Author: bugman
Date: Tue Mar 12 15:52:27 2013
New Revision: 18798
URL: http://svn.gna.org/viewcvs/relax?rev=18798&view=rev
Log:
Merged revisions 18773-18774,18778-18779,18781-18783,18788-18797 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/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@xxxxxxxxxxx/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.
........
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.
........
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.
........
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.
........
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.
........
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_factor[name]()
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.
........
Added:
branches/frame_order_testing/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/init/results
- copied unchanged from r18797,
trunk/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/init/results
branches/frame_order_testing/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/round_1/opt/
- copied from r18797,
trunk/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/round_1/opt/
branches/frame_order_testing/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/round_2/opt/
- copied from r18797,
trunk/test_suite/shared_data/model_free/bug_20563_missing_ri_error/sphere/round_2/opt/
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/compat.py
branches/frame_order_testing/data/__init__.py
branches/frame_order_testing/data/align_tensor.py
branches/frame_order_testing/data/diff_tensor.py
branches/frame_order_testing/devel_scripts/python_multiversion_test_suite.py
branches/frame_order_testing/docs/2to3_checklist
branches/frame_order_testing/docs/CHANGES
branches/frame_order_testing/docs/Release_Checklist
branches/frame_order_testing/generic_fns/pipes.py
branches/frame_order_testing/generic_fns/structure/statistics.py
branches/frame_order_testing/info.py
branches/frame_order_testing/lib/text/table.py
branches/frame_order_testing/multi/result_queue.py
branches/frame_order_testing/relax.py
branches/frame_order_testing/relax_errors.py
branches/frame_order_testing/relax_io.py
branches/frame_order_testing/specific_fns/model_free/macro_base.py
branches/frame_order_testing/specific_fns/model_free/main.py
branches/frame_order_testing/test_suite/gui_tests/base_classes.py
branches/frame_order_testing/test_suite/relax_test_runner.py
branches/frame_order_testing/test_suite/unit_tests/_lib/_text/test_table.py
branches/frame_order_testing/test_suite/unit_tests/_lib/test___init__.py
branches/frame_order_testing/test_suite/unit_tests/package_checking.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/compat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/compat.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/__init__.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/align_tensor.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/diff_tensor.py?rev=18798&r1=18797&r2=18798&view=diff
Modified:
branches/frame_order_testing/devel_scripts/python_multiversion_test_suite.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/devel_scripts/python_multiversion_test_suite.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/docs/2to3_checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/2to3_checklist?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/CHANGES?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/Release_Checklist?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pipes.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/statistics.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/info.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/lib/text/table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/lib/text/table.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/multi/result_queue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/multi/result_queue.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax_errors.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax_io.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/macro_base.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/main.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/test_suite/gui_tests/base_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/gui_tests/base_classes.py?rev=18798&r1=18797&r2=18798&view=diff
Modified: branches/frame_order_testing/test_suite/relax_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/relax_test_runner.py?rev=18798&r1=18797&r2=18798&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_lib/_text/test_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_lib/_text/test_table.py?rev=18798&r1=18797&r2=18798&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_lib/test___init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_lib/test___init__.py?rev=18798&r1=18797&r2=18798&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/package_checking.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/package_checking.py?rev=18798&r1=18797&r2=18798&view=diff
r18798 - in /branches/frame_order_testing: ./ data/ devel_scripts/ docs/ generic_fns/ generic_fns/structure/ lib/text/ multi...