relax SVN archive

Python 3 updates for the frame_order_testing branch.

The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.

Merged revisions 18801-18802 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18801 | bugman | 2013-03-12 16:34:16 +0100 (Tue, 12 Mar 2013) | 6 lines

Added a more informative error message if the platform module is missing.

This is for Python <= 2.2. The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can
simply be copied into the lib/pythonX.X/ directory to fix this.
........
r18802 | bugman | 2013-03-12 16:34:57 +0100 (Tue, 12 Mar 2013) | 3 lines

Slight change to the message printed if the platform module is missing.
........

Slight change to the message printed if the platform module is missing.

Added a more informative error message if the platform module is missing.

This is for Python <= 2.2. The file from http://hg.python.org/cpython/file/2.3/Lib/platform.py can
simply be copied into the lib/pythonX.X/ directory to fix this.

Merged revisions 18799 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18799 | bugman | 2013-03-12 16:20:49 +0100 (Tue, 12 Mar 2013) | 6 lines

Eliminated the os.devnull import flag dep_check.devnull_import.

This is not needed as the compat module defines os.devnull for Python <= 2.3. The devnull module is
no longer part of the relax information printout.
........

Eliminated the os.devnull import flag dep_check.devnull_import.

This is not needed as the compat module defines os.devnull for Python <= 2.3. The devnull module is
no longer part of the relax information printout.

Merged revisions 18773-18774,18778-18779,18781-18783,18788-18797 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18773 | bugman | 2013-03-11 15:47:39 +0100 (Mon, 11 Mar 2013) | 6 lines

Ported the relax 2.2.3 CHANGES file changes back to trunk.

The command used was:
svn merge -r18771:18772 svn+ssh://bugman@.../svn/relax/tags/2.2.3 .
........
r18774 | bugman | 2013-03-11 15:48:09 +0100 (Mon, 11 Mar 2013) | 3 lines

Updated the version number to 2.2.3.
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r18778 | bugman | 2013-03-11 16:35:49 +0100 (Mon, 11 Mar 2013) | 6 lines

Reverted r18774 - the update to version 2.2.3 in the wrong place!

The command used was:
svn merge -r18774:r18773 .
........
r18779 | bugman | 2013-03-11 16:36:22 +0100 (Mon, 11 Mar 2013) | 3 lines

Updated the release checklist document to include the correct instructions for minfx and bmrblib.
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r18781 | bugman | 2013-03-11 16:53:17 +0100 (Mon, 11 Mar 2013) | 6 lines

More fixes for the minfx and bmrblib instructions for the release checklist.

These are the packages bundled with relax (http://gna.org/projects/minfx/ and
http://gna.org/projects/bmrblib/).
........
r18782 | bugman | 2013-03-11 17:11:24 +0100 (Mon, 11 Mar 2013) | 6 lines

Even more fixes for the minfx and bmrblib instructions for the release checklist.

These are the packages bundled with relax (http://gna.org/projects/minfx/ and
http://gna.org/projects/bmrblib/).
........
r18783 | bugman | 2013-03-11 18:00:50 +0100 (Mon, 11 Mar 2013) | 6 lines

Hopefully the last set of fixes for the minfx and bmrblib instructions for the release checklist.

These are the packages bundled with relax (http://gna.org/projects/minfx/ and
http://gna.org/projects/bmrblib/).
........
r18788 | bugman | 2013-03-12 10:52:26 +0100 (Tue, 12 Mar 2013) | 8 lines

Fix for the system tests in the Mac OS X application binary.

The Mf.test_bug_20563_missing_ri_error system test fails in the Mac OS X application binary. The
problem is that the py2app extension used to build the Mac application decides that empty
directories are not to be included in the app, so naturally the test fails when checking for these.
Now empty results files have been added to these directories to trick py2app to include them.
........
r18789 | bugman | 2013-03-12 11:08:39 +0100 (Tue, 12 Mar 2013) | 7 lines

Fixes for the unit test package __all__ list checking.

Now only *.py files and directories are checked. In some cases other files could be present in
the packages, for example the object files when compiling the C modules. These would cause the unit
tests to fail unnecessarily.
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r18790 | bugman | 2013-03-12 11:13:06 +0100 (Tue, 12 Mar 2013) | 7 lines

Fixes for the unit test __all__ list checking for the lib package for the Mac OS X application.

For some reason the py2app extension which creates the app merges the Python installation directory
Resources/lib/python2.7 and the relax lib package into Resources/lib. Now 'python2.7' is
blacklisted when checking the lib package so that the parasitic Python install location is ignored.
........
r18791 | bugman | 2013-03-12 11:21:25 +0100 (Tue, 12 Mar 2013) | 7 lines

Bug fix for the structure RMSD function for when old numpy versions are present.

Older numpy versions do not have the ddof argument for the std() standard deviation function,
therefore relax now catches this, calculates the biased standard deviation formula, and then
multiplies the value by a correction factor to obtain the non-biased estimator.
........
r18792 | bugman | 2013-03-12 11:48:38 +0100 (Tue, 12 Mar 2013) | 3 lines

Docstring editing of the devel_scripts/python_multiversion_test_suite.py development script.
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r18793 | bugman | 2013-03-12 12:16:12 +0100 (Tue, 12 Mar 2013) | 6 lines

Bug fix for the info relax system information module for when spaces are present in the relax path.

If relax is placed into a directory containing spaces, then the determination of the architecture of
the compiled C modules fails.
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r18794 | bugman | 2013-03-12 14:19:35 +0100 (Tue, 12 Mar 2013) | 44 lines

Python 3 fixes for the model-free analysis specific code.

This was causing errors such as:

relax> molmol.macro_write(data_type='rex', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/tmp/tmpuootyr', force=True)
Traceback (most recent call last):
File "/data/edau/relax/relax-trunk/test_suite/system_tests/model_free.py", line 416, in test_bug_20531_molmol_macro_write_relaxfault2
self.interpreter.molmol.macro_write(data_type='rex', dir=ds.tmpdir, force=True)
File "/data/edau/relax/relax-trunk/prompt/uf_objects.py", line 221, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/edau/relax/relax-trunk/generic_fns/molmol.py", line 332, in macro_write
commands = create_macro(data_type=data_type, style=style, colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
File "/data/edau/relax/relax-trunk/generic_fns/molmol.py", line 209, in create_macro
commands = macro(data_type, style, colour_start, colour_end, colour_list)
File "/data/edau/relax/relax-trunk/specific_fns/model_free/macro_base.py", line 505, in create_macro
self.classic_style(data_type, colour_start, colour_end, colour_list, spin_id)
File "/data/edau/relax/relax-trunk/specific_fns/model_free/macro_base.py", line 354, in classic_style
self.classic_rex(res_num, spin.rex, colour_start, colour_end, colour_list)
File "/data/edau/relax/relax-trunk/specific_fns/model_free/macro_base.py", line 448, in classic_rex
frqs.sort()
AttributeError: 'dict_values' object has no attribute 'sort'

and:

relax> grace.write(x_data_type='spin', y_data_type='rex', spin_id=None, plot_data='value', file='rex.agr', dir='/tmp/tmpya6au2', force=True, norm=False)
Opening the file '/tmp/tmpya6au2/rex.agr' for writing.
Traceback (most recent call last):
File "/data/edau/relax/relax-trunk/test_suite/system_tests/model_free.py", line 438, in test_bug_20531_molmol_macro_write_relaxfault2
self.interpreter.grace.write(x_data_type='spin', y_data_type='rex', file='rex.agr', dir=ds.tmpdir, force=True)
File "/data/edau/relax/relax-trunk/prompt/uf_objects.py", line 221, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/edau/relax/relax-trunk/generic_fns/grace.py", line 400, in write
data, set_names, graph_type = get_data(spin_id, x_data_type=x_data_type, y_data_type=y_data_type, plot_data=plot_data)
File "/data/edau/relax/relax-trunk/generic_fns/grace.py", line 244, in get_data
y_val[j] = y_val[j] / y_return_conversion_factor(y_data_type)
File "/data/edau/relax/relax-trunk/specific_fns/api_base.py", line 526, in return_conversion_factor
return self.PARAMS.get_conv_factor(param)
File "/data/edau/relax/relax-trunk/specific_fns/api_objects.py", line 240, in get_conv_factor
return self._conv_factorname
File "/data/edau/relax/relax-trunk/specific_fns/model_free/main.py", line 535, in _conv_factor_rex
frqs.sort()
AttributeError: 'dict_values' object has no attribute 'sort'
........
r18795 | bugman | 2013-03-12 14:27:01 +0100 (Tue, 12 Mar 2013) | 19 lines

Python 3 updates and fixes.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.

The changes to the compat module and multi package were reverted prior to committing.
........
r18796 | bugman | 2013-03-12 15:47:28 +0100 (Tue, 12 Mar 2013) | 11 lines

Improvements for Python 2 and 3 compatibility.

Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and
different Python 3 version compatibility, code has been shifted into the compat module. The
different parts of relax now import from the compat module for modules/packages with different
import semantics for different Python versions.

In addition the different handling of the bz2 and gzip module for reading and writing files has been
shifted from 'relax_io' into 'compat'.
........
r18797 | bugman | 2013-03-12 15:48:04 +0100 (Tue, 12 Mar 2013) | 3 lines

Updated the 2to3 checklist document to include multiple threads for faster operation.
........

Updated the 2to3 checklist document to include multiple threads for faster operation.

Improvements for Python 2 and 3 compatibility.

Much of the Python 2 verses 3 compatibility, as well as different Python 2 version compatibility and
different Python 3 version compatibility, code has been shifted into the compat module. The
different parts of relax now import from the compat module for modules/packages with different
import semantics for different Python versions.

In addition the different handling of the bz2 and gzip module for reading and writing files has been
shifted from 'relax_io' into 'compat'.

Python 3 updates and fixes.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.

The changes to the compat module and multi package were reverted prior to committing.