relax SVN archive

Merged revisions 17780-17806 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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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.
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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.
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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.
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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+.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Merged revisions 17776-17778 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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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/relax/branches/tensor_data
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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/relax/branches/tensor_data

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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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().
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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/relax/branches/tensor_data
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Merged revisions 17693,17697-17737 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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

Finished off the C module compilation testing script.
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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.
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r17709 | bugman | 2012-10-07 15:26:15 +0200 (Sun, 07 Oct 2012) | 3 lines

The manual C module compilation script is now executable.
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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.
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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().
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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.
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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.
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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 .
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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r17725 | bugman | 2012-10-07 19:22:04 +0200 (Sun, 07 Oct 2012) | 3 lines

Small comment edit.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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!
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r17735 | bugman | 2012-10-08 00:47:19 +0200 (Mon, 08 Oct 2012) | 3 lines

Removed some debugging printouts accidentally committed in r17734.
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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.
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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.
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Merged revisions 17689-17691 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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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.
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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.
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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.
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Merged revisions 17677-17687 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17677 | bugman | 2012-10-02 16:35:26 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 integer division to float fix for the frame order analysis.
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r17678 | bugman | 2012-10-02 16:54:57 +0200 (Tue, 02 Oct 2012) | 5 lines

Python 3 fix for the frame order system tests - float to string conversions behave differently.

Now the explicit %.1f formatting is used to force only a single decimal place float.
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r17679 | bugman | 2012-10-02 16:58:40 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 fix for the frame order system tests matching r17678.

As float to string conversions behave differently, the %.1f formatting is used to force only a
single decimal place float.
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r17680 | bugman | 2012-10-02 16:59:22 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 fix - removed the use of the string.lower() function in the OpenDX mapping code.
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r17681 | bugman | 2012-10-02 17:47:23 +0200 (Tue, 02 Oct 2012) | 6 lines

Python 3 fix for the writing out of XML formatted state and results files.

In Python 3, the xmldoc.toprettyxml() returns a string object which needs to be 'encoded' prior to
writing out to file.
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r17682 | bugman | 2012-10-02 17:58:04 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 import fixes for the generic_fns.structure package using relative paths.
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r17683 | bugman | 2012-10-02 18:29:25 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 fix for the format detection of results and save files.
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r17684 | bugman | 2012-10-02 18:34:02 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 2 fix for the relax_io.extract_data() function for a bug introduced at r17669.
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r17685 | bugman | 2012-10-02 18:46:16 +0200 (Tue, 02 Oct 2012) | 5 lines

The relax_io.DummyFileObject now mimics a file object for both Python 2 and 3.

In Python 3, everything from a file is of byte type and no longer string type.
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r17686 | bugman | 2012-10-02 18:48:25 +0200 (Tue, 02 Oct 2012) | 6 lines

The Mf.test_write_results system test can now select the correct file to compare against in Python 3.

The algorithm for determining if the 'final_results_trunc_1.3_v2' or
'final_results_trunc_1.3_pre_py2.7.3_v2' file should be used could not handle Python 3.
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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.
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Merged revisions 17676 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r17676 | bugman | 2012-10-02 16:30:46 +0200 (Tue, 02 Oct 2012) | 3 lines

Python 3 bug fix for the frame order analysis - another int division problem.
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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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