[r17842]
by
bugman
Merged revisions 17677-17687 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
|
2012-10-16 09:00:04
|
Tree
|
[r17841]
by
bugman
Merged revisions 17676 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
|
2012-10-16 08:58:09
|
Tree
|
[r17840]
by
bugman
Merged revisions 17671-17675 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
|
2012-10-16 08:56:13
|
Tree
|
[r17839]
by
bugman
Merged revisions 17661-17670 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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
........
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.
........
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".
........
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.
........
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.
........
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.
........
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.
........
|
2012-10-16 08:52:33
|
Tree
|
[r17838]
by
bugman
Merged revisions 17651-17660 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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
........
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.
........
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.
........
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.
........
r17660 | bugman | 2012-10-02 14:05:50 +0200 (Tue, 02 Oct 2012) | 3 lines
Copyright update.
........
|
2012-10-16 08:52:10
|
Tree
|
[r17837]
by
bugman
Merged revisions 17641-17650 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
r17642 | bugman | 2012-10-01 23:40:37 +0200 (Mon, 01 Oct 2012) | 3 lines
Python 3 - Eliminated an unneeded xrange call.
........
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.
........
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.
........
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().
........
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.
........
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'.
........
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.
........
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.
........
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.
........
|
2012-10-16 08:43:04
|
Tree
|
[r17836]
by
bugman
Merged revisions 17624-17640 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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).
........
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.
........
r17635 | bugman | 2012-10-01 22:51:12 +0200 (Mon, 01 Oct 2012) | 3 lines
Debugging printout removal.
........
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.
........
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.
........
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.
........
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.
........
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.
........
|
2012-10-16 08:42:15
|
Tree
|
[r17835]
by
bugman
Merged revisions 17623 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
|
2012-10-16 08:40:17
|
Tree
|
[r17834]
by
bugman
Merged revisions 17621-17622 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
|
2012-10-16 08:31:23
|
Tree
|
[r17833]
by
bugman
Merged revisions 17601-17620 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
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.
........
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.
........
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.
........
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).
........
r17605 | bugman | 2012-09-28 17:55:25 +0200 (Fri, 28 Sep 2012) | 3 lines
Removed the completely unused gui.components.conversion module.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r17613 | bugman | 2012-09-28 18:55:04 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - absolute module path fix.
........
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.
........
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.
........
r17616 | bugman | 2012-09-28 19:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - absolute module path fixes.
........
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.
........
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.
........
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.
........
r17620 | bugman | 2012-09-28 19:13:30 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparations - removal of some unneeded xrange() calls.
........
|
2012-10-16 08:29:42
|
Tree
|
