Blocked revisions 4481-4493,4523-4527,4529-4547,4549-4551,4567,4569,4571-4572,4575-4577,4579,4585-4586,4618,4621-4623,4659,4662-4671 via svnmerge
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r4481 | bugman | 2008-01-08 14:29:05 +0100 (Tue, 08 Jan 2008) | 3 lines
Shifted the contents of the test_opendx_s2_te_rex() system test into its own script.
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r4482 | bugman | 2008-01-08 14:31:18 +0100 (Tue, 08 Jan 2008) | 5 lines
Bug fix: Removed the 'quit' keyword arg from the call of the prompt() function.
The relax prompt is back again!
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r4483 | bugman | 2008-01-08 14:47:15 +0100 (Tue, 08 Jan 2008) | 3 lines
Converted all of the opt_setup_S2_0_970_te_2048_Rex_0_149() set up function into its own script.
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r4484 | bugman | 2008-01-08 14:51:52 +0100 (Tue, 08 Jan 2008) | 3 lines
All the model-free optimisation tests now run the opt_setup_S2_0_970_te_2048_Rex_0_149.py script.
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r4485 | bugman | 2008-01-08 15:18:10 +0100 (Tue, 08 Jan 2008) | 5 lines
Tidied up the interact_script() function (with comments). The function also returns its status.
The status is obviously only returned if relax doesn't not quit.
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r4486 | bugman | 2008-01-08 15:26:28 +0100 (Tue, 08 Jan 2008) | 5 lines
The status of script execution is now returned by the run() interpreter method.
Nothing currently uses this.
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r4487 | bugman | 2008-01-08 15:36:16 +0100 (Tue, 08 Jan 2008) | 8 lines
prompt.interpreter.interact_script() has been modified to allow RelaxErrors to be raised.
Previously running a script would catch the error, send a nice message to STDERR, and quit. Now
the function can raise the error if asked. This is required for the system tests (because of the
unittest framework). Alternatively the status of the script could have been used by the test, but
this is easier for the test writer and makes the code more flexible.
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r4488 | bugman | 2008-01-08 15:42:44 +0100 (Tue, 08 Jan 2008) | 3 lines
Converted the interact_prompt() args to keyword args and epydoc'd the docstring.
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r4489 | bugman | 2008-01-08 16:19:57 +0100 (Tue, 08 Jan 2008) | 3 lines
Updated the interact_script() docstring for the epydoc format.
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r4490 | bugman | 2008-01-08 16:21:23 +0100 (Tue, 08 Jan 2008) | 3 lines
Updated the prompt() docstring for the epydoc format.
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r4491 | bugman | 2008-01-08 16:22:33 +0100 (Tue, 08 Jan 2008) | 3 lines
Updated the run_script() docstring for the epydoc format.
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r4492 | bugman | 2008-01-08 16:22:58 +0100 (Tue, 08 Jan 2008) | 3 lines
Converted the default quit arg of run_script() to a bool.
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r4493 | bugman | 2008-01-08 16:24:17 +0100 (Tue, 08 Jan 2008) | 3 lines
Updated the runcode() docstring for the epydoc format.
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r4523 | bugman | 2008-01-09 10:50:39 +0100 (Wed, 09 Jan 2008) | 5 lines
Renamed 'print_flag' to 'verbosity' in the calc(), grid_search(), and minimise() user functions.
This arg is not really a flag, and it is the verbosity level, so this makes more sense.
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r4524 | bugman | 2008-01-09 10:53:06 +0100 (Wed, 09 Jan 2008) | 3 lines
Created a new error type for booleans - RelaxBoolError.
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r4525 | bugman | 2008-01-09 10:57:51 +0100 (Wed, 09 Jan 2008) | 3 lines
Converted all the bin args (0/1) to bool args (True/False) in the minimisation user functions.
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r4526 | bugman | 2008-01-09 11:25:14 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all references to 'print_flag' to 'verbosity' in the user function arg unit tests.
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r4527 | bugman | 2008-01-09 11:26:16 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all the bin minimisation arg unit tests to tests for boolean args.
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r4529 | bugman | 2008-01-09 11:37:04 +0100 (Wed, 09 Jan 2008) | 6 lines
Removal of all the old threading code!!!
This will all eventually be replaced by Gary Thompson's multi_processor code, once it is ported to
the new relax design. This threading code was broken, buggy, and not fault tolerant anyway.
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r4530 | bugman | 2008-01-09 11:46:51 +0100 (Wed, 09 Jan 2008) | 6 lines
Updated the relax_io.extract_data() function.
The compression flag has been dropped as it is automatically determined and updated the docstring to
epydoc format.
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r4531 | bugman | 2008-01-09 11:48:33 +0100 (Wed, 09 Jan 2008) | 5 lines
Updated the relax_io.get_file_path() function.
The docstring has been updated to epydoc format.
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r4532 | bugman | 2008-01-09 11:50:27 +0100 (Wed, 09 Jan 2008) | 3 lines
Added the return info to the relax_io.extract_data() function docstring.
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r4533 | bugman | 2008-01-09 11:54:11 +0100 (Wed, 09 Jan 2008) | 6 lines
Updated the relax_io.log() function.
The compression flag has been dropped as it is automatically determined, changed the 'print_flag'
arg to 'verbosity', and updated the docstring to epydoc format.
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r4534 | bugman | 2008-01-09 11:56:14 +0100 (Wed, 09 Jan 2008) | 5 lines
Updated the relax_io.mkdir_nofail() function.
Changed the 'print_flag' arg to 'verbosity' and updated the docstring to epydoc format.
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r4535 | bugman | 2008-01-09 11:58:30 +0100 (Wed, 09 Jan 2008) | 5 lines
Updated the relax_io.open_read_file() function.
Changed the 'print_flag' arg to 'verbosity' and updated the docstring to epydoc format.
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r4536 | bugman | 2008-01-09 12:06:00 +0100 (Wed, 09 Jan 2008) | 5 lines
Spun out the compression determining code of open_read_file() into its own function.
The new function is called determine_compression().
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r4537 | bugman | 2008-01-09 12:06:46 +0100 (Wed, 09 Jan 2008) | 3 lines
Converted the devnull_import variable from a bin value to a boolean.
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r4538 | bugman | 2008-01-09 12:26:39 +0100 (Wed, 09 Jan 2008) | 6 lines
Updated the relax_io.open_write_file() function.
The docstring has been updated for epydoc, the 'print_flag' arg changed to 'verbosity', and a
printed warning shifted to using a RelaxWarning.
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r4539 | bugman | 2008-01-09 14:10:13 +0100 (Wed, 09 Jan 2008) | 3 lines
Updated the docstring of the relax_io.open_write_file() function for epydoc.
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r4540 | bugman | 2008-01-09 14:12:14 +0100 (Wed, 09 Jan 2008) | 3 lines
Bug fix. The compress_type arg is no longer accepted.
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r4541 | bugman | 2008-01-09 14:13:07 +0100 (Wed, 09 Jan 2008) | 3 lines
Bug fix. The compress_type arg is no longer accepted.
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r4542 | bugman | 2008-01-09 14:16:22 +0100 (Wed, 09 Jan 2008) | 6 lines
Updated the generic_fns.state.load_state() function.
The compression flag has been dropped as it is automatically determined and the docstring has been
converted to epydoc format.
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r4543 | bugman | 2008-01-09 14:19:47 +0100 (Wed, 09 Jan 2008) | 5 lines
Updated the generic_fns.state.save_state() function.
The docstring has been converted to epydoc format and the 'force' arg converted to a bool.
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r4544 | bugman | 2008-01-09 14:24:45 +0100 (Wed, 09 Jan 2008) | 3 lines
Bug fix. The relax_io.determine_compression() function now returns the full file path.
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r4545 | bugman | 2008-01-09 14:28:24 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed the 'force' arg of the state.save() user function too a boolean.
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r4546 | bugman | 2008-01-09 14:29:21 +0100 (Wed, 09 Jan 2008) | 3 lines
Fixed a RelaxError import.
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r4547 | bugman | 2008-01-09 14:30:40 +0100 (Wed, 09 Jan 2008) | 5 lines
Updated the force arg unit test of the state.save() user function.
The arg is now a boolean.
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r4549 | bugman | 2008-01-09 14:38:00 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in the generic_fns.minimise module.
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r4550 | bugman | 2008-01-09 14:39:09 +0100 (Wed, 09 Jan 2008) | 3 lines
Removed some unused imports.
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r4551 | bugman | 2008-01-09 14:41:03 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all the 'constraints' and 'scaling' args to be of bool type.
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r4567 | semor | 2008-01-09 17:51:14 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in the prompt for tab_completion.
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r4569 | semor | 2008-01-09 17:54:26 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed 1 instance of the 'print_flag' arg to 'verbosity' in the OpenDX code for 3D isosurfaces.
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r4571 | semor | 2008-01-09 18:02:54 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in the generic directory.
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r4572 | bugman | 2008-01-09 18:13:20 +0100 (Wed, 09 Jan 2008) | 3 lines
Updated the RelaxNoTensorError class to allow for the tensor label to be printed in the traceback.
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r4575 | semor | 2008-01-09 19:20:33 +0100 (Wed, 09 Jan 2008) | 10 lines
Changed almost all instances of the 'print_flag' arg to 'verbosity' in the specific_fns directory.
Exceptions were made for instances in generic_minimise() functions where 'print_flag=print_flag'
becomes 'print_flag=verbosity'.
This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@...>)
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r4576 | semor | 2008-01-09 19:28:21 +0100 (Wed, 09 Jan 2008) | 10 lines
Completed the changes from the previous commit (4575) as the model_free directory had been skipped.
Changed almost all instances of the 'print_flag' arg to 'verbosity' in the specific_fns/model_free
directory. Exceptions were made for instances in generic_minimise() functions where
'print_flag=print_flag' becomes 'print_flag=verbosity'.
This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@...>)
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r4577 | semor | 2008-01-09 19:32:12 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in 'relax_io.py'.
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r4579 | semor | 2008-01-09 19:41:37 +0100 (Wed, 09 Jan 2008) | 3 lines
Fixed a typo that was introduced in the 4576 commit.
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r4585 | bugman | 2008-01-10 14:35:02 +0100 (Thu, 10 Jan 2008) | 22 lines
Manually ported r4584 from the 1.2 line - the fix to bug #8997 (https://gna.org/bugs/?8997).
The command used was:
svn merge -r4583:4584 svn+ssh://bugman@.../svn/relax/1.2
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r4584 | bugman | 2008-01-10 14:30:10 +0100 (Thu, 10 Jan 2008) | 11 lines
Changed paths:
M /1.2/generic_fns/palmer.py
Fix for bug #8997 (https://gna.org/bugs/index.php?8997).
This bug was reported by Carl Diehl (carl dot diehl at bpc dot lu dot se).
The problem was because of a change between relax versions 1.0 and 1.2. Previously the residue
number was being searched for, but the changes used the absolute position to significantly speed up
the code. But the absolute positions are different in a Modelfree 'mfout' file if simulations are
run. The absolute position in this situation is now properly calculated and the test data attached
to the bug report by Seb now works.
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r4586 | bugman | 2008-01-10 15:54:12 +0100 (Thu, 10 Jan 2008) | 3 lines
Removed a few empty __init__() class methods and shifted their docstrings to the class docstring.
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r4618 | bugman | 2008-01-10 21:40:40 +0100 (Thu, 10 Jan 2008) | 17 lines
Ported r4617 from the 1.2 line.
The command used was:
svn merge -r4616:4617 svn+ssh://bugman@.../svn/relax/1.2
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r4617 | bugman | 2008-01-10 21:37:22 +0100 (Thu, 10 Jan 2008) | 6 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py
Modified the full_analysis.py script to be usable when no structure is available.
This is in response to Sebastien's post at
https://mail.gna.org/public/relax-users/2008-01/msg00006.html.
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r4621 | semor | 2008-01-11 04:41:34 +0100 (Fri, 11 Jan 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-2505" from
svn+ssh://semor@.../svn/relax/1.2
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r4622 | semor | 2008-01-11 04:43:05 +0100 (Fri, 11 Jan 2008) | 20 lines
Merged revisions 4619-4620 via svnmerge from
svn+ssh://semor@.../svn/relax/1.2
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r4619 | semor | 2008-01-10 16:38:09 -0500 (Thu, 10 Jan 2008) | 7 lines
Modified the full_analysis.py script so it can handle cases when no residues need to be excluded.
This change was proposed in a post at:
https://mail.gna.org/public/relax-users/2008-01/msg00008.html (Message-id:
<47868730.1030205@...>)
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r4620 | semor | 2008-01-10 16:43:29 -0500 (Thu, 10 Jan 2008) | 6 lines
Corrected a mistake.
The inverse of what was wanted was produced concerning the possibility of not giving a file for
unresolved residues.
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r4623 | bugman | 2008-01-11 09:24:03 +0100 (Fri, 11 Jan 2008) | 9 lines
Reverted r4621, the setting up of svnmerge properties from 1.2 to 1.3.
The following command did not work:
svn merge -r4621:4620 .
So instead the following command was used:
svn propdel svnmerge-integrated
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r4659 | bugman | 2008-01-11 21:31:18 +0100 (Fri, 11 Jan 2008) | 6 lines
An import change to fix a circular import issue uncovered in the consistency_tests_1.3 branch.
This was uncovered by Seb. See the thread starting at
https://mail.gna.org/public/relax-devel/2008-01/msg00042.html.
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r4662 | bugman | 2008-01-13 12:07:18 +0100 (Sun, 13 Jan 2008) | 3 lines
Started to convert the model-free user functions to the new relax design.
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r4663 | bugman | 2008-01-13 12:09:22 +0100 (Sun, 13 Jan 2008) | 6 lines
Deleted the model_free.copy() user function.
This function was not used anywhere within relax and the model-free specific copy() method was
complete rubbish anyway (ancient, unused, broken code).
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r4664 | bugman | 2008-01-13 12:15:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the run argument from all model-free user functions.
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r4665 | bugman | 2008-01-13 12:16:34 +0100 (Sun, 13 Jan 2008) | 3 lines
Copyright update.
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r4666 | bugman | 2008-01-13 12:26:29 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted all the res_num args to spin_id in the model-free user functions.
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r4667 | bugman | 2008-01-13 12:31:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Added the framework for unit tests of the model-free user function args.
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r4668 | bugman | 2008-01-13 12:41:52 +0100 (Sun, 13 Jan 2008) | 3 lines
Wrote 7 unit tests for all args of the model-free user functions.
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r4669 | bugman | 2008-01-13 12:43:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.select_model() user function.
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r4670 | bugman | 2008-01-13 12:44:04 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.create_model() user function.
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r4671 | bugman | 2008-01-13 12:45:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.remove_tm() user function.
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