Author: bugman
Date: Fri Jan 4 18:36:09 2008
New Revision: 4336
URL: http://svn.gna.org/viewcvs/relax?rev=4336&view=rev
Log:
Merged revisions 4302-4335 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r4302 | bugman | 2008-01-04 11:19:35 +0100 (Fri, 04 Jan 2008) | 3 lines
Added 14 unit tests for the setting of relaxation curve fitting parameter
values.
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r4303 | bugman | 2008-01-04 11:22:24 +0100 (Fri, 04 Jan 2008) | 3 lines
Renamed all the previous unit tests from 'test_set_relax_data_xxx' to
'test_set_relax_fit_xxx'.
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r4304 | bugman | 2008-01-04 11:26:36 +0100 (Fri, 04 Jan 2008) | 3 lines
Converted specific_fns.relax_fit.data_init() to the new relax design.
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r4305 | bugman | 2008-01-04 11:28:07 +0100 (Fri, 04 Jan 2008) | 5 lines
Bug fix for the specific_fns.relax_fit.default_value() function.
The Iinf parameter was being checked for as 'te'!!!
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r4307 | bugman | 2008-01-04 11:47:21 +0100 (Fri, 04 Jan 2008) | 7 lines
Modified the structure of the model-free classes containing the model-free
specific functions.
One parent, but empty, class called Model_free now inherits all model-free
specific functions from
the other classes. The Molmol specific class has also been shifted into
its own module as the
initial step for splitting up the original, massive 'model_free.py' file.
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r4308 | bugman | 2008-01-04 11:51:04 +0100 (Fri, 04 Jan 2008) | 3 lines
Prepended 'molmol_' to the start of all the Molmol functions.
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r4309 | bugman | 2008-01-04 13:53:24 +0100 (Fri, 04 Jan 2008) | 3 lines
Updated all of the model-free specific Molmol macro function to the new
relax design.
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r4310 | bugman | 2008-01-04 13:56:47 +0100 (Fri, 04 Jan 2008) | 3 lines
Converted the module from being dependent on Numeric to using numpy.
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r4311 | bugman | 2008-01-04 13:57:34 +0100 (Fri, 04 Jan 2008) | 3 lines
Updated 2 comments relating to the change from Numeric to numpy.
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r4312 | bugman | 2008-01-04 14:06:10 +0100 (Fri, 04 Jan 2008) | 3 lines
Converted all the class methods of the colour module to functions.
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r4313 | bugman | 2008-01-04 14:08:24 +0100 (Fri, 04 Jan 2008) | 3 lines
Removed all of the imports of the now non-existant 'Colour' class.
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r4314 | bugman | 2008-01-04 14:10:10 +0100 (Fri, 04 Jan 2008) | 5 lines
Fixed the appending of the molmol_classic_style docstring.
The function used to be called simply classic.
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r4315 | bugman | 2008-01-04 14:15:01 +0100 (Fri, 04 Jan 2008) | 3 lines
Updated the copyright notice and added some comments.
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r4316 | bugman | 2008-01-04 14:15:56 +0100 (Fri, 04 Jan 2008) | 3 lines
Updated the copyright notice and added some comments.
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r4317 | bugman | 2008-01-04 14:16:47 +0100 (Fri, 04 Jan 2008) | 3 lines
Updated the copyright notice by adding the date the file was originally
created.
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r4318 | bugman | 2008-01-04 14:18:38 +0100 (Fri, 04 Jan 2008) | 3 lines
Removed the import of the now non-existant 'Colour' class.
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r4319 | bugman | 2008-01-04 14:32:41 +0100 (Fri, 04 Jan 2008) | 3 lines
Added the command line option --system-tests to run solely the relax
system/functional tests.
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r4320 | bugman | 2008-01-04 14:34:59 +0100 (Fri, 04 Jan 2008) | 5 lines
Changed the --unit-test command line option to --unit-tests.
The old option still works thanks to the optparse package.
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r4321 | bugman | 2008-01-04 14:42:16 +0100 (Fri, 04 Jan 2008) | 5 lines
Bug fix for running solely the system/functional tests.
The interpeter, which is essential for the tests, is now loaded.
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r4322 | bugman | 2008-01-04 15:34:14 +0100 (Fri, 04 Jan 2008) | 6 lines
A temporary fix for catching stdout during the execution of all unit tests.
The aim is to eventually have stdout collected for each test run and
appended to the failure or
error message if the test was unsuccessful.
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r4323 | bugman | 2008-01-04 16:04:53 +0100 (Fri, 04 Jan 2008) | 5 lines
Update for the generic_fns.sequence.display() function.
Now the function operates correctly with IO redirection of stdout.
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r4324 | bugman | 2008-01-04 16:09:52 +0100 (Fri, 04 Jan 2008) | 3 lines
Replaced the insecure os.tempnam() with tempfile.mktemp().
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r4325 | bugman | 2008-01-04 17:26:07 +0100 (Fri, 04 Jan 2008) | 6 lines
Created the framework for a new unittest runner to replace TextTestRunner.
The point it to capture STDOUT during each test and only print it in the
reports for failures and
errors.
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r4326 | bugman | 2008-01-04 17:33:45 +0100 (Fri, 04 Jan 2008) | 5 lines
Shifted the IO redirection into the RelaxTestRunner.run() method.
This is a temporary change.
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r4327 | bugman | 2008-01-04 17:39:20 +0100 (Fri, 04 Jan 2008) | 5 lines
Created the _RelaxTestResult class as a replacement for _TextTestResult.
This is where the capture of STDOUT should occur.
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r4328 | bugman | 2008-01-04 17:44:32 +0100 (Fri, 04 Jan 2008) | 5 lines
Shifted the STDOUT redirection into the startTest() and stopTest() methods.
These methods are overrides for those in TestResult and _TextTestResult.
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r4329 | bugman | 2008-01-04 17:45:21 +0100 (Fri, 04 Jan 2008) | 3 lines
Restored the run() method accidentally renamed to run2() in the last commit.
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r4330 | bugman | 2008-01-04 17:49:45 +0100 (Fri, 04 Jan 2008) | 3 lines
Added a deliberate unit test failure for implementing the new
RelaxTestRunner code.
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r4331 | bugman | 2008-01-04 17:50:17 +0100 (Fri, 04 Jan 2008) | 3 lines
The normal startTest() code is now run as well.
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r4332 | bugman | 2008-01-04 18:22:42 +0100 (Fri, 04 Jan 2008) | 3 lines
Completed the STDOUT capture and prepending by added an override for
_TextTestResult.addError().
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r4333 | bugman | 2008-01-04 18:24:29 +0100 (Fri, 04 Jan 2008) | 3 lines
Removed the RelaxTestRunner.run() method as it was doing nothing.
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r4334 | bugman | 2008-01-04 18:28:05 +0100 (Fri, 04 Jan 2008) | 6 lines
Reverted the debugging code of r4330.
The command used was:
svn merge -r4330:4329 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r4335 | bugman | 2008-01-04 18:30:19 +0100 (Fri, 04 Jan 2008) | 3 lines
The RelaxTestRunner is used now with the --unit-tests command line option.
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Added:
branches/N_state_model/specific_fns/model_free/molmol.py
- copied unchanged from r4335, 1.3/specific_fns/model_free/molmol.py
branches/N_state_model/test_suite/relax_test_runner.py
- copied unchanged from r4335, 1.3/test_suite/relax_test_runner.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/colour.py
branches/N_state_model/generic_fns/sequence.py
branches/N_state_model/prompt/molmol.py
branches/N_state_model/prompt/pymol.py
branches/N_state_model/relax
branches/N_state_model/specific_fns/model_free/__init__.py
branches/N_state_model/specific_fns/model_free/model_free.py
branches/N_state_model/specific_fns/relax_fit.py
branches/N_state_model/test_suite/runner.py
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
branches/N_state_model/test_suite/unit_tests/unit_test_runner.py
branches/N_state_model/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/colour.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/colour.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/sequence.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/molmol.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/prompt/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/pymol.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/__init__.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/model_free.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/relax_fit.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/test_suite/runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/runner.py?rev=4336&r1=4335&r2=4336&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/sequence_testing_base.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/unit_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/unit_test_runner.py?rev=4336&r1=4335&r2=4336&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/value_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/value_testing_base.py?rev=4336&r1=4335&r2=4336&view=diff
r4336 - in /branches/N_state_model: ./ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/ test_suite/un...