relax SVN archive

Merged revisions 17671-17675 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17671 | bugman | 2012-10-02 15:48:31 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 fix for the user function docstring creation in the prompt UI mode.

Again this is the problem of a division now returning a float rather than an int.
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r17672 | bugman | 2012-10-02 16:05:11 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 fix for the test_write_protein_sequence() unit test.

This is again a string verses byte verses unicode problem.
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r17673 | bugman | 2012-10-02 16:09:58 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 bug fix for the Structure.test_read_pdb_mol_2_model_scientific system tests.

This is again an integer division problem returning a float.
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r17674 | bugman | 2012-10-02 16:12:01 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 2 and 3 support in the generic_fns.relax_data module using 2to3.

One print call was fixed after running 2to3.
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r17675 | bugman | 2012-10-02 16:24:58 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 fixes - eliminated all usage of the dictionary has_key() calls as they are no longer present.
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Merged revisions 17661-17670 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17661 | bugman | 2012-10-02 14:08:22 +0200 (Tue, 02 Oct 2012) | 5 lines

Fix for the test suite summary for Python 3.

The test suite now runs, but fails miserably, under Python 3.
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r17662 | bugman | 2012-10-02 14:16:02 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 fixes - the character '\' is now properly escaped as '\\' in the stereochemistry auto-analysis.
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r17663 | bugman | 2012-10-02 14:18:41 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 fix - the relax_errors.AllRelaxErrors object is now a proper tuple.

Due to bad coding, it was previously a nested tuple. This nested tuple worked in Python 2, but is
fatal for Python 3.
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r17664 | bugman | 2012-10-02 14:23:43 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 preparation - the relax data store (the data package) now supports both Python 2 and 3.

The command used was:
2to3 -w data/__init__.py
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r17665 | bugman | 2012-10-02 14:25:52 +0200 (Tue, 02 Oct 2012) | 5 lines

Better support for both Python 2 and 3 in the relax data store.

The 2to3 script was used on all of the files in the data package.
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r17666 | bugman | 2012-10-02 14:37:01 +0200 (Tue, 02 Oct 2012) | 7 lines

Python 3 bug fix for the state.load user function.

The header line of pickled states (rather than the standard XML states) is of the b'' byte format.
This is now converted to a string, and the search expression is comparing it to the raw string
r"<\?xml".
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r17667 | bugman | 2012-10-02 15:18:32 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 bug fix for the relax_io.read_spin_data() function.

The built in max() function cannot handle the value of None, therefore the filter() function is used
to remove all instances of None from the list.
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r17668 | bugman | 2012-10-02 15:19:32 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 fix for the results.read user function matching that of state.load at r17666.
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r17669 | bugman | 2012-10-02 15:42:37 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 fix for the reading of text from a bz2 file.

In Python 3, the readlines() function was returning a list of bytes types, not a list of strings.
The relax_io.extract_data() function now detects this and converts to string when possible.
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r17670 | bugman | 2012-10-02 15:44:24 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 bug fix for the N-state model target function setup.

The num_tensors variable needs to be an integer, but the Python 3 division will create a float type.
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Merged revisions 17651-17660 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17651 | bugman | 2012-10-02 10:52:35 +0200 (Tue, 02 Oct 2012) | 5 lines

Created the check_types.is_unicode() function for Python 2+3 compatibility.

This is used in the generic_fns.mol_res_spin module.
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r17652 | bugman | 2012-10-02 10:53:34 +0200 (Tue, 02 Oct 2012) | 3 lines

More usage of the is_unicode() function in the generic_fns.mol_res_spin module.
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r17653 | bugman | 2012-10-02 10:54:58 +0200 (Tue, 02 Oct 2012) | 3 lines

Import fix for the OpenDX mapping package, recently broken with the relative import for Python 3 change.
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r17654 | bugman | 2012-10-02 11:04:51 +0200 (Tue, 02 Oct 2012) | 3 lines

The compat module now has the py_version variable specifying if this is Python 2 or 3.
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r17655 | bugman | 2012-10-02 11:39:17 +0200 (Tue, 02 Oct 2012) | 7 lines

For running relax with Python 2, the __builtin__.range() function has been replaced with xrange.

This causes large speed ups (speed that was lost with the earlier xrange() to range() conversions),
and memory decreases. For example on one system, the system test time decreased from 513.029s to
487.586s.
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r17656 | bugman | 2012-10-02 11:47:15 +0200 (Tue, 02 Oct 2012) | 6 lines

Automatically converted the generic_fns.mol_res_spin module to support both Python 2 and 3.

The command used was:
2to3 -w generic_fns/mol_res_spin.py
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r17657 | bugman | 2012-10-02 11:53:17 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 fix for the generic_fns.mol_res_spin.parse_token() function.

Mixed lists for int and string can no longer be sorted. This sort call is not needed anyway.
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r17658 | bugman | 2012-10-02 13:35:59 +0200 (Tue, 02 Oct 2012) | 3 lines

Fix for the test_parse_token_multi_element_name() unit test, as parse_token() no longer sorts.
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r17659 | bugman | 2012-10-02 14:05:17 +0200 (Tue, 02 Oct 2012) | 6 lines

Fix for the running of the test suite under Python 3.

The zip() function used in the loadTestsFromTestCase() function is now an iterator, so it needs to
be passed through the list() function to generate a list.
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r17660 | bugman | 2012-10-02 14:05:50 +0200 (Tue, 02 Oct 2012) | 3 lines

Copyright update.
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Merged revisions 17641-17650 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17641 | bugman | 2012-10-01 23:34:42 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - eliminated the use of the map() function, as this behaves differently in Python 3.
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r17642 | bugman | 2012-10-01 23:40:37 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - Eliminated an unneeded xrange call.
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r17643 | bugman | 2012-10-02 00:37:08 +0200 (Tue, 02 Oct 2012) | 3 lines

Created the special check_types.is_filetype() function for checking for files in all Python versions.
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r17644 | bugman | 2012-10-02 01:16:44 +0200 (Tue, 02 Oct 2012) | 5 lines

Fix for a bug introduced at r17624 in the generic_fns.sequence.validate_sequence() function.

The is_none() function call doesn't seem to be working correctly.
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r17645 | bugman | 2012-10-02 10:23:28 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 preparations - mass conversion of all xrange() calls to range().
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r17646 | bugman | 2012-10-02 10:26:09 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 fixes - the list() function is now used in combination with range() to generate the ordered list.

range() in Python 3 is an iterator object (just as xrange was), so now the list() function has to be
called.
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r17647 | bugman | 2012-10-02 10:35:22 +0200 (Tue, 02 Oct 2012) | 3 lines

Created a new module for simultaneous Python 2 and 3 support in relax called 'compat'.
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r17648 | bugman | 2012-10-02 10:45:46 +0200 (Tue, 02 Oct 2012) | 9 lines

Converted the ScientificPython PDB reader to support both Python 2 and 3.

The command used was:
2to3 extern/scientific_python/IO/PDB.py -w

The __repr__() method was manually modified due to the 'list' variable clashing with the 'list'
type.
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r17649 | bugman | 2012-10-02 10:47:48 +0200 (Tue, 02 Oct 2012) | 3 lines

Converted some raise() function calls to raise statements in preparation for the 2to3 conversion.
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r17650 | bugman | 2012-10-02 10:49:09 +0200 (Tue, 02 Oct 2012) | 3 lines

Another raise() function call to statement change for 2to3 preparations.
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Merged revisions 17624-17640 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17624 | bugman | 2012-10-01 21:33:21 +0200 (Mon, 01 Oct 2012) | 5 lines

Python 3 - removed the use of the types module from generic_fns.sequence.

The relax arg_check module is now being used instead.
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r17625 | bugman | 2012-10-01 21:34:01 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - a pile of relative path fixes for many relax modules.
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r17626 | bugman | 2012-10-01 21:44:20 +0200 (Mon, 01 Oct 2012) | 5 lines

Python 3 - Fix for an os.chmod() call by using the stat module rather than the number 0775.

The number 0755 is no longer valid in Python 3.
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r17627 | bugman | 2012-10-01 21:48:28 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - converted some print statements to function calls in the ScientificPython modules.
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r17628 | bugman | 2012-10-01 21:52:19 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - modified some except statements to be Python 2.4+ compatible in a ScientificPython module.
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r17629 | bugman | 2012-10-01 22:12:24 +0200 (Mon, 01 Oct 2012) | 6 lines

Python 3 - a number of fixes for running the ScientificPython modules in relax on Python 2 and 3.

This includes relative imports, converting raise statements to function calls, removal of the use of
many string module functions which do not exist in Python 3, etc.
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r17630 | bugman | 2012-10-01 22:15:43 +0200 (Mon, 01 Oct 2012) | 6 lines

Python 3 - removal of the use of the string.atoi and string.atof functions.

These have been depreciated since Python 2.0!! They have been replace by the int and float
functions.
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r17631 | bugman | 2012-10-01 22:22:34 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - converted the last of the except error catching statements to be Python 2.4+ compatible.
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r17632 | bugman | 2012-10-01 22:27:00 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - fixes for the renaming of the Queue package.
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r17633 | bugman | 2012-10-01 22:41:26 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 fix - ensure an integer is actually an integer (division now converts ints to floats).
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r17634 | bugman | 2012-10-01 22:43:38 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 fixes for the version module for catching empty lists.
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r17635 | bugman | 2012-10-01 22:51:12 +0200 (Mon, 01 Oct 2012) | 3 lines

Debugging printout removal.
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r17636 | bugman | 2012-10-01 22:54:43 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - relative module paths are now used for the test suite runner.
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r17637 | bugman | 2012-10-01 22:55:29 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - The cStringIO.StringIO import switches to io.StringIO if missing.
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r17638 | bugman | 2012-10-01 23:06:27 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 2 fixes - the Python 3 fixes for the ScientificPython module imports broke Python 2.
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r17639 | bugman | 2012-10-01 23:19:57 +0200 (Mon, 01 Oct 2012) | 5 lines

Python 3 fix for the relax information print out.

The try blocks seem to now operate slightly differently in Python 3.
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r17640 | bugman | 2012-10-01 23:34:08 +0200 (Mon, 01 Oct 2012) | 3 lines

Python 3 - removed the use of the string.lower() function as it is missing in Python 3.
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Merged revisions 17623 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17623 | bugman | 2012-10-01 18:48:11 +0200 (Mon, 01 Oct 2012) | 5 lines

Python 3 preparations - removed all of the string module functions which no longer exist in Python 3.

These functions are part of the strings themselves now.
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Merged revisions 17621-17622 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17621 | bugman | 2012-10-01 14:04:16 +0200 (Mon, 01 Oct 2012) | 3 lines

Fix for bug #20210 (https://gna.org/bugs/?20210) - relax now runs again without having wxPython installed.
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r17622 | bugman | 2012-10-01 18:13:20 +0200 (Mon, 01 Oct 2012) | 5 lines

Improvements for the relax test suite synopsis for when the wxPython module is missing or broken.

This is simply a printout improvement.
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Merged revisions 17601-17620 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17601 | bugman | 2012-09-28 17:17:05 +0200 (Fri, 28 Sep 2012) | 3 lines

More exception handling changes to be Python 2.4+ compatible.
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r17602 | bugman | 2012-09-28 17:22:32 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - eliminated the use of the os.popen3 function from the info module.
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r17603 | bugman | 2012-09-28 17:28:11 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - all os.popen3() instances in relax have been replaced by the subprocess module.
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r17604 | bugman | 2012-09-28 17:28:56 +0200 (Fri, 28 Sep 2012) | 3 lines

Removed an unused import (which was breaking relax in Python 3).
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r17605 | bugman | 2012-09-28 17:55:25 +0200 (Fri, 28 Sep 2012) | 3 lines

Removed the completely unused gui.components.conversion module.
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r17606 | bugman | 2012-09-28 18:08:24 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - all usage of string.split() and string.strip() has been eliminated.
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r17607 | bugman | 2012-09-28 18:11:48 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - compatibility for both the Python 2 cPickle and Python 3 pickle modules.
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r17608 | bugman | 2012-09-28 18:20:48 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - removed the use of the types.ClassType object.
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r17609 | bugman | 2012-09-28 18:32:10 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - converted the relax prompt/script interpreter to be Python 2 and 3 compatible.
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r17610 | bugman | 2012-09-28 18:34:49 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - error handling is now Python 2 and 3 compatible in the relax_io module.
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r17611 | bugman | 2012-09-28 18:50:32 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - all raising of RelaxErrors is now Python 2.4+ compatible.
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r17612 | bugman | 2012-09-28 18:52:10 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - more exception handling updates for all Python 2.4+ versions.
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r17613 | bugman | 2012-09-28 18:55:04 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - absolute module path fix.
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r17614 | bugman | 2012-09-28 18:57:45 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - support for both Python 2 __builtin__ and Python 3 builtins modules.
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r17615 | bugman | 2012-09-28 18:58:47 +0200 (Fri, 28 Sep 2012) | 3 lines

Bug fix for a problem introduced in the last commit.
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r17616 | bugman | 2012-09-28 19:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - absolute module path fixes.
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r17617 | bugman | 2012-09-28 19:04:46 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - eliminated the use of the types.ListType object.
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r17618 | bugman | 2012-09-28 19:06:23 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - the data package now uses absolute imports for all its modules.
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r17619 | bugman | 2012-09-28 19:13:09 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - the data package now really does use the absolute path for its module imports.
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r17620 | bugman | 2012-09-28 19:13:30 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - removal of some unneeded xrange() calls.
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Merged revisions 17581-17600 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17581 | bugman | 2012-09-28 10:58:47 +0200 (Fri, 28 Sep 2012) | 13 lines

Last Python 3 compatibility update for the system tests - they are now both Python 2 and 3 compatible!

The command used was:
2to3 -w \
-f except \
-f import \
-f imports \
-f long \
-f numliterals \
-f xrange \
.
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r17582 | bugman | 2012-09-28 11:00:34 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - removed all xrange() calls from the unit tests, these are not needed.
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r17583 | bugman | 2012-09-28 11:06:47 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - all the _prompt unit tests now use absolute module imports.
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r17584 | bugman | 2012-09-28 11:08:34 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - all of the _generic_fns unit tests now use absolute module imports.
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r17585 | bugman | 2012-09-28 11:09:41 +0200 (Fri, 28 Sep 2012) | 6 lines

Python 3 preparations - the unit tests are now fully Python 2 and 3 compatible.

The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17586 | bugman | 2012-09-28 11:32:12 +0200 (Fri, 28 Sep 2012) | 5 lines

Bug fix for the BMRB system test initialisation for when the bmrblib module is missing.

The base __init__() method needs to be initialised first.
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r17587 | bugman | 2012-09-28 11:32:41 +0200 (Fri, 28 Sep 2012) | 3 lines

Removed some temporary debugging code.
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r17588 | bugman | 2012-09-28 11:34:04 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - the test_suite.gui_tests package now uses absolute module path imports.
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r17589 | bugman | 2012-09-28 11:42:00 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - the queue modules for both Python versions are now supported in the GUI tests.
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r17590 | bugman | 2012-09-28 11:43:29 +0200 (Fri, 28 Sep 2012) | 6 lines

Python 3 preparations - the GUI tests are now fully Python 2 and 3 compatible.

The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17591 | bugman | 2012-09-28 11:45:14 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - the use of the queue module in the status module is now compatible with 2 and 3.
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r17592 | bugman | 2012-09-28 11:49:34 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - the auto_analyses package now uses absolute paths for the module imports.
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r17593 | bugman | 2012-09-28 11:50:34 +0200 (Fri, 28 Sep 2012) | 6 lines

Python 3 preparations - the auto_analyses package is now fully Python 2 and 3 compatible.

The command used was:
2to3 -w -f except -f import -f imports -f long -f numliterals -f xrange .
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r17594 | bugman | 2012-09-28 13:28:49 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - the use of an absolute module path for import.
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r17595 | bugman | 2012-09-28 13:29:29 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - eliminated the unneeded use of xrange().
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r17596 | bugman | 2012-09-28 13:36:50 +0200 (Fri, 28 Sep 2012) | 6 lines

Python 3 preparations - removed all usage of the xrange() in the generic_fns package as none are needed.

The command used was:
2to3 -w -f xrange .
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r17597 | bugman | 2012-09-28 14:23:58 +0200 (Fri, 28 Sep 2012) | 3 lines

Updated the Python 2 to 3 checklist document for the shifting of the 'relax' file to 'relax.py'.
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r17598 | bugman | 2012-09-28 16:40:50 +0200 (Fri, 28 Sep 2012) | 17 lines

Python 3 conversions using 2to3.

The command used was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.
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r17599 | bugman | 2012-09-28 16:57:03 +0200 (Fri, 28 Sep 2012) | 6 lines

Reverted r17598 for the multi.processor module as this breaks in Python 2.

The command used was:
svn merge -r17598:r17597 processor.py
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r17600 | bugman | 2012-09-28 16:58:29 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparations - exception handling fix to be Python 2.4+ compatible.
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Merged revisions 17552-17580 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17552 | bugman | 2012-09-25 13:42:50 +0200 (Tue, 25 Sep 2012) | 7 lines

Fix for bug #20198 (https://gna.org/bugs/?20198) - the relaxation data back-calculation error.

The problem was that the call to the model-free overfit_deselect() method was deselecting any spins
lacking relaxation data! This should not happen, as no spins need to have relaxation data for this
calculation.
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r17553 | bugman | 2012-09-25 14:03:50 +0200 (Tue, 25 Sep 2012) | 5 lines

Added the data_check Boolean argument to all of the specific analysis overfit_deselect() methods.

This allows the unit tests to pass.
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r17554 | bugman | 2012-09-25 14:05:41 +0200 (Tue, 25 Sep 2012) | 7 lines

Added a tryptophan NE1 data set to the sphere model-free model test data.

This is in preparation to catch bug #20197 (https://gna.org/bugs/?20197).

The scripts have also been updated for the newer relax designs.
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r17555 | bugman | 2012-09-25 14:38:21 +0200 (Tue, 25 Sep 2012) | 6 lines

Improved the model-free overfitting deselection printouts prior to optimisation.

Only a single message per spin is now given when the spin is deselected, minimising the amount of
output.
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r17556 | bugman | 2012-09-25 14:53:03 +0200 (Tue, 25 Sep 2012) | 3 lines

More improvements to the model-free over-fitting deselection printouts.
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r17557 | bugman | 2012-09-25 14:58:22 +0200 (Tue, 25 Sep 2012) | 5 lines

Printouts for the over-fitting deselection of spins are suppressed for the back-calculation of relaxation data.

This affects the model-free Monte Carlo simulations, simplifying the output.
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r17558 | bugman | 2012-09-25 15:01:37 +0200 (Tue, 25 Sep 2012) | 3 lines

All overfit_deselect() methods now accept and use the verbose argument.
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r17559 | bugman | 2012-09-25 15:06:25 +0200 (Tue, 25 Sep 2012) | 3 lines

The overfit_deselect() printouts are now regularised and match the model-free printouts.
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r17560 | bugman | 2012-09-25 15:18:23 +0200 (Tue, 25 Sep 2012) | 6 lines

Small change to the sphere model model-free test suite data.

The trptophan indole data is now merged into the last residue (a glycine) to catch bug #20197
(https://gna.org/bugs/?20197).
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r17561 | bugman | 2012-09-25 15:21:43 +0200 (Tue, 25 Sep 2012) | 5 lines

Modified the Mf.test_dauvergne_protocol system test to catch bug #20197 (https://gna.org/bugs/?20197).

The sphere test data NE1 and HE1 data is now being used in this system test, triggering the bug.
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r17562 | bugman | 2012-09-25 16:37:03 +0200 (Tue, 25 Sep 2012) | 3 lines

Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.
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r17563 | bugman | 2012-09-25 16:41:25 +0200 (Tue, 25 Sep 2012) | 3 lines

Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.
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r17564 | bugman | 2012-09-25 16:42:04 +0200 (Tue, 25 Sep 2012) | 3 lines

Fix to the Dasha system test needed for the changes to the relax_data.read user function.
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r17565 | bugman | 2012-09-25 17:02:49 +0200 (Tue, 25 Sep 2012) | 3 lines

Fix for the Relax_data.test_read unit tests for the relax_data.read user function changes.
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r17566 | bugman | 2012-09-25 17:07:18 +0200 (Tue, 25 Sep 2012) | 3 lines

Fix for the Relax_data.test_delete system test for the changes to the relax_data.read user function.
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r17567 | bugman | 2012-09-25 18:46:03 +0200 (Tue, 25 Sep 2012) | 6 lines

Fix for bug #20197 (https://gna.org/bugs/?20197) - the PyMOL and Molmol macro failure.

The macro creation now only operates on spins called 'N' and assumes these are the backbone
nitrogens. The sidechain tryptophan indole NH data will need to be detected and added later.
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r17568 | bugman | 2012-09-27 10:03:08 +0200 (Thu, 27 Sep 2012) | 3 lines

Lots of editing of the model-free GUI section of the user manual.
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r17569 | bugman | 2012-09-27 10:04:04 +0200 (Thu, 27 Sep 2012) | 3 lines

Fix for the comment on the 'Export' button in the BMRB export window.
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r17570 | bugman | 2012-09-27 10:04:22 +0200 (Thu, 27 Sep 2012) | 3 lines

Removed some debugging printouts.
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r17571 | bugman | 2012-09-27 10:05:14 +0200 (Thu, 27 Sep 2012) | 3 lines

Added star versions of the standard spin IDs to the spin ID GUI element (e.g. '@N*', '@H*').
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r17572 | bugman | 2012-09-27 10:07:03 +0200 (Thu, 27 Sep 2012) | 6 lines

The CSA setting in the model-free auto GUI analysis now defaults to the '@N*' spin ID.

Previously no spin ID was being used so that the protons where also having their CSA values set to
that of the nitrogens. Now the execution checking code skips the proton CSA check.
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r17573 | bugman | 2012-09-27 10:08:12 +0200 (Thu, 27 Sep 2012) | 3 lines

Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the recent test suite data changes.
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r17574 | bugman | 2012-09-27 16:14:47 +0200 (Thu, 27 Sep 2012) | 6 lines

Removed the 'force flag' text from the RelaxWarning messages output by the bruker.read user function.

The force flag arguments of the generic_fns.mol_res_spin.name_spin() and
generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.
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r17575 | bugman | 2012-09-27 16:29:40 +0200 (Thu, 27 Sep 2012) | 7 lines

Fix for bug #20201 (https://gna.org/bugs/?20201).

The bruker.read user function can now handle the situation where multiple spins per residue are
already loaded prior to the user function call. The isotope value from the DC file is now
translated to the element name and this is used as part of the spin ID string.
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r17576 | bugman | 2012-09-27 19:19:13 +0200 (Thu, 27 Sep 2012) | 3 lines

Some changes in preparation for Python 3.
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r17577 | bugman | 2012-09-28 10:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines

Fix for a fatal bug introduced in the last revision (r17576).
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r17578 | bugman | 2012-09-28 10:49:08 +0200 (Fri, 28 Sep 2012) | 5 lines

Removed all of the xrange() calls from the system tests as these are not necessary.

This is in preparation for Python 3.
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r17579 | bugman | 2012-09-28 10:55:55 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - changed the import of SystemTestCase to use the absolute module path.
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r17580 | bugman | 2012-09-28 10:57:54 +0200 (Fri, 28 Sep 2012) | 3 lines

Python 3 preparation - the test_suite.system_tests package now uses the absolute module path for imports.
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