Author: bugman
Date: Wed Nov 28 11:09:42 2007
New Revision: 4103
URL: http://svn.gna.org/viewcvs/relax?rev=4103&view=rev
Log:
Merged revisions 4061-4102 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4061 | bugman | 2007-11-26 19:35:34 +0100 (Mon, 26 Nov 2007) | 3 lines
Added the base class framework for testing the relaxation data modules.
........
r4062 | bugman | 2007-11-26 19:39:51 +0100 (Mon, 26 Nov 2007) | 3 lines
Added the framework for the arg unit tests of the relax_data user functions.
........
r4063 | bugman | 2007-11-26 19:53:12 +0100 (Mon, 26 Nov 2007) | 3 lines
Added 13 unit tests for the args of the relax_data.read() user function.
........
r4064 | bugman | 2007-11-26 19:58:45 +0100 (Mon, 26 Nov 2007) | 3 lines
Implemented the relax_data.read() user function interface.
........
r4065 | bugman | 2007-11-26 20:04:57 +0100 (Mon, 26 Nov 2007) | 3 lines
Bug fixes for the arg unit tests of the relax_data.read() user function.
........
r4066 | bugman | 2007-11-26 20:05:49 +0100 (Mon, 26 Nov 2007) | 5 lines
Bug fix for the relax_data.read() user function.
A missing RelaxError import has been added.
........
r4067 | bugman | 2007-11-27 10:28:25 +0100 (Tue, 27 Nov 2007) | 6 lines
Bug fix for the docstring of the
generic_fns.diffusion_tensor.return_data_name() function.
The docstring, because it is joined onto user function docstrings, must
have indentation of 8 spaces
as well!
........
r4068 | bugman | 2007-11-27 11:02:21 +0100 (Tue, 27 Nov 2007) | 6 lines
Removed the formatted docstring file from the repository.
This file needs to be regenerated each time and is an automatically created
file. Its placement in
the repository is not necessary.
........
r4069 | bugman | 2007-11-27 11:06:25 +0100 (Tue, 27 Nov 2007) | 3 lines
Added the last two missing relax base directories for holding unit tests.
........
r4070 | bugman | 2007-11-27 11:07:28 +0100 (Tue, 27 Nov 2007) | 3 lines
Turned the 2 new dirs into modules.
........
r4071 | bugman | 2007-11-27 11:10:44 +0100 (Tue, 27 Nov 2007) | 3 lines
Copyright label update.
........
r4072 | bugman | 2007-11-27 11:23:43 +0100 (Tue, 27 Nov 2007) | 5 lines
Removed the Rx_data class instance from self.relax.specific.
The class instance is now within the module to be imported by who ever
wants it.
........
r4073 | bugman | 2007-11-27 12:00:32 +0100 (Tue, 27 Nov 2007) | 5 lines
Created the new function generic_fns.selection.generate_spin_id().
This will return an ID string for the spin.
........
r4074 | bugman | 2007-11-27 13:17:53 +0100 (Tue, 27 Nov 2007) | 3 lines
Added 5 unit tests for the generic_fns.selection.generate_spin_id()
function.
........
r4075 | bugman | 2007-11-27 13:21:48 +0100 (Tue, 27 Nov 2007) | 3 lines
Created the RelaxNoSpinError class.
........
r4076 | bugman | 2007-11-27 13:23:07 +0100 (Tue, 27 Nov 2007) | 3 lines
Converted the specific_fns.relax_data.read() to the new relax design.
........
r4077 | bugman | 2007-11-27 14:53:43 +0100 (Tue, 27 Nov 2007) | 3 lines
Added the missing import of the specific_fns.relax_data module.
........
r4078 | bugman | 2007-11-27 14:56:08 +0100 (Tue, 27 Nov 2007) | 3 lines
Added 2 missing imports.
........
r4079 | bugman | 2007-11-27 15:07:03 +0100 (Tue, 27 Nov 2007) | 3 lines
Wrote a unit test for the reading of relaxation data.
........
r4080 | bugman | 2007-11-27 18:43:14 +0100 (Tue, 27 Nov 2007) | 3 lines
Bug fix for the RelaxNoSequenceError class.
........
r4081 | bugman | 2007-11-27 18:50:09 +0100 (Tue, 27 Nov 2007) | 5 lines
Bug fix for the specific_fns.relax_data.read() function.
The use of the dummy function sequence_exists() has been replaced with
exists_mol_res_spin_data().
........
r4082 | bugman | 2007-11-28 09:01:54 +0100 (Wed, 28 Nov 2007) | 3 lines
Updated the specific_fns.relax_data.test_labels() function to the new relax
design.
........
r4083 | bugman | 2007-11-28 09:03:01 +0100 (Wed, 28 Nov 2007) | 3 lines
Added a number of missing imports.
........
r4084 | bugman | 2007-11-28 09:17:13 +0100 (Wed, 28 Nov 2007) | 5 lines
Rewrote the specific_fns.relax_data.data_init() function.
This was a big simplification!
........
r4085 | bugman | 2007-11-28 09:21:34 +0100 (Wed, 28 Nov 2007) | 3 lines
Added a base class for the unit tests of the specific_fns.relax_data module.
........
r4086 | bugman | 2007-11-28 09:29:53 +0100 (Wed, 28 Nov 2007) | 3 lines
Wrote 2 unit tests for the specific_fns.relax_data.data_init() function.
........
r4087 | bugman | 2007-11-28 09:31:14 +0100 (Wed, 28 Nov 2007) | 3 lines
Bug fix for the read() function.
........
r4088 | bugman | 2007-11-28 09:35:54 +0100 (Wed, 28 Nov 2007) | 3 lines
Converted specific_fns.relax_data.update_global_data_structures() to the
new relax design.
........
r4089 | bugman | 2007-11-28 09:37:03 +0100 (Wed, 28 Nov 2007) | 3 lines
Added some more missing imports.
........
r4090 | bugman | 2007-11-28 09:42:33 +0100 (Wed, 28 Nov 2007) | 5 lines
Bug fix for the generic_fns.selection.generate_spin_id() function.
The residue and spin names now always start with the identifier ':' or '@'.
........
r4091 | bugman | 2007-11-28 09:43:57 +0100 (Wed, 28 Nov 2007) | 3 lines
Fixes for the unit tests of generic_fns.selection.generate_spin_id().
........
r4092 | bugman | 2007-11-28 09:44:48 +0100 (Wed, 28 Nov 2007) | 3 lines
Added the missing import of RelaxNoSpinError.
........
r4093 | bugman | 2007-11-28 10:00:08 +0100 (Wed, 28 Nov 2007) | 3 lines
Added 2 unit tests for the generic_fns.selection.return_spin() function.
........
r4094 | bugman | 2007-11-28 10:15:55 +0100 (Wed, 28 Nov 2007) | 6 lines
Bug fix to the return_residue() and return_spin() functions.
When a residue or spin is not identified, then this should correspond to
all residues or spins and
not none!
........
r4095 | bugman | 2007-11-28 10:20:18 +0100 (Wed, 28 Nov 2007) | 5 lines
Big bug fix for the generic_fns.residue.create() function.
The mol_to_cont was being set to a ResidueContainer rather than a
MoleculeContainer!!!
........
r4096 | bugman | 2007-11-28 10:33:08 +0100 (Wed, 28 Nov 2007) | 9 lines
Split generic_fns.selection.exists_mol_res_spin_data() into 4 new functions.
The new functions are:
exists_mol_res_spin_data()
exists_mol_data()
exists_res_data()
exists_spin_data()
........
r4097 | bugman | 2007-11-28 10:36:05 +0100 (Wed, 28 Nov 2007) | 5 lines
Bug fix for the generic_fns.residue.copy() function.
The contents of res_to_cont is now checked for, to see if it is empty.
........
r4098 | bugman | 2007-11-28 10:43:17 +0100 (Wed, 28 Nov 2007) | 6 lines
Fixes to the test_return_spin() unit test.
As the setUp() method was modified to add some spin info, the
test_spin_loop_no_selection() unit
test had to be updated as well.
........
r4099 | bugman | 2007-11-28 10:47:17 +0100 (Wed, 28 Nov 2007) | 3 lines
Bug fix for the generic_fns.spin.create() function.
........
r4100 | bugman | 2007-11-28 10:48:45 +0100 (Wed, 28 Nov 2007) | 5 lines
Bug fix for the generic_fns.residue.create() function.
This is the same fix as that for generic_fns.spin.create() in r4099.
........
r4101 | bugman | 2007-11-28 10:59:58 +0100 (Wed, 28 Nov 2007) | 3 lines
Bug fix for the generic_fns.spin.copy() function.
........
r4102 | bugman | 2007-11-28 11:05:31 +0100 (Wed, 28 Nov 2007) | 5 lines
Bug fix for the generic_fns.spin.copy() function.
The wrong pipe was being used for the destination spin container!
........
Added:
branches/N_state_model/test_suite/unit_tests/_dx/
- copied from r4102, 1.3/test_suite/unit_tests/_dx/
branches/N_state_model/test_suite/unit_tests/_prompt/test_relax_data.py
- copied unchanged from r4102,
1.3/test_suite/unit_tests/_prompt/test_relax_data.py
branches/N_state_model/test_suite/unit_tests/_specific_fns/
- copied from r4102, 1.3/test_suite/unit_tests/_specific_fns/
branches/N_state_model/test_suite/unit_tests/relax_data_testing_base.py
- copied unchanged from r4102,
1.3/test_suite/unit_tests/relax_data_testing_base.py
Removed:
branches/N_state_model/docs/latex/docstring.tex
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/diffusion_tensor.py
branches/N_state_model/generic_fns/residue.py
branches/N_state_model/generic_fns/selection.py
branches/N_state_model/generic_fns/spin.py
branches/N_state_model/prompt/relax_data.py
branches/N_state_model/relax_errors.py
branches/N_state_model/specific_fns/main.py
branches/N_state_model/specific_fns/relax_data.py
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_selection.py
[This mail would be too long, it was shortened to contain the URLs only.]
Removed: branches/N_state_model/docs/latex/docstring.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/docs/latex/docstring.tex?rev=4102&view=auto
Modified: branches/N_state_model/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/diffusion_tensor.py?rev=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/generic_fns/residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/residue.py?rev=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/generic_fns/selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/selection.py?rev=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/generic_fns/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/spin.py?rev=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/relax_data.py?rev=4103&r1=4102&r2=4103&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=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/specific_fns/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/main.py?rev=4103&r1=4102&r2=4103&view=diff
Modified: branches/N_state_model/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/relax_data.py?rev=4103&r1=4102&r2=4103&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_generic_fns/test_selection.py?rev=4103&r1=4102&r2=4103&view=diff
r4103 - in /branches/N_state_model: ./ docs/latex/ generic_fns/ prompt/ specific_fns/ test_suite/unit_tests/ test_suite/unit...