Author: bugman
Date: Thu Nov 22 11:18:09 2007
New Revision: 3808
URL: http://svn.gna.org/viewcvs/relax?rev=3808&view=rev
Log:
Merged revisions 3757-3807 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r3757 | bugman | 2007-11-21 12:33:10 +0100 (Wed, 21 Nov 2007) | 3 lines
Added dictionaries to the list of diverse objects for testing the behaviour
of user function args.
........
r3773 | bugman | 2007-11-21 23:42:04 +0100 (Wed, 21 Nov 2007) | 5 lines
Removed the user function sequence.delete() from the redesign document.
This function is redundant and is of no use. It's just a reset.
........
r3774 | bugman | 2007-11-21 23:54:27 +0100 (Wed, 21 Nov 2007) | 3 lines
For the test suite, the Ap4Aase NOE data collected at 600 MHz has been
added to the repository.
........
r3775 | bugman | 2007-11-21 23:57:08 +0100 (Wed, 21 Nov 2007) | 3 lines
Added the base class for the unit tests of the prompt.sequence and
generic_fns.sequence modules.
........
r3776 | bugman | 2007-11-22 00:00:01 +0100 (Thu, 22 Nov 2007) | 3 lines
Added the framework and TestCase class for the unit tests of the
prompt.sequence module.
........
r3777 | bugman | 2007-11-22 00:01:27 +0100 (Thu, 22 Nov 2007) | 3 lines
Fixed the base class name!
........
r3778 | bugman | 2007-11-22 00:03:47 +0100 (Thu, 22 Nov 2007) | 11 lines
Removed all the user functions of prompt.sequence which are not in the
redesign document.
The axed user functions are:
sequence.add()
sequence.copy()
sequnece.delete()
sequence.sort()
These no longer have any use.
........
r3779 | bugman | 2007-11-22 00:40:09 +0100 (Thu, 22 Nov 2007) | 6 lines
Converted the sequence.read() user function to the new relax design.
This function now allows for sequences of molecules, residues, and spins to
be read into the
program.
........
r3780 | bugman | 2007-11-22 00:48:50 +0100 (Thu, 22 Nov 2007) | 3 lines
Added a unit test for the reading of the amino acid sequence out of a
protein NOE data file.
........
r3781 | bugman | 2007-11-22 00:49:57 +0100 (Thu, 22 Nov 2007) | 3 lines
Bug fix for the prompt.sequence module, the correct RelaxErrors are now
imported.
........
r3782 | bugman | 2007-11-22 00:51:05 +0100 (Thu, 22 Nov 2007) | 3 lines
A bug fix for the sequence.read() user function argument checking code.
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r3783 | bugman | 2007-11-22 00:53:24 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the file arg unit test for the sequence.read() user function.
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r3784 | bugman | 2007-11-22 00:56:07 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the dir arg unit test for the sequence.read() user function.
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r3785 | bugman | 2007-11-22 00:59:21 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the mol_name_col arg unit test for the sequence.read() user
function.
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r3786 | bugman | 2007-11-22 01:00:07 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the res_num_col arg unit test for the sequence.read() user
function.
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r3787 | bugman | 2007-11-22 01:00:40 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the res_name_col arg unit test for the sequence.read() user
function.
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r3788 | bugman | 2007-11-22 01:01:22 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the spin_num_col arg unit test for the sequence.read() user
function.
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r3789 | bugman | 2007-11-22 01:02:19 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the spin_name_col arg unit test for the sequence.read() user
function.
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r3790 | bugman | 2007-11-22 01:03:06 +0100 (Thu, 22 Nov 2007) | 3 lines
Bug fix for the argument checking of the sequence.read() user function.
........
r3791 | bugman | 2007-11-22 01:05:15 +0100 (Thu, 22 Nov 2007) | 3 lines
Implemented the sep arg unit test for the sequence.read() user function.
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r3792 | bugman | 2007-11-22 01:14:22 +0100 (Thu, 22 Nov 2007) | 3 lines
Added the framework for the unit tests of the generic_fns.sequence module.
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r3793 | bugman | 2007-11-22 10:23:43 +0100 (Thu, 22 Nov 2007) | 6 lines
Modified the state.load() and state.save() unit tests to use a tmp file
descriptor.
Currently these functions only allow a string file name and don't handle
file descriptors, but this
will be changed.
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r3794 | bugman | 2007-11-22 10:30:34 +0100 (Thu, 22 Nov 2007) | 5 lines
Created the RelaxStrFileError.
This is for when an argument can either be a string or file descriptor.
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r3795 | bugman | 2007-11-22 10:36:30 +0100 (Thu, 22 Nov 2007) | 3 lines
Modified both state.load() and state.save() to accept file descriptor
objects.
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r3796 | bugman | 2007-11-22 10:37:49 +0100 (Thu, 22 Nov 2007) | 3 lines
Modified the arg unit tests of state.load() and state.save() to use 'state'
rather than 'file'.
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r3797 | bugman | 2007-11-22 10:39:53 +0100 (Thu, 22 Nov 2007) | 3 lines
Modified the base class unit tests of state.load() and state.save() to use
the arg 'state'.
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r3798 | bugman | 2007-11-22 10:41:48 +0100 (Thu, 22 Nov 2007) | 3 lines
More fixes for the state.load() and state.save() arg unit tests.
........
r3799 | bugman | 2007-11-22 10:43:31 +0100 (Thu, 22 Nov 2007) | 3 lines
Changed the 'file' arg to 'state' in the functions of the generic_fns.state
module.
........
r3800 | bugman | 2007-11-22 10:49:32 +0100 (Thu, 22 Nov 2007) | 3 lines
Modified open_read_file() and open_write_file() to handle file descriptors,
by returning the arg.
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r3801 | bugman | 2007-11-22 11:01:34 +0100 (Thu, 22 Nov 2007) | 3 lines
Created a simple saved program state file for the state.load() unit tests.
........
r3802 | bugman | 2007-11-22 11:06:46 +0100 (Thu, 22 Nov 2007) | 5 lines
Modified the state base class unit tests to use the new saved state file.
This file is located in test_suite/shared_data/saved_states/.
........
r3803 | bugman | 2007-11-22 11:09:55 +0100 (Thu, 22 Nov 2007) | 3 lines
Changed all the 'dir' args to 'dir_name' in the state.load() and
state.save() user functions.
........
r3804 | bugman | 2007-11-22 11:10:42 +0100 (Thu, 22 Nov 2007) | 3 lines
Changed all the 'dir' args to 'dir_name' in the generic_fns.state module.
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r3805 | bugman | 2007-11-22 11:11:21 +0100 (Thu, 22 Nov 2007) | 3 lines
Fix for the load of program state unit test to use the 'dir_name' arg
instead of 'dir'.
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r3806 | bugman | 2007-11-22 11:12:27 +0100 (Thu, 22 Nov 2007) | 3 lines
Fixed the arg unit tests of state.load() and state.save() to use 'dir_name'
rather than 'dir'.
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r3807 | bugman | 2007-11-22 11:14:25 +0100 (Thu, 22 Nov 2007) | 3 lines
Fixed the directory path for the saved program state (too many '..').
........
Added:
branches/N_state_model/test_suite/shared_data/relaxation_data/
- copied from r3807, 1.3/test_suite/shared_data/relaxation_data/
branches/N_state_model/test_suite/shared_data/saved_states/
- copied from r3807, 1.3/test_suite/shared_data/saved_states/
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_sequence.py
- copied unchanged from r3807,
1.3/test_suite/unit_tests/_generic_fns/test_sequence.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_sequence.py
- copied unchanged from r3807,
1.3/test_suite/unit_tests/_prompt/test_sequence.py
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
- copied unchanged from r3807,
1.3/test_suite/unit_tests/sequence_testing_base.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/docs/data_model_redesign
branches/N_state_model/generic_fns/state.py
branches/N_state_model/prompt/sequence.py
branches/N_state_model/prompt/state.py
branches/N_state_model/relax_errors.py
branches/N_state_model/relax_io.py
branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py
branches/N_state_model/test_suite/unit_tests/state_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/docs/data_model_redesign
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/docs/data_model_redesign?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/generic_fns/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/state.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/sequence.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/prompt/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/state.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_io.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_state.py?rev=3808&r1=3807&r2=3808&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/state_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/state_testing_base.py?rev=3808&r1=3807&r2=3808&view=diff
r3808 - in /branches/N_state_model: ./ docs/ generic_fns/ prompt/ test_suite/shared_data/relaxation_data/ test_suite/shared_...