Author: bugman
Date: Tue Apr 3 13:21:47 2007
New Revision: 3259
URL: http://svn.gna.org/viewcvs/relax?rev=3259&view=rev
Log:
Blocked revisions
3173-3194,3196-3197,3200-3207,3209,3211-3234,3240,3245,3247,3255-3258 via
svnmerge
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r3173 | varioustoxins | 2007-03-13 20:35:15 +1100 (Tue, 13 Mar 2007) | 2
lines
directory independant running of unit tests, improved docs, code cleanup
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r3174 | varioustoxins | 2007-03-13 20:58:31 +1100 (Tue, 13 Mar 2007) | 2
lines
remove annoying debug messages
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r3175 | bugman | 2007-03-13 21:07:52 +1100 (Tue, 13 Mar 2007) | 3 lines
Added the 'test_mol_res_spin' module to the __all__ package variable.
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r3176 | varioustoxins | 2007-03-13 21:17:40 +1100 (Tue, 13 Mar 2007) | 3
lines
corrected lack of return from run function
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r3177 | varioustoxins | 2007-03-13 21:56:38 +1100 (Tue, 13 Mar 2007) | 2
lines
improved messages for bad input
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r3178 | bugman | 2007-03-14 13:45:52 +1100 (Wed, 14 Mar 2007) | 7 lines
Fixed the test suite synopsis (the system/functional tests weren't
returning the test result).
All the contents of the System_tests.__init__() method has been placed into
the run() method as
__init__() needs to return None. This run() method then returns the
global_pass flag to the
Test_suite_runner class or test_suite/runner.py.
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r3179 | bugman | 2007-03-14 16:07:21 +1100 (Wed, 14 Mar 2007) | 3 lines
Removed the svn:executable property from the 'maths_fns/test_chi2.py' unit
test file.
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r3180 | bugman | 2007-03-14 16:09:52 +1100 (Wed, 14 Mar 2007) | 3 lines
Removed the line '#!/usr/bin/env python' from all the unit test modules.
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r3181 | bugman | 2007-03-14 17:08:07 +1100 (Wed, 14 Mar 2007) | 3 lines
Replaced the empty chi2 and dchi2 unit tests with true unit tests for those
functions.
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r3182 | bugman | 2007-03-14 17:32:17 +1100 (Wed, 14 Mar 2007) | 3 lines
Improvements to the docstrings and a comment in the chi-squared value and
gradient unit tests.
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r3183 | bugman | 2007-03-14 17:33:10 +1100 (Wed, 14 Mar 2007) | 3 lines
Added a unit test for the chi-squared Hessian function d2chi2.
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r3184 | bugman | 2007-03-14 17:37:39 +1100 (Wed, 14 Mar 2007) | 3 lines
More docstring improvements for the chi-square function unit tests.
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r3185 | bugman | 2007-03-14 17:38:11 +1100 (Wed, 14 Mar 2007) | 3 lines
Added a tearDown statement to delete the chi-squared Hessian.
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r3186 | bugman | 2007-03-14 17:41:18 +1100 (Wed, 14 Mar 2007) | 3 lines
Simplified the chi2 gradient unit test and added delete statements to
destroy all unit test data.
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r3187 | bugman | 2007-03-14 19:17:32 +1100 (Wed, 14 Mar 2007) | 3 lines
Completion of point 9 of the preparation in the data model redesign
document.
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r3188 | bugman | 2007-03-14 19:30:56 +1100 (Wed, 14 Mar 2007) | 7 lines
Added initial support for the residue user function class.
The file 'prompt/residue.py' was copied from 'prompt/sequence.py' and the
function 'add()' renamed
to 'create' (generating the 'residue.create()' user function). All the
other sequence user
functions still remain unchanged.
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r3189 | bugman | 2007-03-14 19:36:51 +1100 (Wed, 14 Mar 2007) | 3 lines
Created the 'generic_fns.residue' module and started converting the
sequence add() fn to create().
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r3190 | bugman | 2007-03-14 19:37:58 +1100 (Wed, 14 Mar 2007) | 3 lines
Converted the Residue.create() method into a function of the
'generic_fns.residue' module.
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r3191 | bugman | 2007-03-14 19:38:21 +1100 (Wed, 14 Mar 2007) | 3 lines
Removed the 'self' argument to the create() function.
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r3192 | bugman | 2007-03-14 19:42:44 +1100 (Wed, 14 Mar 2007) | 3 lines
Added an import statement for the 'residue' module of the 'generic_fns'
package.
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r3193 | bugman | 2007-03-14 19:53:49 +1100 (Wed, 14 Mar 2007) | 3 lines
A few changes to make the 'residue.create()' user function partially
functional.
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r3194 | varioustoxins | 2007-03-14 21:25:08 +1100 (Wed, 14 Mar 2007) | 4
lines
updates to unit_test_runner, code cleanup, more command line options
changes for the change in name of
unit_tests.unit_test_runner.Unit_test_runner
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r3196 | bugman | 2007-03-15 15:24:38 +1100 (Thu, 15 Mar 2007) | 3 lines
Shifted the unit tests for the relax data storage singleton to the file
'test___init__.py'.
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r3197 | bugman | 2007-03-15 15:57:50 +1100 (Thu, 15 Mar 2007) | 5 lines
Manually reverted most of r3157.
The 'add()' method of the relax data storage singleton has been
reintroduced.
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r3200 | macraild | 2007-03-16 03:58:23 +1100 (Fri, 16 Mar 2007) | 9 lines
Alternative implimentation of the data object as a singleton.
As proposed here:
https://mail.gna.org/public/relax-devel/2007-03/msg00013.html
and agreed here:
https://mail.gna.org/public/relax-devel/2007-03/msg00058.html#
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r3201 | bugman | 2007-03-16 17:45:47 +1100 (Fri, 16 Mar 2007) | 2 lines
Fixes for the unit tests of the relax data storage singleton methods.
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r3202 | bugman | 2007-03-16 17:46:44 +1100 (Fri, 16 Mar 2007) | 2 lines
Wrote two unit tests for testing the generic_fns.residue.create() function.
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r3203 | bugman | 2007-03-16 17:49:27 +1100 (Fri, 16 Mar 2007) | 2 lines
Modified generic_fns.residue.create() to replace the empty first residue if
no residues exist.
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r3204 | bugman | 2007-03-16 17:50:42 +1100 (Fri, 16 Mar 2007) | 6 lines
Important fix for the PipeContainer data structure.
All of the objects of the PipeContainer where being instantiated as objects
of the class rather than
the separate instances. Hence two different PipeContainer instances
contained the same objects!
All object instantiation is now done within the __init__() method to avoid
the problem.
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r3205 | bugman | 2007-03-16 17:53:23 +1100 (Fri, 16 Mar 2007) | 4 lines
Fixed the unit tests for the 'generic_fns.pipes' module.
The relax data storage singleton object is now reset at the start of the
setUp unit test method.
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r3206 | bugman | 2007-03-16 17:56:02 +1100 (Fri, 16 Mar 2007) | 4 lines
Created the 'generic_fns.residue.copy()' function.
Two unit tests for this function have been added.
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r3207 | bugman | 2007-03-16 17:57:46 +1100 (Fri, 16 Mar 2007) | 2 lines
Wrote unit tests for the currently non-existant
'generic_fns.residue.delete()' function.
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r3209 | macraild | 2007-03-17 00:46:23 +1100 (Sat, 17 Mar 2007) | 6 lines
Further modifications for compatibility with the new relax Data object.
The data unit-tests have been fixed, and all import statements in client
modules updated.
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r3211 | bugman | 2007-03-17 12:48:15 +1100 (Sat, 17 Mar 2007) | 5 lines
Updated the residue.delete() user function prompt code.
The code was still that of sequence.delete()!
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r3212 | bugman | 2007-03-17 12:51:44 +1100 (Sat, 17 Mar 2007) | 3 lines
Copied the 'residue.py' files to implement the new 'spin' and 'molecule'
user function classes.
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r3213 | bugman | 2007-03-17 12:52:56 +1100 (Sat, 17 Mar 2007) | 6 lines
Removed the executable property from the test_float.py unit test module.
The command used was:
$ svn propdel svn:executable test_float.py
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r3214 | bugman | 2007-03-17 12:55:35 +1100 (Sat, 17 Mar 2007) | 3 lines
Removed the 'if __name__ == ...' statements and added a copyright statement
for Gary.
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r3215 | bugman | 2007-03-17 12:57:34 +1100 (Sat, 17 Mar 2007) | 3 lines
Removed to unused comment lines.
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r3216 | bugman | 2007-03-17 12:58:48 +1100 (Sat, 17 Mar 2007) | 3 lines
Added to empty unit test modules.
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r3217 | bugman | 2007-03-19 15:47:57 +1100 (Mon, 19 Mar 2007) | 18 lines
Implemented the generic_fns.residue.delete() function (although it doesn't
work yet).
This function has been coded to use the UCSF selection syntax as described
in Gary Thompson's post
located at https://mail.gna.org/public/relax-devel/2007-01/msg00014.html
(Message-id:
<f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>).
The function makes use of three new selection functions - tokenise,
parse_token, and molecule_loop.
The first two are described at
https://mail.gna.org/public/relax-devel/2007-01/msg00036.html
(Message-ID: <1168883717.7569.511.camel@mrspell>). The last function is
similar to the spin_loop
function described in the same post. All three are yet to be implemented
(although stubs have been
created for the functions).
The RelaxError 'RelaxSpinSelectDisallowError' has been created to prevent
spins from being selected
by the user function.
The unit tests for generic_fns.residue.delete() have been updated and two
more added:
test_delete_all() and test_delete_shift().
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r3218 | bugman | 2007-03-19 15:56:04 +1100 (Mon, 19 Mar 2007) | 4 lines
Converted all the class methods of the 'generic_fns.selection' module into
functions.
The unsel_*() methods have been renamed to desel_*() and the functions
alphabetically sorted.
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r3219 | bugman | 2007-03-19 15:59:48 +1100 (Mon, 19 Mar 2007) | 2 lines
Wrote a unit test for the generic_fns.selection.reverse() function.
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r3220 | bugman | 2007-03-19 16:04:31 +1100 (Mon, 19 Mar 2007) | 2 lines
Bug fix. Removed the import of the now non-existant Selection class.
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r3221 | bugman | 2007-03-19 16:19:33 +1100 (Mon, 19 Mar 2007) | 5 lines
Fixed the select.reverse() user function.
The generic_fns.selection.reverse() function still does not work as the
spin_loop() function needs
to be implemented.
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r3222 | bugman | 2007-03-19 16:20:13 +1100 (Mon, 19 Mar 2007) | 12 lines
Wrote the spin_loop() generator function for looping over and returning
spin containers.
For more info, see my post at
https://mail.gna.org/public/relax-devel/2006-10/msg00057.html
(Message-id:
<1160557041.9523.74.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>). The idea
of the
generator function, using the yield statement, to return the spin data
containers was given by Gary
Thompson at https://mail.gna.org/public/relax-devel/2007-01/msg00014.html
(Message-id:
<f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>). More
details are given by Chris
MacRaild at https://mail.gna.org/public/relax-devel/2007-01/msg00036.html
(Message-ID:
<1168883717.7569.511.camel@mrspell>).
The full generator function is generic_fns.selection.spin_loop().
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r3223 | bugman | 2007-03-19 16:20:44 +1100 (Mon, 19 Mar 2007) | 4 lines
Wrote the molecule_loop() generator function for looping over and returning
molecule containers.
The full generator function is generic_fns.selection.molecule_loop().
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r3224 | bugman | 2007-03-19 16:21:14 +1100 (Mon, 19 Mar 2007) | 2 lines
Created the RelaxMolSelectDisallowError and RelaxResSelectDisallowError
errors.
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r3225 | bugman | 2007-03-19 16:21:47 +1100 (Mon, 19 Mar 2007) | 4 lines
Multiple unit tests for the spin_loop(), residue_loop(), and
molecule_loop() generator functions.
These generator functions belong to the 'generic_fns.selection' module.
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r3226 | bugman | 2007-03-19 16:22:33 +1100 (Mon, 19 Mar 2007) | 6 lines
Bug fix.
The spin_loop() and molecule_loop() generator functions now accept zero
arguments for the selection
of everything. This fixes two of the unit tests. The
test_molecule_loop_no_selection() unit test
has also been fixed.
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r3227 | bugman | 2007-03-19 16:23:18 +1100 (Mon, 19 Mar 2007) | 2 lines
Implemented the generic_fns.selection.residue_loop() generator function.
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r3228 | bugman | 2007-03-19 16:23:48 +1100 (Mon, 19 Mar 2007) | 2 lines
Small bug fix for the test_residue_loop_no_selection() unit test.
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r3229 | bugman | 2007-03-19 16:24:23 +1100 (Mon, 19 Mar 2007) | 4 lines
Wrote the generic_fns.selection.tokenise() function and 28 unit tests
covering the function!
The unit tests attempt to cover all proper and improper combinations of the
selection string.
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r3230 | bugman | 2007-03-19 16:25:03 +1100 (Mon, 19 Mar 2007) | 5 lines
Wrote the generic_fns.selection.parse_token() function and 13 unit tests
covering the function!
The unit tests attempt to cover all proper and improper combinations of the
supplied token including
numbers (integers), names, and number ranges.
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r3231 | bugman | 2007-03-19 16:25:57 +1100 (Mon, 19 Mar 2007) | 5 lines
Updated the data model redesign document.
The spin_loop() generator function and selection syntax parsing functions
tokenise() and
parse_token() are now implemented.
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r3232 | bugman | 2007-03-19 16:26:45 +1100 (Mon, 19 Mar 2007) | 5 lines
Wrote the identification string documentation.
This documentation is the string 'generic_fns.selection.id_string_doc'.
The residue.delete() user
function docstring has had this string added to the end.
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r3233 | bugman | 2007-03-19 16:27:21 +1100 (Mon, 19 Mar 2007) | 4 lines
Fixed the generic_fns.residue.delete() function and its associated unit
tests.
An additional unit test for deletion using residue names has been added.
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r3234 | bugman | 2007-03-19 17:20:17 +1100 (Mon, 19 Mar 2007) | 3 lines
Updated the unit test runner to be cross platform compatible.
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r3240 | bugman | 2007-03-26 15:25:28 +1000 (Mon, 26 Mar 2007) | 10 lines
Bug fix.
This issue was reported by Gary Thompson at
https://mail.gna.org/public/relax-devel/2007-03/msg00084.html (Message-id:
<45FE68E4.4010000@xxxxxxxxxxxxxxx>).
The module separator character '.' had been replace by os.curdir in a
number of places in the unit
test runner. This has now been fixed.
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r3245 | macraild | 2007-03-30 02:46:15 +1000 (Fri, 30 Mar 2007) | 13 lines
A proposal for a modified mol-res-spin selection mechanism.
This simple modification, based on a selection object, permits
the use of booleans in selection strings, eg:
':leu@xxxxxxx | :val@CG1,CG2'
selects leucine and valine methyls.
Also, modification of Selection.__contains__() will allow for
wildcards, regex, etc as desired.
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r3247 | macraild | 2007-03-30 04:40:50 +1000 (Fri, 30 Mar 2007) | 3 lines
This time booleans actually work!
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r3255 | macraild | 2007-03-30 23:35:39 +1000 (Fri, 30 Mar 2007) | 3 lines
Improvements and unit-tests for spin selection
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r3256 | varioustoxins | 2007-03-30 23:55:16 +1000 (Fri, 30 Mar 2007) | 3
lines
unit_test_runner.py no longersilently ignores TestCases with syntax
errors. They now produce a dummy test case that prints the SyntaxError
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r3257 | varioustoxins | 2007-03-31 00:11:44 +1000 (Sat, 31 Mar 2007) | 3
lines
unit_test_runner emits a better warning messages that no tests from
a module with a syntax error will be run
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r3258 | macraild | 2007-03-31 02:41:01 +1000 (Sat, 31 Mar 2007) | 3 lines
Further mol-res-spin selection improvements. Work still needed on
boolean logic.
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Modified:
1.2/ (props changed)
Propchange: 1.2/
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r3259 - /1.2/