Replace all references to StringIO/cStringIO to six.moves

libtbx/command_line/easy_qsub.py

@@ -17,14 +17,14 @@
 import os
 import re
 import subprocess
-import StringIO
 import sys
 import time
 import stat
 
 from libtbx import easy_run
 from libtbx.utils import Sorry
 from six.moves import range
+from six.moves import StringIO
 
 key_words = {
   "phenix_source"    : str,
@@ -275,7 +275,7 @@ def process_args(args):
 def get_queue_machine_details():
   cmd = "qstat -f"
   ero = easy_run.fully_buffered(command = cmd)
-  out = StringIO.StringIO()
+  out = StringIO()
   ero.show_stdout(out = out)
   rc = {}
   for line in out.getvalue().split("\n"):
@@ -525,7 +525,7 @@ def _cmp_gap(k1, k2):
 
   # Run the command, and then find the job id in the output
   ero = easy_run.fully_buffered(command = cmd)
-  out = StringIO.StringIO()
+  out = StringIO()
   ero.show_stdout(out = out)
   # Line looks like:
   # "Your job-array 5436256.1-122:1 ("easy_qsub") has been submitted"

libtbx/command_line/import_all_python.py

@@ -4,7 +4,7 @@
 import libtbx.load_env
 from libtbx.utils import multi_out
 from optparse import OptionParser
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import os.path as op
 import os
 import sys

libtbx/command_line/parallel_simple.py

@@ -64,7 +64,7 @@ def run_one_cmd(cmd_info):
         join_stdout_stderr=True,
         stdout_splitlines=False)
     except: # intentional
-      from cStringIO import StringIO
+      from six.moves import cStringIO as StringIO
       sio = StringIO()
       show_traceback(file=sio)
       buffers = None

libtbx/command_line/py_compile_all.py

@@ -1,14 +1,14 @@
 from __future__ import division
 import compileall
-import cStringIO
 import sys, os
+from six.moves import cStringIO as StringIO
 
 def run():
   dirs = sys.argv[1:]
   if (len(dirs) == 0):
     dirs = [os.getcwd()]
-  sys.stdout = cStringIO.StringIO()
-  sys.stderr = cStringIO.StringIO()
+  sys.stdout = StringIO()
+  sys.stderr = StringIO()
   for dir in dirs:
     compileall.compile_dir(dir, 100)
 

libtbx/easy_mp.py

@@ -4,11 +4,11 @@
 from libtbx.str_utils import show_string
 from libtbx.math_utils import ifloor
 from libtbx import Auto
-from cStringIO import StringIO
 import traceback
 import os
 import sys
 from six.moves import range
+from six.moves import cStringIO as StringIO
 
 _have_maxtasksperchild = (sys.version_info[:2] >= (2,7))
 

libtbx/easy_run.py

@@ -215,7 +215,7 @@ def call(command):
   return subprocess.call(args=command, shell=True)
 
 def exercise(args=None):
-  from cStringIO import StringIO
+  from six.moves import cStringIO as StringIO
   import sys
   if (args is None): args = sys.argv[1:]
   verbose = "--verbose" in args

libtbx/env_config.py

@@ -14,7 +14,7 @@
   import six.moves.cPickle as pickle
 except ImportError:
   import pickle
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import re
 import site, sys, os
 op = os.path

libtbx/find_reference_cycles.py

@@ -1,7 +1,7 @@
 from __future__ import division
 from __future__ import print_function
 from types import FrameType
-from StringIO import StringIO
+from six.moves import StringIO
 import gc
 import sys
 

libtbx/introspection.py

@@ -63,7 +63,7 @@ def print_trace(frame, event, arg):
 
 def start_print_trace():
   if ("pydoc" in sys.modules):
-    from cStringIO import StringIO
+    from six.moves import cStringIO as StringIO
     s = StringIO()
     show_stack(out=s)
     for line in s.getvalue().splitlines():

libtbx/phil/__init__.py

@@ -7,7 +7,7 @@
 from libtbx.utils import Sorry, format_exception, import_python_object
 from itertools import count
 from libtbx import Auto, slots_getstate_setstate
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import tokenize as python_tokenize
 import warnings
 import math

libtbx/phil/tst.py

@@ -9,7 +9,7 @@
 from libtbx import easy_pickle
 from libtbx import Auto
 import warnings
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import copy
 import sys, os
 from six.moves import range

libtbx/phil/tst_interface.py

@@ -5,7 +5,7 @@
 from libtbx.phil import interface
 import libtbx.load_env
 import libtbx.phil
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import sys
 
 def exercise () :

libtbx/runtime_utils.py

@@ -17,7 +17,8 @@
 from libtbx import adopt_init_args, group_args
 import libtbx.load_env
 import libtbx.phil
-import cStringIO
+from six.moves import cStringIO as StringIO
+
 import traceback
 import signal
 import stat
@@ -488,7 +489,7 @@ def run (args) :
 class simple_client (detached_process_client) :
   def __init__ (self, *args, **kwds) :
     self.n_cb = 0
-    self.out = cStringIO.StringIO()
+    self.out = StringIO()
     detached_process_client.__init__(self, *args, **kwds)
 
   def callback_error (self, error, traceback_info) :

libtbx/server/SocketServer.py

@@ -414,10 +414,10 @@ class DatagramRequestHandler(BaseRequestHandler):
     """Define self.rfile and self.wfile for datagram sockets."""
 
     def setup(self):
-        import StringIO
+        from six.moves import StringIO
         self.packet, self.socket = self.request
-        self.rfile = StringIO.StringIO(self.packet)
-        self.wfile = StringIO.StringIO(self.packet)
+        self.rfile = StringIO(self.packet)
+        self.wfile = StringIO(self.packet)
 
     def finish(self):
         self.socket.sendto(self.wfile.getvalue(), self.client_address)

libtbx/smart_open.py

@@ -3,7 +3,7 @@
 from libtbx.utils import escape_sh_double_quoted, gzip_open, bz2_open
 from libtbx import easy_run
 from libtbx.str_utils import show_string
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import os
 
 def for_reading(file_name, mode="r", gzip_mode="rb"):

libtbx/sphinx/phil.py

@@ -21,7 +21,7 @@ class PhilDirective(Directive):
                  'attributes-level': directives.nonnegative_int}
 
   def run(self):
-    from cStringIO import StringIO
+    from six.moves import cStringIO as StringIO
 
     phil_include = self.arguments[0]
     expert_level = self.options.get('expert-level', None)

libtbx/str_utils.py

@@ -1,7 +1,7 @@
 
 from __future__ import division, absolute_import
 from __future__ import print_function
-import cStringIO
+from six.moves import cStringIO
 import sys
 import six
 from six.moves import zip
@@ -291,7 +291,7 @@ def next_non_empty(self):
 # cStringIO with pickling support
 class StringIO (object) :
   def __init__ (self, *args, **kwds) :
-    self._buffer = cStringIO.StringIO(*args, **kwds)
+    self._buffer = cStringIO(*args, **kwds)
 
   def __getattr__ (self, *args, **kwds) :
     return getattr(self._buffer, *args, **kwds)

libtbx/table_utils.py

@@ -9,7 +9,8 @@
 ##
 from __future__ import absolute_import
 import libtbx.forward_compatibility # for sum
-import cStringIO,operator
+import operator
+from six.moves import cStringIO as StringIO
 from functools import reduce
 from six.moves import map
 from six.moves import range
@@ -62,7 +63,7 @@ def row_wrapper(row):
                     + len(delim)*(len(max_widths)-1))
     # select the appropriate justify method
     justify = {'center':str.center, 'right':str.rjust, 'left':str.ljust}[justify.lower()]
-    output=cStringIO.StringIO()
+    output=StringIO()
 
     total_row_width=0
     line=None
@@ -316,7 +317,7 @@ def show(self,message,out,columns_to_print=['Limit','Population','MeanI']):
       self.printTable(columns_to_print,printed_rows=to_print,out=out)
       print(legend, file=out)
 
-  OC = cStringIO.StringIO()
+  OC = StringIO()
   derived_1 = typical_use_case_1()
   derived_1.show(message="Analysis of signals after noise suppression",out=OC)
   assert "\n".join([i.rstrip() for i in OC.getvalue().split("\n")]) == \
@@ -358,7 +359,7 @@ def show(self,default=['Limit','Population','Fract','adjustPop'],out=None):
       self.printTable(default,out=out)
       #print >>out,"0"
 
-  OC = cStringIO.StringIO()
+  OC = StringIO()
   derived_2 = typical_use_case_2()
   derived_2.show(out=OC)
 

libtbx/test_utils/__init__.py

@@ -667,7 +667,7 @@ def run_command(
   return cmd_result
 
 def exercise():
-  from cStringIO import StringIO
+  from six.moves import cStringIO as StringIO
   assert approx_equal(1, 1)
   out = StringIO()
   assert not approx_equal(1, 0, out=out)

libtbx/test_utils/parallel.py

@@ -8,7 +8,7 @@
 from libtbx.utils import import_python_object, Sorry, multi_out
 from libtbx import group_args, Auto
 from multiprocessing import Pool, cpu_count
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import traceback
 import time
 import os

libtbx/tst_easy_mp.py

@@ -4,7 +4,7 @@
 from libtbx import unpicklable
 from libtbx.test_utils import Exception_expected
 from libtbx import Auto
-from cStringIO import StringIO
+from six.moves import cStringIO as StringIO
 import sys
 from six.moves import range
 from six.moves import zip

libtbx/tst_path.py

@@ -125,7 +125,7 @@ def exercise_move_old_create_new_directory():
 
 def exercise_cleanup () :
   from libtbx.path import clean_out_directory
-  from cStringIO import StringIO
+  from six.moves import cStringIO as StringIO
   import shutil
   import os
   if os.path.isdir("tmp_libtbx_path_cleanup") :

libtbx/tst_str_utils.py

@@ -2,6 +2,8 @@
 from __future__ import print_function
 from __future__ import absolute_import
 from six.moves import range
+from six.moves import cStringIO as StringIO
+
 def exercise():
   from libtbx.test_utils import show_diff, Exception_expected
   import six.moves.cPickle
@@ -61,8 +63,7 @@ def exercise():
 ^world """ % " "
   #
   from libtbx.str_utils import show_sorted_by_counts
-  import cStringIO
-  out = cStringIO.StringIO()
+  out = StringIO()
   assert show_sorted_by_counts(
     label_count_pairs=[("b", 3), ("a", 3), ("c", -2)],
     out=out, prefix="%")
@@ -71,7 +72,7 @@ def exercise():
 %"b"  3
 %"c" -2
 """)
-  out = cStringIO.StringIO()
+  out = StringIO()
   assert show_sorted_by_counts(
     label_count_pairs=[("b", -3), ("a", -3), ("c", 2)], reverse=False,
      out=out, prefix="%", annotations=[None, "", "x"])
@@ -92,10 +93,10 @@ def exercise():
       ["this is", "a very", "long", "sentence", "indeed"])]:
     assert [block for block in line_breaker(string, width=7)]==expected_result
   #
-  from libtbx.str_utils import StringIO
-  out1 = cStringIO.StringIO()
-  out2 = StringIO()
-  out3 = StringIO("Hello world!\n")
+  from libtbx.str_utils import StringIO as pickleStringIO
+  out1 = StringIO()
+  out2 = pickleStringIO()
+  out3 = pickleStringIO("Hello world!\n")
   print("Hello world!", file=out1)
   print("Hello world!", file=out2)
   try :

libtbx/tst_thread_utils.py

@@ -8,6 +8,7 @@
 import time
 import sys
 from six.moves import range
+from six.moves import cStringIO as StringIO
 
 ########################################################################
 # THREADING ONLY
@@ -182,8 +183,7 @@ def _target_function04 (args, kwds, connection) :
   return _tst_print(*args, **kwds)
 
 def tst_stdout () :
-  import cStringIO
-  tmpout = cStringIO.StringIO()
+  tmpout = StringIO()
   _tst_print(tmpout)
 
   for buffer_stdout in [True, False] :
@@ -254,8 +254,7 @@ def tst_abort_2 () :
 
 def _target_function08 (args, kwds, connection) :
   import libtbx.callbacks # import dependency
-  import cStringIO
-  log = cStringIO.StringIO()
+  log = StringIO()
   libtbx.call_back.set_warning_log(log)
   time.sleep(1)
   libtbx.warn("Hello, world!")

libtbx/tst_utils.py

@@ -3,14 +3,14 @@
 from __future__ import absolute_import
 from libtbx import utils
 from libtbx.test_utils import Exception_expected, approx_equal, show_diff
-from cStringIO import StringIO
 import warnings
 import random
 import time
 import os
 import stat
 import tempfile
 from six.moves import range
+from six.moves import cStringIO as StringIO
 
 def exercise_forward_compatibility():
   import itertools
@@ -349,7 +349,6 @@ def exercise_str_unicode():
 
 def exercise_group_args():
   from libtbx import group_args
-  from cStringIO import StringIO
   out = StringIO()
   a = group_args(
       a=1,