % 10 == 0): diff --git a/gltbx/wx_scene.py b/gltbx/wx_scene.py index 4261a576c7..1e5a721e24 100644 --- a/gltbx/wx_scene.py +++ b/gltbx/wx_scene.py @@ -16,6 +16,7 @@ import math import sys import atexit +from six.moves import range def v3distsq(a,b): diff --git a/gltbx/wx_viewer.py b/gltbx/wx_viewer.py index 13c90f734f..938bc4cf4b 100644 --- a/gltbx/wx_viewer.py +++ b/gltbx/wx_viewer.py @@ -13,6 +13,7 @@ import scitbx.math from scitbx import matrix import six +from six.moves import range try: import wx except ImportError: @@ -794,7 +795,7 @@ def draw_minimum_covering_sphere(self): gray = 0.3 glColor3f(gray,gray,gray) glBegin(GL_POLYGON) - for i in xrange(360): + for i in range(360): a = i * math.pi / 180 rs = r * math.sin(a) rc = r * math.cos(a) diff --git a/libtbx/clear_paths.py b/libtbx/clear_paths.py index 93c6b0af66..bc5022e0ac 100644 --- a/libtbx/clear_paths.py +++ b/libtbx/clear_paths.py @@ -5,6 +5,7 @@ import stat import os import os.path as op +from six.moves import range def make_paths_writable_if_possible(paths): os_stat = os.stat diff --git a/libtbx/cluster.py b/libtbx/cluster.py index 0ec9f5a2d9..5407fa6bf1 100644 --- a/libtbx/cluster.py +++ b/libtbx/cluster.py @@ -21,6 +21,7 @@ # from builtins import range +from six.moves import range class ClusteringError(Exception): pass diff --git a/libtbx/command_line/easy_qsub.py b/libtbx/command_line/easy_qsub.py index 0a2a743686..5580f1db35 100644 --- a/libtbx/command_line/easy_qsub.py +++ b/libtbx/command_line/easy_qsub.py @@ -22,6 +22,7 @@ from libtbx import easy_run from libtbx.utils import Sorry +from six.moves import range key_words = { "phenix_source" : str, diff --git a/libtbx/command_line/install.py b/libtbx/command_line/install.py index d7de1b1038..9a51cef5f2 100644 --- a/libtbx/command_line/install.py +++ b/libtbx/command_line/install.py @@ -7,6 +7,7 @@ import shutil import sys from optparse import SUPPRESS_HELP, OptionParser +from six.moves import range try: import procrunner diff --git a/libtbx/command_line/parallel_simple.py b/libtbx/command_line/parallel_simple.py index 94cc9297d4..dbc609caf8 100644 --- a/libtbx/command_line/parallel_simple.py +++ b/libtbx/command_line/parallel_simple.py @@ -3,6 +3,7 @@ import re import time import sys, os +from six.moves import range op = os.path def show_traceback(file): diff --git a/libtbx/command_line/show_dist_paths.py b/libtbx/command_line/show_dist_paths.py index 28d8915a69..1d23e329d6 100644 --- a/libtbx/command_line/show_dist_paths.py +++ b/libtbx/command_line/show_dist_paths.py @@ -1,4 +1,5 @@ from __future__ import absolute_import, division, print_function +from six.moves import range def run(args): import libtbx.load_env diff --git a/libtbx/command_line/show_python_dependencies.py b/libtbx/command_line/show_python_dependencies.py index 6279794e7e..4e40e3e7cb 100644 --- a/libtbx/command_line/show_python_dependencies.py +++ b/libtbx/command_line/show_python_dependencies.py @@ -15,6 +15,7 @@ import libtbx.pkg_utils from libtbx.pkg_utils import pkg_resources from libtbx.pkg_utils import packaging +from six.moves import range BOLD = "\033[1m" diff --git a/libtbx/easy_mp.py b/libtbx/easy_mp.py index bf4405ca5c..514d7e096c 100644 --- a/libtbx/easy_mp.py +++ b/libtbx/easy_mp.py @@ -7,6 +7,7 @@ import traceback import os import sys +from six.moves import range _have_maxtasksperchild = (sys.version_info[:2] >= (2,7)) diff --git a/libtbx/easy_profile.py b/libtbx/easy_profile.py index 6c85616c7e..a502e2b166 100644 --- a/libtbx/easy_profile.py +++ b/libtbx/easy_profile.py @@ -1,5 +1,6 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range class easy_profile(object): """ cProfile.Profile easy-to-use wrapper """ diff --git a/libtbx/easy_run.py b/libtbx/easy_run.py index 74195f7ca9..fb2632caf2 100644 --- a/libtbx/easy_run.py +++ b/libtbx/easy_run.py @@ -6,6 +6,7 @@ import sys import threading import signal +from six.moves import range def _show_lines(lines, out, prefix): if (out is None): out = sys.stdout diff --git a/libtbx/math_utils.py b/libtbx/math_utils.py index 27016a1c39..1bfccee77f 100644 --- a/libtbx/math_utils.py +++ b/libtbx/math_utils.py @@ -1,6 +1,7 @@ from __future__ import absolute_import, division, print_function from builtins import object, range import math +from six.moves import range def round2(x, d=0): ''' diff --git a/libtbx/option_parser.py b/libtbx/option_parser.py index 379e853547..9ed436f960 100644 --- a/libtbx/option_parser.py +++ b/libtbx/option_parser.py @@ -6,6 +6,7 @@ import sys from optparse import * +from six.moves import range def check_bool(option, opt, value): v = value.strip().lower() diff --git a/libtbx/path.py b/libtbx/path.py index 30b4ed8763..253e011379 100644 --- a/libtbx/path.py +++ b/libtbx/path.py @@ -4,6 +4,7 @@ import shutil import os import sys +from six.moves import range op = os.path def norm_join(*args): diff --git a/libtbx/phil/tst.py b/libtbx/phil/tst.py index c49ccb2da6..511b400845 100644 --- a/libtbx/phil/tst.py +++ b/libtbx/phil/tst.py @@ -11,6 +11,7 @@ from six.moves import cStringIO as StringIO import copy import sys, os +from six.moves import range def exercise_string_quote_and_tokenize(): n_ok = [0] diff --git a/libtbx/pyframe.py b/libtbx/pyframe.py index 0eec1ace0e..0e643eaab4 100644 --- a/libtbx/pyframe.py +++ b/libtbx/pyframe.py @@ -2,6 +2,7 @@ from __future__ import absolute_import, division, print_function from builtins import range import inspect +from six.moves import range class error(Exception): """ libtbx.python_frame error """ diff --git a/libtbx/queuing_system_utils/looping.py b/libtbx/queuing_system_utils/looping.py index 301aaba281..498362de68 100644 --- a/libtbx/queuing_system_utils/looping.py +++ b/libtbx/queuing_system_utils/looping.py @@ -1,4 +1,5 @@ from __future__ import absolute_import, division, print_function +from six.moves import range def isodd(n): return n & 1 and True or False diff --git a/libtbx/queuing_system_utils/lsf.py b/libtbx/queuing_system_utils/lsf.py index 0652ba609d..86dcdba95e 100644 --- a/libtbx/queuing_system_utils/lsf.py +++ b/libtbx/queuing_system_utils/lsf.py @@ -3,6 +3,7 @@ import subprocess #import sys import os +from six.moves import range class Job: def __init__(self, name, execObj, modules=[], pythonExec='python'): diff --git a/libtbx/queuing_system_utils/scheduling.py b/libtbx/queuing_system_utils/scheduling.py index cde6c61753..ba4d0464ef 100644 --- a/libtbx/queuing_system_utils/scheduling.py +++ b/libtbx/queuing_system_utils/scheduling.py @@ -6,6 +6,7 @@ import time from collections import deque +from six.moves import range class Identifier(object): """ diff --git a/libtbx/queuing_system_utils/sge_utils.py b/libtbx/queuing_system_utils/sge_utils.py index d4f3b2a9b2..b7cd66ae72 100644 --- a/libtbx/queuing_system_utils/sge_utils.py +++ b/libtbx/queuing_system_utils/sge_utils.py @@ -5,6 +5,7 @@ import sys import os +from six.moves import range def int_or_none(v): if (v is None or v == "undefined"): return None diff --git a/libtbx/queuing_system_utils/tst.py b/libtbx/queuing_system_utils/tst.py index 04d7ffb8db..f2af07fecc 100644 --- a/libtbx/queuing_system_utils/tst.py +++ b/libtbx/queuing_system_utils/tst.py @@ -1,4 +1,5 @@ from __future__ import absolute_import, division, print_function +from six.moves import range # XXX this is intended to be a simple template for debugging queueing system # support issues, not a full regression test. diff --git a/libtbx/runtime_utils.py b/libtbx/runtime_utils.py index c00e33d16e..e3b32f5f98 100644 --- a/libtbx/runtime_utils.py +++ b/libtbx/runtime_utils.py @@ -23,6 +23,7 @@ import time import os import sys +from six.moves import range process_master_phil = libtbx.phil.parse(""" run_file = None diff --git a/libtbx/scheduling/file_queue.py b/libtbx/scheduling/file_queue.py index a6d250afc5..d51b999106 100644 --- a/libtbx/scheduling/file_queue.py +++ b/libtbx/scheduling/file_queue.py @@ -5,6 +5,7 @@ import fcntl import tempfile import os +from six.moves import range class instant(object): diff --git a/libtbx/scheduling/parallel_for.py b/libtbx/scheduling/parallel_for.py index 609d2d2b80..8f1a048b0e 100644 --- a/libtbx/scheduling/parallel_for.py +++ b/libtbx/scheduling/parallel_for.py @@ -2,6 +2,7 @@ from builtins import object, range from collections import deque +from six.moves import range class single_pooler(object): """ @@ -73,7 +74,7 @@ def __init__(self, size): def submit_one_job(self, calcsiter, manager): - calculations = [ c for ( i, c ) in zip( range( self.size), calcsiter ) ] + calculations = [ c for ( i, c ) in zip( range(self.size), calcsiter ) ] if not calculations: raise StopIteration diff --git a/libtbx/scheduling/socket_queue.py b/libtbx/scheduling/socket_queue.py index a40e573e4e..e5b7858240 100644 --- a/libtbx/scheduling/socket_queue.py +++ b/libtbx/scheduling/socket_queue.py @@ -1,6 +1,7 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range class MultiQueue(object): def __init__(self): diff --git a/libtbx/sphinx/pubmed.py b/libtbx/sphinx/pubmed.py index 23eb89f2cb..34911df6b2 100644 --- a/libtbx/sphinx/pubmed.py +++ b/libtbx/sphinx/pubmed.py @@ -2,6 +2,7 @@ from builtins import range import docutils.parsers.rst +from six.moves import range def setup(app): app.add_directive('pubmed', PubMedDirective) diff --git a/libtbx/table_utils.py b/libtbx/table_utils.py index fd51867e1e..aa3eacad07 100644 --- a/libtbx/table_utils.py +++ b/libtbx/table_utils.py @@ -7,6 +7,7 @@ ## slightly modifed functionality. ## from builtins import range +from six.moves import range try: # Python 3 from itertools import zip_longest except ImportError: # Python 2 diff --git a/libtbx/test_utils/__init__.py b/libtbx/test_utils/__init__.py index 43a4da7c24..acec7a2b08 100644 --- a/libtbx/test_utils/__init__.py +++ b/libtbx/test_utils/__init__.py @@ -14,6 +14,7 @@ import types import six +from six.moves import range try: import threading except ImportError: diff --git a/libtbx/tst_binary_search.py b/libtbx/tst_binary_search.py index d8ab0ce20c..b5bf4c63c7 100644 --- a/libtbx/tst_binary_search.py +++ b/libtbx/tst_binary_search.py @@ -3,6 +3,7 @@ from libtbx import binary_search import random import sys +from six.moves import range class random_callback(object): diff --git a/libtbx/tst_easy_mp.py b/libtbx/tst_easy_mp.py index dec164193e..a5a6fbb6d7 100644 --- a/libtbx/tst_easy_mp.py +++ b/libtbx/tst_easy_mp.py @@ -5,6 +5,7 @@ from libtbx import Auto from six.moves import cStringIO as StringIO import sys +from six.moves import range def exercise_func_wrapper_sub_directories(): from libtbx.easy_mp import func_wrapper_sub_directories as f diff --git a/libtbx/tst_easy_mp_state.py b/libtbx/tst_easy_mp_state.py index 33fdfb9f2d..682cbfc9ea 100644 --- a/libtbx/tst_easy_mp_state.py +++ b/libtbx/tst_easy_mp_state.py @@ -6,6 +6,7 @@ import string import threading import time +from six.moves import range class state_object(): ''' A simple thread-safe object keeping an internal state. ''' diff --git a/libtbx/tst_easy_pickle.py b/libtbx/tst_easy_pickle.py index f5d2aa7aa9..5bdd93d598 100644 --- a/libtbx/tst_easy_pickle.py +++ b/libtbx/tst_easy_pickle.py @@ -1,5 +1,6 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range def exercise(n, use_dumps=False): from libtbx import easy_pickle import time diff --git a/libtbx/tst_math_utils.py b/libtbx/tst_math_utils.py index b9c4d8b66f..56fdb08c90 100644 --- a/libtbx/tst_math_utils.py +++ b/libtbx/tst_math_utils.py @@ -1,6 +1,7 @@ from __future__ import absolute_import, division, print_function from builtins import range from libtbx.test_utils import approx_equal +from six.moves import range def exercise_integer(): from libtbx.math_utils import iround, iceil, ifloor, nearest_integer diff --git a/libtbx/tst_object_oriented_patterns.py b/libtbx/tst_object_oriented_patterns.py index cba4f5d41f..42287f69ba 100644 --- a/libtbx/tst_object_oriented_patterns.py +++ b/libtbx/tst_object_oriented_patterns.py @@ -3,6 +3,7 @@ from builtins import range from libtbx import object_oriented_patterns as oop from libtbx.test_utils import approx_equal, Exception_expected +from six.moves import range def exercise_injector(): class a(object): diff --git a/libtbx/tst_path.py b/libtbx/tst_path.py index 4974609af5..a756554b17 100644 --- a/libtbx/tst_path.py +++ b/libtbx/tst_path.py @@ -1,5 +1,6 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range def exercise_posix_relpath(f, enable_abspath_if_through_root): # based on .test_relpath() in Python-2.7.2/Lib/test/test_posixpath.py import os diff --git a/libtbx/tst_representation.py b/libtbx/tst_representation.py index 84e28bf00c..60086a3ead 100644 --- a/libtbx/tst_representation.py +++ b/libtbx/tst_representation.py @@ -1,6 +1,7 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range if (__name__ == "__main__"): for x in range(30): J = 7205759403792790 + x diff --git a/libtbx/tst_scheduling.py b/libtbx/tst_scheduling.py index a45d546da4..61395fc06a 100644 --- a/libtbx/tst_scheduling.py +++ b/libtbx/tst_scheduling.py @@ -2,6 +2,7 @@ import unittest import time +from six.moves import range def normal_function(arg, wait): diff --git a/libtbx/tst_str_utils.py b/libtbx/tst_str_utils.py index 3af075107b..8b0b444384 100644 --- a/libtbx/tst_str_utils.py +++ b/libtbx/tst_str_utils.py @@ -1,4 +1,5 @@ from __future__ import absolute_import, division, print_function +from six.moves import range def exercise(): from libtbx.test_utils import show_diff, Exception_expected from six.moves import cPickle as pickle diff --git a/libtbx/tst_thread_utils.py b/libtbx/tst_thread_utils.py index 95e64f6226..04d5d2300d 100644 --- a/libtbx/tst_thread_utils.py +++ b/libtbx/tst_thread_utils.py @@ -9,6 +9,7 @@ from libtbx.utils import Sorry, Abort import time import sys +from six.moves import range ######################################################################## # THREADING ONLY diff --git a/libtbx/tst_topological_sort.py b/libtbx/tst_topological_sort.py index e471d27489..f85e69151d 100644 --- a/libtbx/tst_topological_sort.py +++ b/libtbx/tst_topological_sort.py @@ -1,5 +1,6 @@ from __future__ import absolute_import, division, print_function from builtins import range +from six.moves import range def exercise_specific(): from libtbx.topological_sort import stable from libtbx.topological_sort import strongly_connected_components as scc diff --git a/libtbx/tst_utils.py b/libtbx/tst_utils.py index a63fe3c5ce..c04dd49a63 100644 --- a/libtbx/tst_utils.py +++ b/libtbx/tst_utils.py @@ -9,6 +9,7 @@ import os import stat import tempfile +from six.moves import range def exercise_misc(): utils.host_and_user().show(prefix="### ") diff --git a/libtbx/utils.py b/libtbx/utils.py index fafd6d7d58..3de272ed7f 100644 --- a/libtbx/utils.py +++ b/libtbx/utils.py @@ -19,6 +19,7 @@ from libtbx.queuing_system_utils import pbs_utils, sge_utils from libtbx.math_utils import round2 from libtbx.str_utils import show_string +from six.moves import range try: import gzip except ImportError: gzip = None diff --git a/libtbx/xmlrpc_utils.py b/libtbx/xmlrpc_utils.py index 163b59013c..47dbfde495 100644 --- a/libtbx/xmlrpc_utils.py +++ b/libtbx/xmlrpc_utils.py @@ -67,6 +67,7 @@ import random import os import sys +from six.moves import range # http://stackoverflow.com/questions/372365/set-timeout-for-xmlrpclib-serverproxy class TimeoutTransport(xmlrpclib.Transport): diff --git a/rstbx/bpcx/compare_mosflm_xds.py b/rstbx/bpcx/compare_mosflm_xds.py index d839b6b689..b646c6d81d 100644 --- a/rstbx/bpcx/compare_mosflm_xds.py +++ b/rstbx/bpcx/compare_mosflm_xds.py @@ -31,6 +31,7 @@ from annlib_ext import AnnAdaptor as ann_adaptor from cctbx.sgtbx import space_group, space_group_symbols from cctbx.miller import map_to_asu +from six.moves import range def meansd(values): assert(len(values) > 3) diff --git a/rstbx/bpcx/detector_model/detector.py b/rstbx/bpcx/detector_model/detector.py index 085f03075f..7a73866158 100644 --- a/rstbx/bpcx/detector_model/detector.py +++ b/rstbx/bpcx/detector_model/detector.py @@ -3,6 +3,7 @@ from scitbx import matrix from rstbx.bpcx import sensor +from six.moves import range class detector: '''An abstract class definition for X-ray detectors which are assumed to diff --git a/rstbx/bpcx/ersatz_misset.py b/rstbx/bpcx/ersatz_misset.py index 0e349dd53c..852e45e33d 100644 --- a/rstbx/bpcx/ersatz_misset.py +++ b/rstbx/bpcx/ersatz_misset.py @@ -6,6 +6,7 @@ from scitbx.math import r3_rotation_axis_and_angle_as_matrix from rstbx.cftbx.coordinate_frame_converter import coordinate_frame_converter +from six.moves import range # ersatz_misset - # diff --git a/rstbx/bpcx/uc1_2_positions.py b/rstbx/bpcx/uc1_2_positions.py index dd9cf50104..88a165a03d 100644 --- a/rstbx/bpcx/uc1_2_positions.py +++ b/rstbx/bpcx/uc1_2_positions.py @@ -13,6 +13,7 @@ from cctbx.array_family import flex from annlib_ext import AnnAdaptor as ann_adaptor from scitbx import matrix +from six.moves import range def meansd(values): diff --git a/rstbx/bpcx/uc1_2_positions_idx.py b/rstbx/bpcx/uc1_2_positions_idx.py index 42703f619d..40aa754e48 100644 --- a/rstbx/bpcx/uc1_2_positions_idx.py +++ b/rstbx/bpcx/uc1_2_positions_idx.py @@ -13,6 +13,7 @@ from cctbx.array_family import flex from annlib_ext import AnnAdaptor as ann_adaptor from scitbx import matrix +from six.moves import range def meansd(values): diff --git a/rstbx/bpcx/uc1_2_validate.py b/rstbx/bpcx/uc1_2_validate.py index b1e253ef5d..ce23a4e4a3 100644 --- a/rstbx/bpcx/uc1_2_validate.py +++ b/rstbx/bpcx/uc1_2_validate.py @@ -12,6 +12,7 @@ from cctbx.array_family import flex from annlib_ext import AnnAdaptor as ann_adaptor from scitbx import matrix +from six.moves import range def meansd(values): diff --git a/rstbx/cftbx/coordinate_frame_helpers.py b/rstbx/cftbx/coordinate_frame_helpers.py index bcdb2e0410..e627475b68 100644 --- a/rstbx/cftbx/coordinate_frame_helpers.py +++ b/rstbx/cftbx/coordinate_frame_helpers.py @@ -3,6 +3,7 @@ import random from scitbx import matrix from cctbx import sgtbx +from six.moves import range class coordinate_frame_information: '''A bucket class to store coordinate frame information.''' diff --git a/rstbx/diffraction/tst_ewald_sphere.py b/rstbx/diffraction/tst_ewald_sphere.py index 2e236b7198..a44e7dc4b4 100644 --- a/rstbx/diffraction/tst_ewald_sphere.py +++ b/rstbx/diffraction/tst_ewald_sphere.py @@ -7,6 +7,7 @@ from rstbx.diffraction import rotation_angles, reflection_prediction from rstbx.bpcx import sensor from libtbx.test_utils import approx_equal +from six.moves import range # This script (provided by Graeme Winter) will take the quartz structure and # simulate a rotation around the 0 0 1 reflection and 1 0 1 reflection. diff --git a/rstbx/slip_viewer/ring_frame.py b/rstbx/slip_viewer/ring_frame.py index 7c811ae882..7238d071eb 100644 --- a/rstbx/slip_viewer/ring_frame.py +++ b/rstbx/slip_viewer/ring_frame.py @@ -4,6 +4,7 @@ # $Id$ import wx +from six.moves import range class RingSettingsFrame(wx.MiniFrame): diff --git a/rstbx/slip_viewer/slip_display.py b/rstbx/slip_viewer/slip_display.py index 21b6751d81..f07dbae367 100644 --- a/rstbx/slip_viewer/slip_display.py +++ b/rstbx/slip_viewer/slip_display.py @@ -31,6 +31,7 @@ from . import pyslip from . import tile_generation +from six.moves import range pyslip._Tiles = tile_generation._Tiles ###### diff --git a/rstbx/viewer/__init__.py b/rstbx/viewer/__init__.py index 1e91060bbd..3f7457f15b 100644 --- a/rstbx/viewer/__init__.py +++ b/rstbx/viewer/__init__.py @@ -5,6 +5,7 @@ from libtbx.str_utils import format_value from libtbx.utils import Sorry import math +from six.moves import range pi_over_180 = math.pi / 180 diff --git a/rstbx/viewer/pixels3d.py b/rstbx/viewer/pixels3d.py index 7e3254d705..728b252e1e 100644 --- a/rstbx/viewer/pixels3d.py +++ b/rstbx/viewer/pixels3d.py @@ -8,6 +8,7 @@ from scitbx.array_family import flex from math import log import wx +from six.moves import range def glbox(xyz1, xyz2): x1 = min(xyz1[0], xyz2[0]) diff --git a/simtbx/nanoBragg/nanoBragg_gui_frames.py b/simtbx/nanoBragg/nanoBragg_gui_frames.py index bc658aa34a..deec3e3c4a 100644 --- a/simtbx/nanoBragg/nanoBragg_gui_frames.py +++ b/simtbx/nanoBragg/nanoBragg_gui_frames.py @@ -20,6 +20,7 @@ from simtbx.nanoBragg import nanoBragg_threads as thr from iota.components import iota_ui_controls as ct from iota.components.iota_utils import InputFinder, WxFlags, noneset +from six.moves import range ginp = InputFinder() import time diff --git a/simtbx/nanoBragg/tst_gaussian_mosaicity.py b/simtbx/nanoBragg/tst_gaussian_mosaicity.py index 925ea6a09a..3e2e3ac5e0 100644 --- a/simtbx/nanoBragg/tst_gaussian_mosaicity.py +++ b/simtbx/nanoBragg/tst_gaussian_mosaicity.py @@ -5,6 +5,7 @@ import libtbx.load_env # possibly implicit import math from libtbx.test_utils import approx_equal +from six.moves import range class plotter: def __init__(self, tophat, normal): diff --git a/simtbx/nanoBragg/tst_nanoBragg_multipanel.py b/simtbx/nanoBragg/tst_nanoBragg_multipanel.py index 4b87f25a67..d0b5a660f4 100644 --- a/simtbx/nanoBragg/tst_nanoBragg_multipanel.py +++ b/simtbx/nanoBragg/tst_nanoBragg_multipanel.py @@ -11,6 +11,7 @@ from dxtbx.model.beam import BeamFactory from dxtbx.model.crystal import CrystalFactory from dxtbx.model.detector import DetectorFactory, Detector, Panel +from six.moves import range # dxtbx beam model description diff --git a/simtbx/nanoBragg/tst_nanoBragg_pilatus.py b/simtbx/nanoBragg/tst_nanoBragg_pilatus.py index 4d96b068b3..6cf9393ca6 100644 --- a/simtbx/nanoBragg/tst_nanoBragg_pilatus.py +++ b/simtbx/nanoBragg/tst_nanoBragg_pilatus.py @@ -11,6 +11,7 @@ import libtbx.load_env # possibly implicit from cctbx import crystal from cctbx import miller +from six.moves import range assert miller pdb_lines = """HEADER TEST diff --git a/spotfinder/servers/mp_spotfinder_server_read_file.py b/spotfinder/servers/mp_spotfinder_server_read_file.py index 5ed1824c54..79c4e594a4 100644 --- a/spotfinder/servers/mp_spotfinder_server_read_file.py +++ b/spotfinder/servers/mp_spotfinder_server_read_file.py @@ -4,6 +4,7 @@ from multiprocessing import Process, current_process from urlparse import urlparse +from six.moves import range #backward compatibility with Python 2.5 try: from urlparse import parse_qs except Exception: from cgi import parse_qs