Author: semor
Date: Thu Aug 25 14:43:50 2011
New Revision: 14450
URL: http://svn.gna.org/viewcvs/relax?rev=14450&view=rev
Log:
Merged revisions 14428-14429,14431,14433,14436-14442,14446-14447 via svnmerge
from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r14428 | bugman | 2011-08-25 11:41:18 +0200 (Thu, 25 Aug 2011) | 5 lines
Deleted the STDOUT and STDERR capture mess in MF_minimise_command!
This was a horrible design breaking both the GUI and the test suite!!!
........
r14429 | bugman | 2011-08-25 11:42:03 +0200 (Thu, 25 Aug 2011) | 5 lines
The uni-processor call to capture_stdio() has been removed.
No IO redirection will be performed in uni-processor mode.
........
r14431 | bugman | 2011-08-25 11:49:34 +0200 (Thu, 25 Aug 2011) | 6 lines
Removed the IO redirection from the uni-processor return_object() method.
IO redirection in the 'multi' package is a bad, bad idea and destroys all
IO redirection any Python
program is attempting to do.
........
r14433 | bugman | 2011-08-25 11:55:56 +0200 (Thu, 25 Aug 2011) | 6 lines
Eliminated the restore_stdio() method from the multi package.
The redirection of IO streams is totally incompatible with an IO
redirection performed by the
underlying Python program.
........
r14436 | bugman | 2011-08-25 12:12:25 +0200 (Thu, 25 Aug 2011) | 5 lines
Fix for the RelaxError system - the status singleton was not being imported.
This was a result of a faulty merger of the gui_testing branch.
........
r14437 | bugman | 2011-08-25 12:13:07 +0200 (Thu, 25 Aug 2011) | 5 lines
Removed the _sys_exit module variable from the mpi4py processor.
This is unnecessary.
........
r14438 | bugman | 2011-08-25 12:18:40 +0200 (Thu, 25 Aug 2011) | 3 lines
Removed a pile of unused code from the mpi4py processor module.
........
r14439 | bugman | 2011-08-25 12:19:59 +0200 (Thu, 25 Aug 2011) | 6 lines
Reverted r14438 as the code actually was used.
The command used was:
svn merge -r14438:14437 .
........
r14440 | bugman | 2011-08-25 12:22:17 +0200 (Thu, 25 Aug 2011) | 3 lines
Some cleaning up of the mpi4py processor module.
........
r14441 | bugman | 2011-08-25 12:24:18 +0200 (Thu, 25 Aug 2011) | 6 lines
Reverted r14437 as _sys_exit is necessary for the mpi4py processor module.
The command used was:
svn merge -r14437:14436 .
........
r14442 | bugman | 2011-08-25 12:26:31 +0200 (Thu, 25 Aug 2011) | 3 lines
Fix for the pymol.write user function - the file name can be set to None!
........
r14446 | bugman | 2011-08-25 12:53:45 +0200 (Thu, 25 Aug 2011) | 3 lines
Fix for the GUI test mode - the mode variable should be a class variable.
........
r14447 | bugman | 2011-08-25 12:55:11 +0200 (Thu, 25 Aug 2011) | 5 lines
Some more fixes for the 'mode' class variable.
These problems were due to the multi-processor code merger.
........
Modified:
branches/inversion-recovery/ (props changed)
branches/inversion-recovery/multi/mpi4py_processor.py
branches/inversion-recovery/multi/multi_processor_base.py
branches/inversion-recovery/multi/processor.py
branches/inversion-recovery/multi/uni_processor.py
branches/inversion-recovery/prompt/pymol_control.py
branches/inversion-recovery/relax.py
branches/inversion-recovery/relax_errors.py
branches/inversion-recovery/specific_fns/model_free/multi_processor_commands.py
Propchange: branches/inversion-recovery/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Aug 25 14:43:50 2011
@@ -1,1 +1,1 @@
-/1.3:1-14425
+/1.3:1-14449
Modified: branches/inversion-recovery/multi/mpi4py_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/multi/mpi4py_processor.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/multi/mpi4py_processor.py (original)
+++ branches/inversion-recovery/multi/mpi4py_processor.py Thu Aug 25 14:43:50
2011
@@ -60,9 +60,12 @@
break
-# wrapper sys.exit function
-# CHECKME is status ok
def exit(status=None):
+ """Wrapper for the sys.exit function."""
+
+ # CHECKME is status ok
+
+ # Execution on the slave.
if MPI.COMM_WORLD.rank != 0:
if in_main_loop:
raise Exception('sys.exit unexpectedley called on slave!')
@@ -75,10 +78,10 @@
sys.__stderr__.write('***********************************************\n')
sys.__stderr__.write('\n')
MPI.COMM_WORLD.Abort()
+
+ # Execution on the master.
else:
- #print 'here'
exit_mpi()
- #MPI.COMM_WORLD.Abort(1)
_sys_exit(status)
@@ -86,6 +89,7 @@
if MPI.Is_initialized() and not MPI.Is_finalized() and
MPI.COMM_WORLD.rank == 0:
broadcast_command(Exit_command())
ditch_all_results()
+
class Mpi4py_processor(Multi_processor):
Modified: branches/inversion-recovery/multi/multi_processor_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/multi/multi_processor_base.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/multi/multi_processor_base.py (original)
+++ branches/inversion-recovery/multi/multi_processor_base.py Thu Aug 25
14:43:50 2011
@@ -1,6 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2007 Gary S Thompson (https://gna.org/users/varioustoxins)
#
+# Copyright (C) 2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -144,8 +145,6 @@
def post_run(self):
-
- self.restore_stdio()
super(Multi_processor, self).post_run()
Modified: branches/inversion-recovery/multi/processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/multi/processor.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/multi/processor.py (original)
+++ branches/inversion-recovery/multi/processor.py Thu Aug 25 14:43:50 2011
@@ -430,10 +430,6 @@
self._processor_size = processor_size
'''Number of slave processors available in this processor.'''
- # Default STDOUT and STDERR for restoring later on.
- self.orig_stdout = sys.__stdout__
- self.orig_stderr = sys.__stderr__
-
# Capture the STDIO.
self.setup_stdio_capture(stdio_capture)
@@ -677,21 +673,6 @@
'''
return int(math.ceil(math.log10(self.processor_size())))
-
-
- def restore_stdio(self):
- '''Restore sys.stdout and sys.stderr to the system defaults.
-
- @note: sys.stdout and sys.stderr are replaced with sys.__stdout__
ans sys.__stderr__.
- '''
-
- # First flush.
- sys.stdout.flush()
- sys.stderr.flush()
-
- # Then restore the IO streams.
- sys.stdout = self.orig_stdout
- sys.stderr = self.orig_stderr
def return_object(self, result):
Modified: branches/inversion-recovery/multi/uni_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/multi/uni_processor.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/multi/uni_processor.py (original)
+++ branches/inversion-recovery/multi/uni_processor.py Thu Aug 25 14:43:50
2011
@@ -1,7 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2007 Gary S Thompson (https://gna.org/users/varioustoxins)
#
-# Copyright (C) 2010 Edward d'Auvergne
#
+# Copyright (C) 2010-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -111,10 +111,6 @@
def return_object(self, result):
- local_save_stdout = sys.stdout
- local_save_stderr = sys.stderr
- self.restore_stdio()
-
if isinstance(result, Exception):
#FIXME: clear command queue
# and finalise mpi (or restart it if we can!
@@ -132,8 +128,6 @@
else:
message = 'Unexpected result type \n%s \nvalue%s'
%(result.__class__.__name__, result)
raise Exception(message)
- sys.stdout = local_save_stdout
- sys.stderr = local_save_stderr
def run(self):
@@ -152,9 +146,7 @@
for i, command in enumerate(self.command_queue):
completed = (i == last_command)
- self.capture_stdio(self.std_stdio_capture(pre_strings=('', '')))
command.run(self, completed)
- self.restore_stdio()
#self.run_command_queue()
#TODO: add cheques for empty queues and maps if now warn
Modified: branches/inversion-recovery/prompt/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/prompt/pymol_control.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/prompt/pymol_control.py (original)
+++ branches/inversion-recovery/prompt/pymol_control.py Thu Aug 25 14:43:50
2011
@@ -321,7 +321,7 @@
arg_check.is_str_or_num_list(colour_start, 'starting colour of the
linear gradient', size=3, can_be_none=True)
arg_check.is_str_or_num_list(colour_end, 'ending colour of the
linear gradient', size=3, can_be_none=True)
arg_check.is_str(colour_list, 'colour list', can_be_none=True)
- arg_check.is_str_or_inst(file, 'file name')
+ arg_check.is_str_or_inst(file, 'file name', can_be_none=True)
arg_check.is_str(dir, 'directory name', can_be_none=True)
arg_check.is_bool(force, 'force flag')
Modified: branches/inversion-recovery/relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/relax.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/relax.py (original)
+++ branches/inversion-recovery/relax.py Thu Aug 25 14:43:50 2011
@@ -214,7 +214,7 @@
runner.run_unit_tests()
# Execute the relax GUI tests.
- elif mode == 'GUI tests':
+ elif self.mode == 'GUI tests':
# Run the tests.
runner = Test_suite_runner(self.tests)
runner.run_gui_tests()
@@ -229,7 +229,7 @@
# Unknown mode.
else:
- raise relax_errors.RelaxError("The '%s' mode is unknown." % mode)
+ raise relax_errors.RelaxError("The '%s' mode is unknown." %
self.mode)
def arguments(self):
@@ -351,7 +351,7 @@
elif options.unit_tests:
self.mode = 'unit tests'
elif options.gui_tests:
- mode = 'GUI tests'
+ self.mode = 'GUI tests'
# Set the status flag.
status.test_mode = True
Modified: branches/inversion-recovery/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/relax_errors.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
--- branches/inversion-recovery/relax_errors.py (original)
+++ branches/inversion-recovery/relax_errors.py Thu Aug 25 14:43:50 2011
@@ -36,6 +36,7 @@
import time
from types import ClassType
+
# Text variables.
BIN = 'a binary number (0 or 1)'
BOOL = 'a Boolean (True or False)'
@@ -98,6 +99,7 @@
"""Modify the behaviour of the error system."""
# Save the state if the pedantic flag is turned on.
+ from status import Status; status = Status()
if status.pedantic:
save_state()
Modified:
branches/inversion-recovery/specific_fns/model_free/multi_processor_commands.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/model_free/multi_processor_commands.py?rev=14450&r1=14449&r2=14450&view=diff
==============================================================================
---
branches/inversion-recovery/specific_fns/model_free/multi_processor_commands.py
(original)
+++
branches/inversion-recovery/specific_fns/model_free/multi_processor_commands.py
Thu Aug 25 14:43:50 2011
@@ -1,7 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2007 Gary S Thompson (https://gna.org/users/varioustoxins)
#
-# Copyright (C) 2008, 2010 Edward d'Auvergne
#
+# Copyright (C) 2008-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -134,15 +134,7 @@
# Disassemble the results list.
param_vector, func, iter, fc, gc, hc, warning = results
- # Get the STDOUT and STDERR messages.
- #FIXME: we need to interleave stdout and stderr
- (stdout, stderr)= processor.get_stdio_capture()
- result_string = stdout.getvalue() + stderr.getvalue()
- stdout.truncate(0)
- stderr.truncate(0)
-
processor.return_object(MF_result_command(processor,
self.memo_id, param_vector, func, iter, fc, gc, hc, warning, completed=False))
- processor.return_object(Result_string(processor, result_string,
completed=completed))
# An error occurred.
except Exception, e :
r14450 - in /branches/inversion-recovery: ./ multi/ prompt/ specific_fns/model_free/