bugrelax - Bugs: bug #20213, duplicate_data / deepcopy:...

 
 
Show feedback again

bug #20213: duplicate_data / deepcopy: IndexError: list assignment index out of range

Submitted by:  Martin Ballaschk <mab>
Submitted on:  Tue 02 Oct 2012 03:48:51 PM UTC  
 
Category: relax's source codeSpecific analysis category: None
Priority: 5 - NormalSeverity: 3 - Normal
Status: FixedAssigned to: Edward d Auvergne <bugman>
Originator Name: Open/Closed: Closed
Release: 2.1.1Operating System: All systems

Add a New Comment (Rich MarkupRich Markup):
   

You are not logged in

Please log in, so followups can be emailed to you.

 

(Jump to the original submission Jump to the original submission)

Tue 16 Oct 2012 09:03:18 AM UTC, SVN revision 17844:

Merged revisions 17693,17697-17737 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

........
r17693 | bugman | 2012-10-03 22:46:34 +0200 (Wed, 03 Oct 2012) | 6 lines

Fix to the DummyFileObject to allow Python 2.5 and lower to run relax.

The byte arrays are now placed in eval() statements to allow the 2.5 and lower interpreters to parse
the code.
........
r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines

Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.

The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.
........
r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines

The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
........
r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines

Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.

https://gna.org/bugs/?20213.
........
r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines

Fix for bug #20213 (https://gna.org/bugs/?20213).

The problem was that the generic_fns.sequence.generate() function was searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two spins with the same name
but different numbers were treated as the same spin, and only data from one was being generated via
the copy() function.
........
r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines

Created the relax_io.readlines method for handling the bz2 and gzip module byte strings in Python 3.

The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings from their readlines()
methods in Python 3. This causes failures all over relax. This behaviour is probably a bug in
these classes. The relax_io.readlines method is a workaround for this problem, to have a list of
standard strings returned.
........
r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines

Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using relax_io.readlines().
........

[...] r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] First attempt at making the relaxation curve-fitting C module Python 3 compatible.

[...]........

[...] r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.

[...]........

[...] r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines

[...]

[...] The relax_fit specific analysis module now supports both Python 2 and 3.

[...]

[...] The command used was:

[...] 2to3 -w specific_fns/relax_fit.py

[...]........

[...] r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added a script for testing out the C module compilation on multiple python targets.

[...]........

[...] r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Finished off the C module compilation testing script.

[...]........

[...] r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.

[...]........

[...] r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The manual C module compilation script is now executable.

[...]........

[...] r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added the IO module to the relax information print out and dependency checks.

[...]........

[...] r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines

[...]

[...] The relax_io.open_read_file() now supports all Python versions over 2.4.

[...]

[...] This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed

[...] classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped

[...] around io.TextIOWrapper().

[...]........

[...] r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines

[...]

[...] Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and r17669.

[...]

[...] The command used were:

[...] svn merge -r17702:17669 relax_io.py

[...] svn merge -r17702:r17701 /data/relax/relax-trunk/generic_fns/structure/internal.py

[...]

[...] The relax_io module should now handle all files as text, independent of compression. These reverted

[...] revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1 and 3.2. But now the

[...] io.TextIOWrapper() class is being used to eliminate the byte streams, which should be text streams.

[...]........

[...] r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The C module compilation testing script now accepts the Python version as a first argument.

[...]........

[...] r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Reverted r17681 as file objects in relax are now always treated as text, so byte streams are not needed.

[...]

[...] The command used was:

[...] svn merge -r17681:r17680 .

[...]........

[...] r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the Pipes.test_pipe_bundle() system test.

[...]

[...] The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.

[...]........

[...] r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places.

[...]

[...] This increased precision will only be of use in the relax test suite.

[...]........

[...] r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.

[...]........

[...] r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines

[...]

[...] Python 3 fix for the relax_io.open_write_file() function.

[...]

[...] This now matches the behaviour of open_read_file() in that there are three different behaviours for

[...] opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for

[...] Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as

[...] open_write_file() is for creating text files.

[...]........

[...] r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to Grace files at r17716.

[...]........

[...] r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix - removed the use of the string module from generic_fns.spectrum.

[...]........

[...] r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the ability to save and restore states using the pickle module.

[...]

[...] A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now

[...] everything defaults to the XML formatted output.

[...]........

[...] r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.

[...]........

[...] r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Removed the pickle format information and arguments from the state user function definitions.

[...]........

[...] r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 support for Modelfree4 and Dasha.

[...]

[...] The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python

[...] objects are now interconverted when the Python 3 encode() and decode() methods are detected.

[...]........

[...] r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Small comment edit.

[...]........

[...] r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the Mf.test_latex_table system test.

[...]

[...] The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw

[...] string format r"""Text""" is now used.

[...]........

[...] r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The OMP model-free results file generation script now outputs for any relax version.

[...]........

[...] r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the Python 3 byte array hack which should have been removed earlier.

[...]

[...] This code is from r17669 which should have been removed at r17712 but was accidentally left out.

[...] Instead of reverting, the code has been deleted as r17669 contained another useful change.

[...]........

[...] r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Added a Python 3 version of the truncated OMP model-free results file.

[...]

[...] This was created with trunk which is during the 2.1 relax releases.

[...]........

[...] r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The messsage about skipping the GUI tests due to wxPython being missing is now more specific.

[...]

[...] This was being shown for all runs of the test suite when it only needs to appear if GUI tests have

[...] been run.

[...]........

[...] r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The relaxation curve-fitting system tests are now skipped if the module is missing or broken.

[...]

[...] This improves the printouts from the test suite and shows a summary of skipped tests rather than a

[...] pile of traceback messages and errors.

[...]........

[...] r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines

[...]

[...] Python 3 fix for the model-free results file reading tests.

[...]

[...] The ordering of dictionaries is different in Python 3, so now these are properly converted from

[...] strings to dictionaries before comparison. This was not happening because of the XML changes from

[...] Python 2.7.3 onwards.

[...]........

[...] r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the setting of diffusion and alignment tensor simulation values.

[...]

[...] The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.

[...]........

[...] r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] The fix of r17733 actually broke Python 2.

[...]

[...] The list.__setattr__() method is fundamentally different between Python 2 and 3!

[...]........

[...] r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed some debugging printouts accidentally committed in r17734.

[...]........

[...] r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fix of r17734 which attempted to fix r17733.

[...]

[...] The Python version is now being detected.

[...]........

[...] r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Updated the relax version numbers and 'trunk' used relax user manual.

[...]

[...] For example the information about checking out the main development line was still talking about 1.3

[...] rather than the trunk.

[...]........

[...]

[...]

(Browse SVN revision 17844)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 15 Oct 2012 01:26:32 PM UTC, SVN revision 17811:

Merged revisions 17697-17737,17776-17778,17780-17806,17808 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines

Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.

The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.
................
r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines

The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
................
r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines

Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.

https://gna.org/bugs/?20213.
................
r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines

Fix for bug #20213 (https://gna.org/bugs/?20213).

The problem was that the generic_fns.sequence.generate() function was searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two spins with the same name
but different numbers were treated as the same spin, and only data from one was being generated via
the copy() function.
................
r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines

Created the relax_io.readlines method for handling the bz2 and gzip module byte strings in Python 3.

The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings from their readlines()
methods in Python 3. This causes failures all over relax. This behaviour is probably a bug in
these classes. The relax_io.readlines method is a workaround for this problem, to have a list of
standard strings returned.
................
r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines

Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using relax_io.readlines().
................
r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines

First attempt at making the relaxation curve-fitting C module Python 3 compatible.
................
r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines

The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.

[...]................

[...] r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines

[...]

[...] The relax_fit specific analysis module now supports both Python 2 and 3.

[...]

[...] The command used was:

[...] 2to3 -w specific_fns/relax_fit.py

[...]................

[...] r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added a script for testing out the C module compilation on multiple python targets.

[...]................

[...] r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Finished off the C module compilation testing script.

[...]................

[...] r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.

[...]................

[...] r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The manual C module compilation script is now executable.

[...]................

[...] r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added the IO module to the relax information print out and dependency checks.

[...]................

[...] r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines

[...]

[...] The relax_io.open_read_file() now supports all Python versions over 2.4.

[...]

[...] This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed

[...] classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped

[...] around io.TextIOWrapper().

[...]................

[...] r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines

[...]

[...] Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and r17669.

[...]

[...] The command used were:

[...] svn merge -r17702:17669 relax_io.py

[...] svn merge -r17702:r17701 /data/relax/relax-trunk/generic_fns/structure/internal.py

[...]

[...] The relax_io module should now handle all files as text, independent of compression. These reverted

[...] revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1 and 3.2. But now the

[...] io.TextIOWrapper() class is being used to eliminate the byte streams, which should be text streams.

[...]................

[...] r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The C module compilation testing script now accepts the Python version as a first argument.

[...]................

[...] r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Reverted r17681 as file objects in relax are now always treated as text, so byte streams are not needed.

[...]

[...] The command used was:

[...] svn merge -r17681:r17680 .

[...]................

[...] r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the Pipes.test_pipe_bundle() system test.

[...]

[...] The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.

[...]................

[...] r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places.

[...]

[...] This increased precision will only be of use in the relax test suite.

[...]................

[...] r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.

[...]................

[...] r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines

[...]

[...] Python 3 fix for the relax_io.open_write_file() function.

[...]

[...] This now matches the behaviour of open_read_file() in that there are three different behaviours for

[...] opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for

[...] Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as

[...] open_write_file() is for creating text files.

[...]................

[...] r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to Grace files at r17716.

[...]................

[...] r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix - removed the use of the string module from generic_fns.spectrum.

[...]................

[...] r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the ability to save and restore states using the pickle module.

[...]

[...] A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now

[...] everything defaults to the XML formatted output.

[...]................

[...] r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.

[...]................

[...] r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Removed the pickle format information and arguments from the state user function definitions.

[...]................

[...] r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 support for Modelfree4 and Dasha.

[...]

[...] The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python

[...] objects are now interconverted when the Python 3 encode() and decode() methods are detected.

[...]................

[...] r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Small comment edit.

[...]................

[...] r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the Mf.test_latex_table system test.

[...]

[...] The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw

[...] string format r"""Text""" is now used.

[...]................

[...] r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The OMP model-free results file generation script now outputs for any relax version.

[...]................

[...] r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the Python 3 byte array hack which should have been removed earlier.

[...]

[...] This code is from r17669 which should have been removed at r17712 but was accidentally left out.

[...] Instead of reverting, the code has been deleted as r17669 contained another useful change.

[...]................

[...] r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Added a Python 3 version of the truncated OMP model-free results file.

[...]

[...] This was created with trunk which is during the 2.1 relax releases.

[...]................

[...] r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The messsage about skipping the GUI tests due to wxPython being missing is now more specific.

[...]

[...] This was being shown for all runs of the test suite when it only needs to appear if GUI tests have

[...] been run.

[...]................

[...] r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The relaxation curve-fitting system tests are now skipped if the module is missing or broken.

[...]

[...] This improves the printouts from the test suite and shows a summary of skipped tests rather than a

[...] pile of traceback messages and errors.

[...]................

[...] r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines

[...]

[...] Python 3 fix for the model-free results file reading tests.

[...]

[...] The ordering of dictionaries is different in Python 3, so now these are properly converted from

[...] strings to dictionaries before comparison. This was not happening because of the XML changes from

[...] Python 2.7.3 onwards.

[...]................

[...] r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the setting of diffusion and alignment tensor simulation values.

[...]

[...] The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.

[...]................

[...] r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] The fix of r17733 actually broke Python 2.

[...]

[...] The list.__setattr__() method is fundamentally different between Python 2 and 3!

[...]................

[...] r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed some debugging printouts accidentally committed in r17734.

[...]................

[...] r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fix of r17734 which attempted to fix r17733.

[...]

[...] The Python version is now being detected.

[...]................

[...] r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Updated the relax version numbers and 'trunk' used relax user manual.

[...]

[...] For example the information about checking out the main development line was still talking about 1.3

[...] rather than the trunk.

[...]................

[...] r17776 | bugman | 2012-10-09 00:59:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Initialized merge tracking via "svnmerge" with revisions "1-17738" from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17777 | bugman | 2012-10-09 01:01:34 +0200 (Tue, 09 Oct 2012) | 180 lines

[...]

[...] Merged revisions 17739-17774 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]

[...] ........

[...] r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The diffusion tensor data structure has been completely converted into a read-only structure.

[...]

[...] The _setattr_() method now will always raise a RelaxError, and the diffusion tensor simulation

[...] data structure objects _setitem_() method will raise the same error.

[...] ........

[...] r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the initialisation of the diffusion tensor data structure, now that it is read-only.

[...] ........

[...] r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The new diffusion tensor fixed() method has been created to allow the fixed flag to be changed.

[...] ........

[...] r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Created the diffusion tensor data structure type() method for setting the tensor type.

[...]

[...] This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of relax, as the structure is

[...] now read only.

[...] ........

[...] r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Renamed the diffusion tensor data structure type() method to set_type().

[...]

[...] This is because the type is stored as the 'type' object, clashing with the method name.

[...] ........

[...] r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Converted the old diffusion tensor _setattr_() method into the set() method.

[...]

[...] This is the only way in which diffusion tensor parameters, errors and simulations can be set.

[...] ........

[...] r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Improvements to the diffusion tensor set() method.

[...]

[...] The parameters, errors and simulations are now properly differentiated and stored.

[...] ........

[...] r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] A number of private diffusion tensor objects and methods have switched to the single leading '_' format.

[...] ........

[...] r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed all the unused imports from specific_fns.model_free.main.

[...] ........

[...] r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Redesigned how diffusion tensor simulation structures are handled.

[...]

[...] The design is now much cleaner and works with all Python versions.

[...] ........

[...] r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Modified the setUp() method for the diffusion tensor system tests to use the new design.

[...] ........

[...] r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.

[...] ........

[...] r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the diffusion tensor _deepcopy_() replacement method for the new design.

[...] ........

[...] r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The setting of list values for the DiffTensorSimList object now works correctly.

[...]

[...] The private _set() method now works correctly by calling the base class method, and the normal

[...] setting of diffusion tensor simulation values produces a RelaxError.

[...] ........

[...] r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the Diffusion_tensor.test_copy system test - the simulation parameters are now read-only.

[...]

[...] Instead, the diffusion tensor set() method needs to be called.

[...] ........

[...] r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the diffusion tensor data structure from_xml() method to the new tensor design.

[...] ........

[...] r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the diffusion tensor to_xml() method for the new design.

[...]

[...] For some reason the methods of the Element class are no longer blacklisted.

[...] ........

[...] r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the model-free specific analysis duplicate_data() method for the new design.

[...]

[...] The diffusion tensor _mod_attr_ object is now called _mod_attr.

[...] ........

[...] r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.

[...] ........

[...] r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The fix user function now uses the diffusion tensor set_fixed() method.

[...] ........

[...] r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().

[...] ........

[...] r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the palmer.extract user function to use the new diffusion tensor design.

[...] ........

[...] r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.

[...]

[...] This was the previous behaviour and is needed for the test suite to pass.

[...] ........

[...] r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fixing of parameters in the model-free analyses.

[...]

[...] The diffusion tensor set_fixed() method is now used.

[...] ........

[...] r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the diffusion_tensor.init user function - it was not completely converted.

[...] ........

[...] r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.

[...] ........

[...] r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.

[...] ........

[...] r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the fold_angles() diffusion tensor function - again an incomplete design conversion.

[...] ........

[...] r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of relax 1.2 model-free results files for the diffusion tensor structure redesign.

[...] ........

[...] r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of model-free results files from relax 1.2 when simulation data is missing.

[...] ........

[...] r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Updated all of the diffusion tensor unit tests to the new design.

[...] ........

[...] r17770 | bugman | 2012-10-08 22:36:00 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Cleaned up the docstring of the diffusion tensor data object _setattr_() method.

[...] ........

[...] r17771 | bugman | 2012-10-08 22:36:47 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed the now unused _update_sim_append() method from the diffusion tensor data structure.

[...] ........

[...] r17772 | bugman | 2012-10-08 22:38:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Deleted the now unused _update_sim_set() method of the diffusion tensor data structure.

[...] ........

[...] r17773 | bugman | 2012-10-08 22:49:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Small clean ups of the diffusion tensor data structure code.

[...] ........

[...] r17774 | bugman | 2012-10-09 00:24:34 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensor.

[...]

[...] This large set of changes matches all of those revisions for the diffusion tensor already committed in

[...] this branch. The alignment tensor data structures are now read only, and can only be modified via the

[...] set() method. This is a much simplified design which works on all Python versions.

[...] ........

[...]................

[...] r17778 | bugman | 2012-10-09 01:02:04 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Removed merge tracking for "svnmerge" for

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17780 | bugman | 2012-10-09 10:26:13 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the model-free BMRB export - many string module methods no longer exist.

[...]................

[...] r17781 | bugman | 2012-10-09 10:29:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] More Python 3 fixes for the use of now non-existent string module functions.

[...]................

[...] r17782 | bugman | 2012-10-09 11:53:02 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails.

[...]

[...] This removes a pile of useless error messages from the test, and presents a table of skipped tests

[...] at the end.

[...]................

[...] r17783 | bugman | 2012-10-09 12:03:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.5 and lower fix for the test_write_protein_sequence() unit test.

[...]

[...] The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the code

[...] without failing, and the byte array comparison is now only used for Python 3+.

[...]................

[...] r17784 | bugman | 2012-10-09 12:09:45 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] The Results system tests are no longer dependent on the relaxation curve-fitting C modules.

[...]

[...] This allows these tests to run when the module cannot be imported.

[...]................

[...] r17785 | bugman | 2012-10-09 12:50:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Created a special script for testing out relax with Python versions 1.0 all the way to 3.3.

[...]

[...] This builds the C modules for each Python version in ~/bin and then runs the test suite, outputting

[...] everything to log files.

[...]................

[...] r17786 | bugman | 2012-10-09 12:52:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 fixes - the ctypes module does not exist in Python versions 2.4 and lower.

[...]

[...] This is only used for some non-essential functionality on MS Windows, so now it is deactivated if

[...] not present.

[...]................

[...] r17787 | bugman | 2012-10-09 12:59:11 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 and lower fix for the pipe_loop() generator method.

[...]

[...] In these Python versions, a 'try' block with a 'finally' statement cannot contain 'yield'

[...] statements! This work around should be compatible with all Python versions.

[...]................

[...] r17788 | bugman | 2012-10-09 13:36:46 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Fix for the test_write_protein_sequence() unit test for a recently introduced bug.

[...]................

[...] r17789 | bugman | 2012-10-09 14:28:30 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Reactivated support for Python 2.3.

[...]

[...] This mainly skips the missing 'subprocess' module. This however decreases relax's functionality a

[...] little.

[...]................

[...] r17790 | bugman | 2012-10-09 14:35:38 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Small improvements to the multiple python version test suite testing script.

[...]................

[...] r17791 | bugman | 2012-10-09 15:59:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for Python 3.1.

[...]

[...] The XML version in Python 3.1 is the old style! Therefore the old results file is being used to

[...] check this Python 3.1 result.

[...]................

[...] r17792 | bugman | 2012-10-09 20:47:25 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Better Python 2.3 support.

[...]

[...] The compat module is now imported at the very start to allow the builtins to be set before any other

[...] imports. The sorted() builtin method is now mimicked and the os.devnull string set for Python 2.3

[...] and earlier.

[...]................

[...] r17793 | bugman | 2012-10-09 20:59:17 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 2.4 fix - the unit test runner no longer uses the builtin set() method.

[...]................

[...] r17794 | bugman | 2012-10-09 21:06:42 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] Python 2.4 and earlier fix for the GUI.

[...]

[...] Try-except-finally statement blocks are not supported, so these have to nested in two try statements.

[...]................

[...] r17795 | bugman | 2012-10-10 16:37:34 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for the Python 3 versions.

[...]

[...] The logic for determining Python 3 versions was broken and the incorrect files was used for Python

[...] 3.1.

[...]................

[...] r17796 | bugman | 2012-10-10 16:44:00 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.

[...]

[...] The object comparison method no longer converts dictionaries to strings for the comparison, as the

[...] string version is different in different Python versions.

[...]................

[...] r17797 | bugman | 2012-10-11 10:53:47 +0200 (Thu, 11 Oct 2012) | 5 lines

[...]

[...] Disabled the initial relax intro print out from the GUI when running the test suite.

[...]

[...] This prevents the intro text from appearing in the first failed test.

[...]................

[...] r17798 | bugman | 2012-10-12 11:48:22 +0200 (Fri, 12 Oct 2012) | 10 lines

[...]

[...] Redesigned the reset user function backend.

[...]

[...] This now no only clears out the relax data store, but it also resets the GUI if present. Some of

[...] the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI

[...] window are closed and the relax controller gauges are set to zero and the log window text cleared.

[...]

[...] These changes should allow GUI tests after an error or failure to pass, something which is currently

[...] problematic.

[...]................

[...] r17799 | bugman | 2012-10-15 10:21:37 +0200 (Mon, 15 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the ScientificPython PDB reader unit tests.

[...]

[...] The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now

[...] they are sorted prior to comparison.

[...]................

[...] r17800 | bugman | 2012-10-15 10:31:28 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3 fix - eliminated the superfluous operator.itemgetter() call in the diffusion tensor code.

[...]................

[...] r17801 | bugman | 2012-10-15 10:39:20 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix - the subprocess module is only imported when present.

[...]

[...] This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.

[...]................

[...] r17802 | bugman | 2012-10-15 10:42:56 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.

[...]

[...] The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.

[...]................

[...] r17803 | bugman | 2012-10-15 10:48:09 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped if the subprocess module is missing.

[...]................

[...] r17804 | bugman | 2012-10-15 13:50:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.

[...]

[...] This allows the test suite to terminate normally. With different Python versions on different

[...] operating systems, this could sometimes cause the test suite to freeze at the end, the final

[...] printout to be missing, or other strange behaviour.

[...]................

[...] r17805 | bugman | 2012-10-15 14:24:14 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Removed an unused import of the Queue module from the multi-processor.

[...]................

[...] r17806 | bugman | 2012-10-15 14:25:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Python 2.4 and earlier fixes for the Queuing module.

[...]

[...] The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+

[...] has been added to the compat module. This module is now used for all imports of the Queue class for

[...] all Python versions.

[...]................

[...] r17808 | bugman | 2012-10-15 15:01:36 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Added support for Python 2.2 and earlier for the compilation of the C modules.

[...]................

[...]

[...]

(Browse SVN revision 17811)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 15 Oct 2012 01:07:06 PM UTC, SVN revision 17810:

Merged revisions 17689-17691,17693,17697-17737,17776-17778,17780-17806,17808 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r17689 | bugman | 2012-10-02 23:51:32 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 bug fix for the geometric structure module - another integer division to float problem.
................
r17690 | bugman | 2012-10-03 00:09:30 +0200 (Wed, 03 Oct 2012) | 3 lines

The Python 3 dictionary values() method no longer returns a list, so a list() call is needed.
................
r17691 | bugman | 2012-10-03 01:26:26 +0200 (Wed, 03 Oct 2012) | 6 lines

Bug fix for wxPython 2.9.4.0 - the unsetting of the alpha mask for all bitmap images should now work.

The wx.Bitmap.SetMaskColour(None) call does not work, so instead a wx.Colour() instance is passed in
instead.
................
r17693 | bugman | 2012-10-03 22:46:34 +0200 (Wed, 03 Oct 2012) | 6 lines

Fix to the DummyFileObject to allow Python 2.5 and lower to run relax.

The byte arrays are now placed in eval() statements to allow the 2.5 and lower interpreters to parse
the code.
................
r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines

Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.

The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.
................
r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines

The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
................
r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines

Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.

https://gna.org/bugs/?20213.
................
r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines

Fix for bug #20213 (https://gna.org/bugs/?20213).

The problem was that the generic_fns.sequence.generate() function was searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two spins with the same name
but different numbers were treated as the same spin, and only data from one was being generated via

[...] the copy() function.

[...]................

[...] r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines

[...]

[...] Created the relax_io.readlines method for handling the bz2 and gzip module byte strings in Python 3.

[...]

[...] The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings from their readlines()

[...] methods in Python 3. This causes failures all over relax. This behaviour is probably a bug in

[...] these classes. The relax_io.readlines method is a workaround for this problem, to have a list of

[...] standard strings returned.

[...]................

[...] r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using relax_io.readlines().

[...]................

[...] r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] First attempt at making the relaxation curve-fitting C module Python 3 compatible.

[...]................

[...] r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.

[...]................

[...] r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines

[...]

[...] The relax_fit specific analysis module now supports both Python 2 and 3.

[...]

[...] The command used was:

[...] 2to3 -w specific_fns/relax_fit.py

[...]................

[...] r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added a script for testing out the C module compilation on multiple python targets.

[...]................

[...] r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Finished off the C module compilation testing script.

[...]................

[...] r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.

[...]................

[...] r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The manual C module compilation script is now executable.

[...]................

[...] r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added the IO module to the relax information print out and dependency checks.

[...]................

[...] r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines

[...]

[...] The relax_io.open_read_file() now supports all Python versions over 2.4.

[...]

[...] This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed

[...] classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped

[...] around io.TextIOWrapper().

[...]................

[...] r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines

[...]

[...] Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and r17669.

[...]

[...] The command used were:

[...] svn merge -r17702:17669 relax_io.py

[...] svn merge -r17702:r17701 /data/relax/relax-trunk/generic_fns/structure/internal.py

[...]

[...] The relax_io module should now handle all files as text, independent of compression. These reverted

[...] revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1 and 3.2. But now the

[...] io.TextIOWrapper() class is being used to eliminate the byte streams, which should be text streams.

[...]................

[...] r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The C module compilation testing script now accepts the Python version as a first argument.

[...]................

[...] r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Reverted r17681 as file objects in relax are now always treated as text, so byte streams are not needed.

[...]

[...] The command used was:

[...] svn merge -r17681:r17680 .

[...]................

[...] r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the Pipes.test_pipe_bundle() system test.

[...]

[...] The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.

[...]................

[...] r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places.

[...]

[...] This increased precision will only be of use in the relax test suite.

[...]................

[...] r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.

[...]................

[...] r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines

[...]

[...] Python 3 fix for the relax_io.open_write_file() function.

[...]

[...] This now matches the behaviour of open_read_file() in that there are three different behaviours for

[...] opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for

[...] Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as

[...] open_write_file() is for creating text files.

[...]................

[...] r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to Grace files at r17716.

[...]................

[...] r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix - removed the use of the string module from generic_fns.spectrum.

[...]................

[...] r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the ability to save and restore states using the pickle module.

[...]

[...] A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now

[...] everything defaults to the XML formatted output.

[...]................

[...] r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.

[...]................

[...] r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Removed the pickle format information and arguments from the state user function definitions.

[...]................

[...] r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 support for Modelfree4 and Dasha.

[...]

[...] The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python

[...] objects are now interconverted when the Python 3 encode() and decode() methods are detected.

[...]................

[...] r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Small comment edit.

[...]................

[...] r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the Mf.test_latex_table system test.

[...]

[...] The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw

[...] string format r"""Text""" is now used.

[...]................

[...] r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The OMP model-free results file generation script now outputs for any relax version.

[...]................

[...] r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the Python 3 byte array hack which should have been removed earlier.

[...]

[...] This code is from r17669 which should have been removed at r17712 but was accidentally left out.

[...] Instead of reverting, the code has been deleted as r17669 contained another useful change.

[...]................

[...] r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Added a Python 3 version of the truncated OMP model-free results file.

[...]

[...] This was created with trunk which is during the 2.1 relax releases.

[...]................

[...] r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The messsage about skipping the GUI tests due to wxPython being missing is now more specific.

[...]

[...] This was being shown for all runs of the test suite when it only needs to appear if GUI tests have

[...] been run.

[...]................

[...] r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The relaxation curve-fitting system tests are now skipped if the module is missing or broken.

[...]

[...] This improves the printouts from the test suite and shows a summary of skipped tests rather than a

[...] pile of traceback messages and errors.

[...]................

[...] r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines

[...]

[...] Python 3 fix for the model-free results file reading tests.

[...]

[...] The ordering of dictionaries is different in Python 3, so now these are properly converted from

[...] strings to dictionaries before comparison. This was not happening because of the XML changes from

[...] Python 2.7.3 onwards.

[...]................

[...] r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the setting of diffusion and alignment tensor simulation values.

[...]

[...] The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.

[...]................

[...] r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] The fix of r17733 actually broke Python 2.

[...]

[...] The list.__setattr__() method is fundamentally different between Python 2 and 3!

[...]................

[...] r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed some debugging printouts accidentally committed in r17734.

[...]................

[...] r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fix of r17734 which attempted to fix r17733.

[...]

[...] The Python version is now being detected.

[...]................

[...] r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Updated the relax version numbers and 'trunk' used relax user manual.

[...]

[...] For example the information about checking out the main development line was still talking about 1.3

[...] rather than the trunk.

[...]................

[...] r17776 | bugman | 2012-10-09 00:59:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Initialized merge tracking via "svnmerge" with revisions "1-17738" from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17777 | bugman | 2012-10-09 01:01:34 +0200 (Tue, 09 Oct 2012) | 180 lines

[...]

[...] Merged revisions 17739-17774 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]

[...] ........

[...] r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The diffusion tensor data structure has been completely converted into a read-only structure.

[...]

[...] The _setattr_() method now will always raise a RelaxError, and the diffusion tensor simulation

[...] data structure objects _setitem_() method will raise the same error.

[...] ........

[...] r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the initialisation of the diffusion tensor data structure, now that it is read-only.

[...] ........

[...] r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The new diffusion tensor fixed() method has been created to allow the fixed flag to be changed.

[...] ........

[...] r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Created the diffusion tensor data structure type() method for setting the tensor type.

[...]

[...] This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of relax, as the structure is

[...] now read only.

[...] ........

[...] r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Renamed the diffusion tensor data structure type() method to set_type().

[...]

[...] This is because the type is stored as the 'type' object, clashing with the method name.

[...] ........

[...] r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Converted the old diffusion tensor _setattr_() method into the set() method.

[...]

[...] This is the only way in which diffusion tensor parameters, errors and simulations can be set.

[...] ........

[...] r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Improvements to the diffusion tensor set() method.

[...]

[...] The parameters, errors and simulations are now properly differentiated and stored.

[...] ........

[...] r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] A number of private diffusion tensor objects and methods have switched to the single leading '_' format.

[...] ........

[...] r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed all the unused imports from specific_fns.model_free.main.

[...] ........

[...] r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Redesigned how diffusion tensor simulation structures are handled.

[...]

[...] The design is now much cleaner and works with all Python versions.

[...] ........

[...] r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Modified the setUp() method for the diffusion tensor system tests to use the new design.

[...] ........

[...] r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.

[...] ........

[...] r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the diffusion tensor _deepcopy_() replacement method for the new design.

[...] ........

[...] r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The setting of list values for the DiffTensorSimList object now works correctly.

[...]

[...] The private _set() method now works correctly by calling the base class method, and the normal

[...] setting of diffusion tensor simulation values produces a RelaxError.

[...] ........

[...] r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the Diffusion_tensor.test_copy system test - the simulation parameters are now read-only.

[...]

[...] Instead, the diffusion tensor set() method needs to be called.

[...] ........

[...] r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the diffusion tensor data structure from_xml() method to the new tensor design.

[...] ........

[...] r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the diffusion tensor to_xml() method for the new design.

[...]

[...] For some reason the methods of the Element class are no longer blacklisted.

[...] ........

[...] r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the model-free specific analysis duplicate_data() method for the new design.

[...]

[...] The diffusion tensor _mod_attr_ object is now called _mod_attr.

[...] ........

[...] r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.

[...] ........

[...] r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The fix user function now uses the diffusion tensor set_fixed() method.

[...] ........

[...] r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().

[...] ........

[...] r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the palmer.extract user function to use the new diffusion tensor design.

[...] ........

[...] r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.

[...]

[...] This was the previous behaviour and is needed for the test suite to pass.

[...] ........

[...] r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fixing of parameters in the model-free analyses.

[...]

[...] The diffusion tensor set_fixed() method is now used.

[...] ........

[...] r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the diffusion_tensor.init user function - it was not completely converted.

[...] ........

[...] r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.

[...] ........

[...] r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.

[...] ........

[...] r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the fold_angles() diffusion tensor function - again an incomplete design conversion.

[...] ........

[...] r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of relax 1.2 model-free results files for the diffusion tensor structure redesign.

[...] ........

[...] r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of model-free results files from relax 1.2 when simulation data is missing.

[...] ........

[...] r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Updated all of the diffusion tensor unit tests to the new design.

[...] ........

[...] r17770 | bugman | 2012-10-08 22:36:00 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Cleaned up the docstring of the diffusion tensor data object _setattr_() method.

[...] ........

[...] r17771 | bugman | 2012-10-08 22:36:47 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed the now unused _update_sim_append() method from the diffusion tensor data structure.

[...] ........

[...] r17772 | bugman | 2012-10-08 22:38:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Deleted the now unused _update_sim_set() method of the diffusion tensor data structure.

[...] ........

[...] r17773 | bugman | 2012-10-08 22:49:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Small clean ups of the diffusion tensor data structure code.

[...] ........

[...] r17774 | bugman | 2012-10-09 00:24:34 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensor.

[...]

[...] This large set of changes matches all of those revisions for the diffusion tensor already committed in

[...] this branch. The alignment tensor data structures are now read only, and can only be modified via the

[...] set() method. This is a much simplified design which works on all Python versions.

[...] ........

[...]................

[...] r17778 | bugman | 2012-10-09 01:02:04 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Removed merge tracking for "svnmerge" for

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17780 | bugman | 2012-10-09 10:26:13 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the model-free BMRB export - many string module methods no longer exist.

[...]................

[...] r17781 | bugman | 2012-10-09 10:29:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] More Python 3 fixes for the use of now non-existent string module functions.

[...]................

[...] r17782 | bugman | 2012-10-09 11:53:02 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails.

[...]

[...] This removes a pile of useless error messages from the test, and presents a table of skipped tests

[...] at the end.

[...]................

[...] r17783 | bugman | 2012-10-09 12:03:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.5 and lower fix for the test_write_protein_sequence() unit test.

[...]

[...] The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the code

[...] without failing, and the byte array comparison is now only used for Python 3+.

[...]................

[...] r17784 | bugman | 2012-10-09 12:09:45 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] The Results system tests are no longer dependent on the relaxation curve-fitting C modules.

[...]

[...] This allows these tests to run when the module cannot be imported.

[...]................

[...] r17785 | bugman | 2012-10-09 12:50:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Created a special script for testing out relax with Python versions 1.0 all the way to 3.3.

[...]

[...] This builds the C modules for each Python version in ~/bin and then runs the test suite, outputting

[...] everything to log files.

[...]................

[...] r17786 | bugman | 2012-10-09 12:52:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 fixes - the ctypes module does not exist in Python versions 2.4 and lower.

[...]

[...] This is only used for some non-essential functionality on MS Windows, so now it is deactivated if

[...] not present.

[...]................

[...] r17787 | bugman | 2012-10-09 12:59:11 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 and lower fix for the pipe_loop() generator method.

[...]

[...] In these Python versions, a 'try' block with a 'finally' statement cannot contain 'yield'

[...] statements! This work around should be compatible with all Python versions.

[...]................

[...] r17788 | bugman | 2012-10-09 13:36:46 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Fix for the test_write_protein_sequence() unit test for a recently introduced bug.

[...]................

[...] r17789 | bugman | 2012-10-09 14:28:30 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Reactivated support for Python 2.3.

[...]

[...] This mainly skips the missing 'subprocess' module. This however decreases relax's functionality a

[...] little.

[...]................

[...] r17790 | bugman | 2012-10-09 14:35:38 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Small improvements to the multiple python version test suite testing script.

[...]................

[...] r17791 | bugman | 2012-10-09 15:59:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for Python 3.1.

[...]

[...] The XML version in Python 3.1 is the old style! Therefore the old results file is being used to

[...] check this Python 3.1 result.

[...]................

[...] r17792 | bugman | 2012-10-09 20:47:25 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Better Python 2.3 support.

[...]

[...] The compat module is now imported at the very start to allow the builtins to be set before any other

[...] imports. The sorted() builtin method is now mimicked and the os.devnull string set for Python 2.3

[...] and earlier.

[...]................

[...] r17793 | bugman | 2012-10-09 20:59:17 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 2.4 fix - the unit test runner no longer uses the builtin set() method.

[...]................

[...] r17794 | bugman | 2012-10-09 21:06:42 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] Python 2.4 and earlier fix for the GUI.

[...]

[...] Try-except-finally statement blocks are not supported, so these have to nested in two try statements.

[...]................

[...] r17795 | bugman | 2012-10-10 16:37:34 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for the Python 3 versions.

[...]

[...] The logic for determining Python 3 versions was broken and the incorrect files was used for Python

[...] 3.1.

[...]................

[...] r17796 | bugman | 2012-10-10 16:44:00 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.

[...]

[...] The object comparison method no longer converts dictionaries to strings for the comparison, as the

[...] string version is different in different Python versions.

[...]................

[...] r17797 | bugman | 2012-10-11 10:53:47 +0200 (Thu, 11 Oct 2012) | 5 lines

[...]

[...] Disabled the initial relax intro print out from the GUI when running the test suite.

[...]

[...] This prevents the intro text from appearing in the first failed test.

[...]................

[...] r17798 | bugman | 2012-10-12 11:48:22 +0200 (Fri, 12 Oct 2012) | 10 lines

[...]

[...] Redesigned the reset user function backend.

[...]

[...] This now no only clears out the relax data store, but it also resets the GUI if present. Some of

[...] the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI

[...] window are closed and the relax controller gauges are set to zero and the log window text cleared.

[...]

[...] These changes should allow GUI tests after an error or failure to pass, something which is currently

[...] problematic.

[...]................

[...] r17799 | bugman | 2012-10-15 10:21:37 +0200 (Mon, 15 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the ScientificPython PDB reader unit tests.

[...]

[...] The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now

[...] they are sorted prior to comparison.

[...]................

[...] r17800 | bugman | 2012-10-15 10:31:28 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3 fix - eliminated the superfluous operator.itemgetter() call in the diffusion tensor code.

[...]................

[...] r17801 | bugman | 2012-10-15 10:39:20 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix - the subprocess module is only imported when present.

[...]

[...] This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.

[...]................

[...] r17802 | bugman | 2012-10-15 10:42:56 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.

[...]

[...] The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.

[...]................

[...] r17803 | bugman | 2012-10-15 10:48:09 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped if the subprocess module is missing.

[...]................

[...] r17804 | bugman | 2012-10-15 13:50:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.

[...]

[...] This allows the test suite to terminate normally. With different Python versions on different

[...] operating systems, this could sometimes cause the test suite to freeze at the end, the final

[...] printout to be missing, or other strange behaviour.

[...]................

[...] r17805 | bugman | 2012-10-15 14:24:14 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Removed an unused import of the Queue module from the multi-processor.

[...]................

[...] r17806 | bugman | 2012-10-15 14:25:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Python 2.4 and earlier fixes for the Queuing module.

[...]

[...] The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+

[...] has been added to the compat module. This module is now used for all imports of the Queue class for

[...] all Python versions.

[...]................

[...] r17808 | bugman | 2012-10-15 15:01:36 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Added support for Python 2.2 and earlier for the compilation of the C modules.

[...]................

[...]

[...]

(Browse SVN revision 17810)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Mon 15 Oct 2012 12:54:26 PM UTC, SVN revision 17807:

Merged revisions 17687,17689-17691,17693,17697-17737,17776-17778,17780-17806 via svnmerge from
svn+ssh://bugman@svn.gna.org/svn/relax/trunk

................
r17687 | bugman | 2012-10-02 18:55:31 +0200 (Tue, 02 Oct 2012) | 5 lines

Another Python 3 fix for the relax_io.extract_data() function.

Sometimes this function sees byte types, sometimes string types. The function can now handle both.
................
r17689 | bugman | 2012-10-02 23:51:32 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 bug fix for the geometric structure module - another integer division to float problem.
................
r17690 | bugman | 2012-10-03 00:09:30 +0200 (Wed, 03 Oct 2012) | 3 lines

The Python 3 dictionary values() method no longer returns a list, so a list() call is needed.
................
r17691 | bugman | 2012-10-03 01:26:26 +0200 (Wed, 03 Oct 2012) | 6 lines

Bug fix for wxPython 2.9.4.0 - the unsetting of the alpha mask for all bitmap images should now work.

The wx.Bitmap.SetMaskColour(None) call does not work, so instead a wx.Colour() instance is passed in
instead.
................
r17693 | bugman | 2012-10-03 22:46:34 +0200 (Wed, 03 Oct 2012) | 6 lines

Fix to the DummyFileObject to allow Python 2.5 and lower to run relax.

The byte arrays are now placed in eval() statements to allow the 2.5 and lower interpreters to parse
the code.
................
r17697 | bugman | 2012-10-04 18:20:51 +0200 (Thu, 04 Oct 2012) | 7 lines

Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.

The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.
................
r17698 | bugman | 2012-10-04 18:23:16 +0200 (Thu, 04 Oct 2012) | 3 lines

The Mf.test_bug_20213_asn_sidechain() system test now uses a temporary directory for output.
................
r17699 | bugman | 2012-10-04 18:37:56 +0200 (Thu, 04 Oct 2012) | 5 lines

Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.

https://gna.org/bugs/?20213.
................
r17700 | bugman | 2012-10-04 19:02:08 +0200 (Thu, 04 Oct 2012) | 8 lines

[...]

[...] Fix for bug #20213 (https://gna.org/bugs/?20213).

[...]

[...] The problem was that the generic_fns.sequence.generate() function was searching for a spin based on

[...] its spin ID generated from the spin name and not spin number. Hence two spins with the same name

[...] but different numbers were treated as the same spin, and only data from one was being generated via

[...] the copy() function.

[...]................

[...] r17701 | bugman | 2012-10-05 18:42:15 +0200 (Fri, 05 Oct 2012) | 8 lines

[...]

[...] Created the relax_io.readlines method for handling the bz2 and gzip module byte strings in Python 3.

[...]

[...] The bz2.BZ2File and gzip.GzipFile classes now return lists of bytes strings from their readlines()

[...] methods in Python 3. This causes failures all over relax. This behaviour is probably a bug in

[...] these classes. The relax_io.readlines method is a workaround for this problem, to have a list of

[...] standard strings returned.

[...]................

[...] r17702 | bugman | 2012-10-05 18:43:11 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] Python 3 bug fix for the internal PDB and XYZ 3D structure readers by using relax_io.readlines().

[...]................

[...] r17703 | bugman | 2012-10-05 19:39:17 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] First attempt at making the relaxation curve-fitting C module Python 3 compatible.

[...]................

[...] r17704 | bugman | 2012-10-05 19:45:46 +0200 (Fri, 05 Oct 2012) | 3 lines

[...]

[...] The relaxation curve-fitting C module now supports compilation on both Python 2 and 3.

[...]................

[...] r17705 | bugman | 2012-10-05 19:48:03 +0200 (Fri, 05 Oct 2012) | 6 lines

[...]

[...] The relax_fit specific analysis module now supports both Python 2 and 3.

[...]

[...] The command used was:

[...] 2to3 -w specific_fns/relax_fit.py

[...]................

[...] r17706 | bugman | 2012-10-07 15:00:19 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added a script for testing out the C module compilation on multiple python targets.

[...]................

[...] r17707 | bugman | 2012-10-07 15:13:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Finished off the C module compilation testing script.

[...]................

[...] r17708 | bugman | 2012-10-07 15:16:28 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the scripts.

[...]................

[...] r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The manual C module compilation script is now executable.

[...]................

[...] r17710 | bugman | 2012-10-07 15:37:52 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Added the IO module to the relax information print out and dependency checks.

[...]................

[...] r17711 | bugman | 2012-10-07 15:40:50 +0200 (Sun, 07 Oct 2012) | 7 lines

[...]

[...] The relax_io.open_read_file() now supports all Python versions over 2.4.

[...]

[...] This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed

[...] classes overriding the incomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped

[...] around io.TextIOWrapper().

[...]................

[...] r17712 | bugman | 2012-10-07 15:50:10 +0200 (Sun, 07 Oct 2012) | 11 lines

[...]

[...] Reverted revisions r17702, r17701, r17693, r17687, r17685, r17684, and r17669.

[...]

[...] The command used were:

[...] svn merge -r17702:17669 relax_io.py

[...] svn merge -r17702:r17701 /data/relax/relax-trunk/generic_fns/structure/internal.py

[...]

[...] The relax_io module should now handle all files as text, independent of compression. These reverted

[...] revisions were attempts at fixing the buggy behaviour of Python 3.0, 3.1 and 3.2. But now the

[...] io.TextIOWrapper() class is being used to eliminate the byte streams, which should be text streams.

[...]................

[...] r17713 | bugman | 2012-10-07 15:56:44 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The C module compilation testing script now accepts the Python version as a first argument.

[...]................

[...] r17714 | bugman | 2012-10-07 16:15:02 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Reverted r17681 as file objects in relax are now always treated as text, so byte streams are not needed.

[...]

[...] The command used was:

[...] svn merge -r17681:r17680 .

[...]................

[...] r17715 | bugman | 2012-10-07 16:29:56 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the Pipes.test_pipe_bundle() system test.

[...]

[...] The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3.

[...]................

[...] r17716 | bugman | 2012-10-07 16:38:01 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] For consistency between Python 2 and 3, the grace.write user function outputs to 15 decimal places.

[...]

[...] This increased precision will only be of use in the relax test suite.

[...]................

[...] r17717 | bugman | 2012-10-07 16:38:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the Noe.test_noe_analysis() system test for the grace.write precision changes.

[...]................

[...] r17718 | bugman | 2012-10-07 18:12:33 +0200 (Sun, 07 Oct 2012) | 8 lines

[...]

[...] Python 3 fix for the relax_io.open_write_file() function.

[...]

[...] This now matches the behaviour of open_read_file() in that there are three different behaviours for

[...] opening bz2 and gz files for writing to for the different Python versions (one for Python 2, one for

[...] Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as

[...] open_write_file() is for creating text files.

[...]................

[...] r17719 | bugman | 2012-10-07 18:45:38 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Fix for the Relax_fit.test_bug_12670_12679() system test for the changes to Grace files at r17716.

[...]................

[...] r17720 | bugman | 2012-10-07 18:53:30 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Python 3 fix - removed the use of the string module from generic_fns.spectrum.

[...]................

[...] r17721 | bugman | 2012-10-07 18:59:12 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the ability to save and restore states using the pickle module.

[...]

[...] A pickled state is of no use to relax anymore. It's removal is needed for Python 3 support. So now

[...] everything defaults to the XML formatted output.

[...]................

[...] r17722 | bugman | 2012-10-07 18:59:43 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Eliminated the State.test_state_pickle() system test as pickled states are no longer supported.

[...]................

[...] r17723 | bugman | 2012-10-07 19:12:26 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Removed the pickle format information and arguments from the state user function definitions.

[...]................

[...] r17724 | bugman | 2012-10-07 19:21:06 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 support for Modelfree4 and Dasha.

[...]

[...] The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python

[...] objects are now interconverted when the Python 3 encode() and decode() methods are detected.

[...]................

[...] r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] Small comment edit.

[...]................

[...] r17726 | bugman | 2012-10-07 20:56:21 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the Mf.test_latex_table system test.

[...]

[...] The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw

[...] string format r"""Text""" is now used.

[...]................

[...] r17727 | bugman | 2012-10-07 20:59:22 +0200 (Sun, 07 Oct 2012) | 3 lines

[...]

[...] The OMP model-free results file generation script now outputs for any relax version.

[...]................

[...] r17728 | bugman | 2012-10-07 21:54:24 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] Removed the Python 3 byte array hack which should have been removed earlier.

[...]

[...] This code is from r17669 which should have been removed at r17712 but was accidentally left out.

[...] Instead of reverting, the code has been deleted as r17669 contained another useful change.

[...]................

[...] r17729 | bugman | 2012-10-07 21:58:58 +0200 (Sun, 07 Oct 2012) | 5 lines

[...]

[...] Added a Python 3 version of the truncated OMP model-free results file.

[...]

[...] This was created with trunk which is during the 2.1 relax releases.

[...]................

[...] r17730 | bugman | 2012-10-07 22:06:49 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The messsage about skipping the GUI tests due to wxPython being missing is now more specific.

[...]

[...] This was being shown for all runs of the test suite when it only needs to appear if GUI tests have

[...] been run.

[...]................

[...] r17731 | bugman | 2012-10-07 22:11:43 +0200 (Sun, 07 Oct 2012) | 6 lines

[...]

[...] The relaxation curve-fitting system tests are now skipped if the module is missing or broken.

[...]

[...] This improves the printouts from the test suite and shows a summary of skipped tests rather than a

[...] pile of traceback messages and errors.

[...]................

[...] r17732 | bugman | 2012-10-08 00:11:32 +0200 (Mon, 08 Oct 2012) | 7 lines

[...]

[...] Python 3 fix for the model-free results file reading tests.

[...]

[...] The ordering of dictionaries is different in Python 3, so now these are properly converted from

[...] strings to dictionaries before comparison. This was not happening because of the XML changes from

[...] Python 2.7.3 onwards.

[...]................

[...] r17733 | bugman | 2012-10-08 00:34:46 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Python 3 fix for the setting of diffusion and alignment tensor simulation values.

[...]

[...] The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.

[...]................

[...] r17734 | bugman | 2012-10-08 00:41:24 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] The fix of r17733 actually broke Python 2.

[...]

[...] The list.__setattr__() method is fundamentally different between Python 2 and 3!

[...]................

[...] r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed some debugging printouts accidentally committed in r17734.

[...]................

[...] r17736 | bugman | 2012-10-08 00:48:50 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fix of r17734 which attempted to fix r17733.

[...]

[...] The Python version is now being detected.

[...]................

[...] r17737 | bugman | 2012-10-08 11:04:32 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Updated the relax version numbers and 'trunk' used relax user manual.

[...]

[...] For example the information about checking out the main development line was still talking about 1.3

[...] rather than the trunk.

[...]................

[...] r17776 | bugman | 2012-10-09 00:59:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Initialized merge tracking via "svnmerge" with revisions "1-17738" from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17777 | bugman | 2012-10-09 01:01:34 +0200 (Tue, 09 Oct 2012) | 180 lines

[...]

[...] Merged revisions 17739-17774 via svnmerge from

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]

[...] ........

[...] r17739 | bugman | 2012-10-08 11:36:44 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The diffusion tensor data structure has been completely converted into a read-only structure.

[...]

[...] The _setattr_() method now will always raise a RelaxError, and the diffusion tensor simulation

[...] data structure objects _setitem_() method will raise the same error.

[...] ........

[...] r17740 | bugman | 2012-10-08 11:37:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the initialisation of the diffusion tensor data structure, now that it is read-only.

[...] ........

[...] r17741 | bugman | 2012-10-08 11:37:54 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The new diffusion tensor fixed() method has been created to allow the fixed flag to be changed.

[...] ........

[...] r17742 | bugman | 2012-10-08 11:42:23 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] Created the diffusion tensor data structure type() method for setting the tensor type.

[...]

[...] This is to remove the "cdp.diff_tensor.type = 'x'" code from the core of relax, as the structure is

[...] now read only.

[...] ........

[...] r17743 | bugman | 2012-10-08 11:44:02 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Renamed the diffusion tensor data structure type() method to set_type().

[...]

[...] This is because the type is stored as the 'type' object, clashing with the method name.

[...] ........

[...] r17744 | bugman | 2012-10-08 14:04:54 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Converted the old diffusion tensor _setattr_() method into the set() method.

[...]

[...] This is the only way in which diffusion tensor parameters, errors and simulations can be set.

[...] ........

[...] r17745 | bugman | 2012-10-08 14:13:34 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Improvements to the diffusion tensor set() method.

[...]

[...] The parameters, errors and simulations are now properly differentiated and stored.

[...] ........

[...] r17746 | bugman | 2012-10-08 14:19:03 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] A number of private diffusion tensor objects and methods have switched to the single leading '_' format.

[...] ........

[...] r17747 | bugman | 2012-10-08 16:32:48 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed all the unused imports from specific_fns.model_free.main.

[...] ........

[...] r17748 | bugman | 2012-10-08 17:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Redesigned how diffusion tensor simulation structures are handled.

[...]

[...] The design is now much cleaner and works with all Python versions.

[...] ........

[...] r17749 | bugman | 2012-10-08 17:17:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Modified the setUp() method for the diffusion tensor system tests to use the new design.

[...] ........

[...] r17750 | bugman | 2012-10-08 17:22:42 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.

[...] ........

[...] r17751 | bugman | 2012-10-08 17:57:50 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the diffusion tensor _deepcopy_() replacement method for the new design.

[...] ........

[...] r17752 | bugman | 2012-10-08 18:00:05 +0200 (Mon, 08 Oct 2012) | 6 lines

[...]

[...] The setting of list values for the DiffTensorSimList object now works correctly.

[...]

[...] The private _set() method now works correctly by calling the base class method, and the normal

[...] setting of diffusion tensor simulation values produces a RelaxError.

[...] ........

[...] r17753 | bugman | 2012-10-08 18:01:36 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the Diffusion_tensor.test_copy system test - the simulation parameters are now read-only.

[...]

[...] Instead, the diffusion tensor set() method needs to be called.

[...] ........

[...] r17754 | bugman | 2012-10-08 18:27:08 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the diffusion tensor data structure from_xml() method to the new tensor design.

[...] ........

[...] r17755 | bugman | 2012-10-08 18:44:12 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the diffusion tensor to_xml() method for the new design.

[...]

[...] For some reason the methods of the Element class are no longer blacklisted.

[...] ........

[...] r17756 | bugman | 2012-10-08 18:46:31 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the model-free specific analysis duplicate_data() method for the new design.

[...]

[...] The diffusion tensor _mod_attr_ object is now called _mod_attr.

[...] ........

[...] r17757 | bugman | 2012-10-08 18:50:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the 'fixed' object.

[...] ........

[...] r17758 | bugman | 2012-10-08 18:50:46 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The fix user function now uses the diffusion tensor set_fixed() method.

[...] ........

[...] r17759 | bugman | 2012-10-08 18:54:29 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed().

[...] ........

[...] r17760 | bugman | 2012-10-08 19:00:43 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Converted the palmer.extract user function to use the new diffusion tensor design.

[...] ........

[...] r17761 | bugman | 2012-10-08 19:15:40 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.

[...]

[...] This was the previous behaviour and is needed for the test suite to pass.

[...] ........

[...] r17762 | bugman | 2012-10-08 19:16:25 +0200 (Mon, 08 Oct 2012) | 5 lines

[...]

[...] Fix for the fixing of parameters in the model-free analyses.

[...]

[...] The diffusion tensor set_fixed() method is now used.

[...] ........

[...] r17763 | bugman | 2012-10-08 19:20:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the diffusion_tensor.init user function - it was not completely converted.

[...] ........

[...] r17764 | bugman | 2012-10-08 19:27:45 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.

[...] ........

[...] r17765 | bugman | 2012-10-08 19:30:25 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.

[...] ........

[...] r17766 | bugman | 2012-10-08 19:36:16 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Another fix for the fold_angles() diffusion tensor function - again an incomplete design conversion.

[...] ........

[...] r17767 | bugman | 2012-10-08 19:56:55 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of relax 1.2 model-free results files for the diffusion tensor structure redesign.

[...] ........

[...] r17768 | bugman | 2012-10-08 20:04:53 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Fix for the reading of model-free results files from relax 1.2 when simulation data is missing.

[...] ........

[...] r17769 | bugman | 2012-10-08 22:21:31 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Updated all of the diffusion tensor unit tests to the new design.

[...] ........

[...] r17770 | bugman | 2012-10-08 22:36:00 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Cleaned up the docstring of the diffusion tensor data object _setattr_() method.

[...] ........

[...] r17771 | bugman | 2012-10-08 22:36:47 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Removed the now unused _update_sim_append() method from the diffusion tensor data structure.

[...] ........

[...] r17772 | bugman | 2012-10-08 22:38:18 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Deleted the now unused _update_sim_set() method of the diffusion tensor data structure.

[...] ........

[...] r17773 | bugman | 2012-10-08 22:49:38 +0200 (Mon, 08 Oct 2012) | 3 lines

[...]

[...] Small clean ups of the diffusion tensor data structure code.

[...] ........

[...] r17774 | bugman | 2012-10-09 00:24:34 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensor.

[...]

[...] This large set of changes matches all of those revisions for the diffusion tensor already committed in

[...] this branch. The alignment tensor data structures are now read only, and can only be modified via the

[...] set() method. This is a much simplified design which works on all Python versions.

[...] ........

[...]................

[...] r17778 | bugman | 2012-10-09 01:02:04 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Removed merge tracking for "svnmerge" for

[...] svn+ssh://bugman@svn.gna.org/svn/relax/branches/tensor_data

[...]................

[...] r17780 | bugman | 2012-10-09 10:26:13 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 3 fix for the model-free BMRB export - many string module methods no longer exist.

[...]................

[...] r17781 | bugman | 2012-10-09 10:29:53 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] More Python 3 fixes for the use of now non-existent string module functions.

[...]................

[...] r17782 | bugman | 2012-10-09 11:53:02 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails.

[...]

[...] This removes a pile of useless error messages from the test, and presents a table of skipped tests

[...] at the end.

[...]................

[...] r17783 | bugman | 2012-10-09 12:03:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.5 and lower fix for the test_write_protein_sequence() unit test.

[...]

[...] The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the code

[...] without failing, and the byte array comparison is now only used for Python 3+.

[...]................

[...] r17784 | bugman | 2012-10-09 12:09:45 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] The Results system tests are no longer dependent on the relaxation curve-fitting C modules.

[...]

[...] This allows these tests to run when the module cannot be imported.

[...]................

[...] r17785 | bugman | 2012-10-09 12:50:29 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Created a special script for testing out relax with Python versions 1.0 all the way to 3.3.

[...]

[...] This builds the C modules for each Python version in ~/bin and then runs the test suite, outputting

[...] everything to log files.

[...]................

[...] r17786 | bugman | 2012-10-09 12:52:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 fixes - the ctypes module does not exist in Python versions 2.4 and lower.

[...]

[...] This is only used for some non-essential functionality on MS Windows, so now it is deactivated if

[...] not present.

[...]................

[...] r17787 | bugman | 2012-10-09 12:59:11 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Python 2.4 and lower fix for the pipe_loop() generator method.

[...]

[...] In these Python versions, a 'try' block with a 'finally' statement cannot contain 'yield'

[...] statements! This work around should be compatible with all Python versions.

[...]................

[...] r17788 | bugman | 2012-10-09 13:36:46 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Fix for the test_write_protein_sequence() unit test for a recently introduced bug.

[...]................

[...] r17789 | bugman | 2012-10-09 14:28:30 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Reactivated support for Python 2.3.

[...]

[...] This mainly skips the missing 'subprocess' module. This however decreases relax's functionality a

[...] little.

[...]................

[...] r17790 | bugman | 2012-10-09 14:35:38 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Small improvements to the multiple python version test suite testing script.

[...]................

[...] r17791 | bugman | 2012-10-09 15:59:34 +0200 (Tue, 09 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for Python 3.1.

[...]

[...] The XML version in Python 3.1 is the old style! Therefore the old results file is being used to

[...] check this Python 3.1 result.

[...]................

[...] r17792 | bugman | 2012-10-09 20:47:25 +0200 (Tue, 09 Oct 2012) | 7 lines

[...]

[...] Better Python 2.3 support.

[...]

[...] The compat module is now imported at the very start to allow the builtins to be set before any other

[...] imports. The sorted() builtin method is now mimicked and the os.devnull string set for Python 2.3

[...] and earlier.

[...]................

[...] r17793 | bugman | 2012-10-09 20:59:17 +0200 (Tue, 09 Oct 2012) | 3 lines

[...]

[...] Python 2.4 fix - the unit test runner no longer uses the builtin set() method.

[...]................

[...] r17794 | bugman | 2012-10-09 21:06:42 +0200 (Tue, 09 Oct 2012) | 5 lines

[...]

[...] Python 2.4 and earlier fix for the GUI.

[...]

[...] Try-except-finally statement blocks are not supported, so these have to nested in two try statements.

[...]................

[...] r17795 | bugman | 2012-10-10 16:37:34 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_write_results() system test for the Python 3 versions.

[...]

[...] The logic for determining Python 3 versions was broken and the incorrect files was used for Python

[...] 3.1.

[...]................

[...] r17796 | bugman | 2012-10-10 16:44:00 +0200 (Wed, 10 Oct 2012) | 6 lines

[...]

[...] Fix for the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2.

[...]

[...] The object comparison method no longer converts dictionaries to strings for the comparison, as the

[...] string version is different in different Python versions.

[...]................

[...] r17797 | bugman | 2012-10-11 10:53:47 +0200 (Thu, 11 Oct 2012) | 5 lines

[...]

[...] Disabled the initial relax intro print out from the GUI when running the test suite.

[...]

[...] This prevents the intro text from appearing in the first failed test.

[...]................

[...] r17798 | bugman | 2012-10-12 11:48:22 +0200 (Fri, 12 Oct 2012) | 10 lines

[...]

[...] Redesigned the reset user function backend.

[...]

[...] This now no only clears out the relax data store, but it also resets the GUI if present. Some of

[...] the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI

[...] window are closed and the relax controller gauges are set to zero and the log window text cleared.

[...]

[...] These changes should allow GUI tests after an error or failure to pass, something which is currently

[...] problematic.

[...]................

[...] r17799 | bugman | 2012-10-15 10:21:37 +0200 (Mon, 15 Oct 2012) | 6 lines

[...]

[...] Python 3 fix for the ScientificPython PDB reader unit tests.

[...]

[...] The order of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now

[...] they are sorted prior to comparison.

[...]................

[...] r17800 | bugman | 2012-10-15 10:31:28 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3 fix - eliminated the superfluous operator.itemgetter() call in the diffusion tensor code.

[...]................

[...] r17801 | bugman | 2012-10-15 10:39:20 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix - the subprocess module is only imported when present.

[...]

[...] This is for the stereochem_analysis auto-analysis, but the import kills all of the auto-analyses.

[...]................

[...] r17802 | bugman | 2012-10-15 10:42:56 +0200 (Mon, 15 Oct 2012) | 5 lines

[...]

[...] Python 2.3 and earlier fix for the Test_relax_re.test_search() unit test.

[...]

[...] The unittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.

[...]................

[...] r17803 | bugman | 2012-10-15 10:48:09 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Python 2.3- fixes - the Modelfree4 and Dasha system tests are now skipped if the subprocess module is missing.

[...]................

[...] r17804 | bugman | 2012-10-15 13:50:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Test suite bug fix - the GUI tests now cleanly terminate the interpreter thread.

[...]

[...] This allows the test suite to terminate normally. With different Python versions on different

[...] operating systems, this could sometimes cause the test suite to freeze at the end, the final

[...] printout to be missing, or other strange behaviour.

[...]................

[...] r17805 | bugman | 2012-10-15 14:24:14 +0200 (Mon, 15 Oct 2012) | 3 lines

[...]

[...] Removed an unused import of the Queue module from the multi-processor.

[...]................

[...] r17806 | bugman | 2012-10-15 14:25:51 +0200 (Mon, 15 Oct 2012) | 7 lines

[...]

[...] Python 2.4 and earlier fixes for the Queuing module.

[...]

[...] The TaskQueue class from http://code.activestate.com/recipes/475160/ which was added to Python 2.5+

[...] has been added to the compat module. This module is now used for all imports of the Queue class for

[...] all Python versions.

[...]................

[...]

[...]

(Browse SVN revision 17807)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 04 Oct 2012 05:02:08 PM UTC, SVN revision 17700:

Fix for bug #20213 (https://gna.org/bugs/?20213).

The problem was that the generic_fns.sequence.generate() function was searching for a spin based on
its spin ID generated from the spin name and not spin number. Hence two spins with the same name
but different numbers were treated as the same spin, and only data from one was being generated via
the copy() function.

(Browse SVN revision 17700)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 04 Oct 2012 04:37:57 PM UTC, SVN revision 17699:

Created the simple Sequence.test_sequence_copy() system test to catch bug #20213.

https://gna.org/bugs/?20213.

(Browse SVN revision 17699)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 04 Oct 2012 04:20:51 PM UTC, SVN revision 17697:

Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.

The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from the analysis.

(Browse SVN revision 17697)

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Thu 04 Oct 2012 04:07:22 PM UTC, comment #1:

This bug is caused by the loading of Asn and Gln sidechain nitrogen spins, but relax should handle this.

Edward d Auvergne <bugman>
Project AdministratorIn charge of this item.
Tue 02 Oct 2012 03:48:51 PM UTC, original submission:

Hi Edward,

during or after fitting tm, relax gives me the following error:

File "/opt/relax-2.1.0/specific_fns/model_free/main.py", line 1537, in duplicate_data
dp_to.mol[mol_index].res[res_index].spin[spin_index] = deepcopy(spin2)
IndexError: list assignment index out of range

The full traceback:

Model-free model of spin '#1U06-H_mol1:47@N'.
Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion
tm0 - mf (Tue Oct 2 17:14:03 2012) 1 6 1051.35716 1053.35716
tm1 - mf (Tue Oct 2 17:14:03 2012) 2 6 28.84022 32.84022
tm2 - mf (Tue Oct 2 17:14:03 2012) 3 6 25.50256 31.50256
tm3 - mf (Tue Oct 2 17:14:03 2012) 3 6 3.76695 9.76695
tm4 - mf (Tue Oct 2 17:14:03 2012) 4 6 3.76695 11.76695
tm5 - mf (Tue Oct 2 17:14:03 2012) 4 6 25.50256 33.50256
tm6 - mf (Tue Oct 2 17:14:03 2012) 5 6 25.50256 35.50256
tm7 - mf (Tue Oct 2 17:14:03 2012) 5 6 3.76695 13.76695
tm8 - mf (Tue Oct 2 17:14:03 2012) 6 6 3.76695 15.76695
tm9 - mf (Tue Oct 2 17:14:03 2012) 2 6 683.15687 687.15687
The model from the data pipe 'tm3 - mf (Tue Oct 2 17:14:03 2012)' has been selected.
Exception raised in thread.

Traceback (most recent call last):
File "/opt/relax-2.1.0/gui/analyses/execute.py", line 87, in run
self.run_analysis()
File "/opt/relax-2.1.0/gui/analyses/auto_model_free.py", line 803, in run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, diff_model=self.data.global_models, mf_models=self.data.mf_models, local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, conv_loop=self.data.conv_loop)
File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 235, in _init_
self.execute()
File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 562, in execute
self.model_selection(modsel_pipe=self.name_pipe('aic'), dir=self.base_dir + 'aic')
File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 769, in model_selection
self.interpreter.model_selection(method='AIC', modsel_pipe=modsel_pipe, bundle=self.pipe_bundle, pipes=self.pipes)
File "/opt/relax-2.1.0/prompt/uf_objects.py", line 219, in _call_
self._backend(*new_args, **uf_kargs)
File "/opt/relax-2.1.0/generic_fns/model_selection.py", line 298, in select
duplicate_data[best_model](best_model, modsel_pipe, model_info, global_stats=global_flag, verbose=False)
File "/opt/relax-2.1.0/specific_fns/model_free/main.py", line 1537, in duplicate_data
dp_to.mol[mol_index].res[res_index].spin[spin_index] = deepcopy(spin2)
IndexError: list assignment index out of range

The full error log is in log5.txt.

I used a reduced data set of only 10 residues, still relax chokes on residue 47.

I have no idea where this comes from. With a different crystal structure / pdb file (1shg) and relax version everything worked well and I got quite meaningful results. I wnated to re-run relax with another pdb structure, just for the heck of it.

Please have a look into the "prep.py" file, that's the script I used to prepare the setup.

I'd be very grateful if you could tell me what went wrong.

The recorded data are not confidential and I could make them accessible at any time.

Martin Ballaschk <mab>

 

(Note: upload size limit is set to 1024 kB, after insertion of the required escape characters.)

Attach File(s):
   
   
Comment:
   

Attached Files
file #16625:  run.py added by None (4kB - text/x-python-script - Full script and single-spin demo data which reproduces deep-copy error)
file #16626:  sh3-47.2.zip added by None (364kB - application/zip - Full script and single-spin demo data which reproduces deep-copy error)
file #16621:  sh3-47.zip added by mab (100kB - application/zip)
file #16619:  log5.txt added by mab (613kB - text/plain)
file #16620:  prep.py added by mab (3kB - text/x-python-script)

 

Depends on the following items: None found

Items that depend on this one: None found

 

Carbon-Copy List
  • -unavailable- added by bugman (Updated the item)
  • -unavailable- added by mab (Submitted the item)
  •  

    Do you think this task is very important?
    If so, you can click here to add your encouragement to it.
    This task has 0 encouragements so far.

    Only logged-in users can vote.

     

    Please enter the title of George Orwell's famous dystopian book (it's a date):

     

     

    Follow 13 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Thu 04 Oct 2012 05:02:18 PM UTCbugmanStatusIn Progress=>Fixed
      Open/ClosedOpen=>Closed
    Thu 04 Oct 2012 04:07:22 PM UTCbugmanCategoryGUI=>relax's source code
      StatusConfirmed=>In Progress
      Release2.1.0=>2.1.1
      Operating SystemGNU/Linux=>All systems
    Thu 04 Oct 2012 02:25:37 PM UTCbugmanStatusNone=>Confirmed
      Assigned toNone=>bugman
    Thu 04 Oct 2012 01:14:31 PM UTCNoneAttached File-=>Added run.py, #16625
      Attached File-=>Added sh3-47.2.zip, #16626
    Tue 02 Oct 2012 03:50:15 PM UTCmabAttached File-=>Added sh3-47.zip, #16621
    Tue 02 Oct 2012 03:48:51 PM UTCmabAttached File-=>Added log5.txt, #16619
      Attached File-=>Added prep.py, #16620
    Show feedback again

    Back to the top


    Powered by Savane 3.1-cleanup