Author: bugman
Date: Wed Oct 15 21:19:57 2008
New Revision: 7708
URL: http://svn.gna.org/viewcvs/relax?rev=7708&view=rev
Log:
Merged revisions 7529-7707 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r7530 | bugman | 2008-10-06 22:13:43 +0200 (Mon, 06 Oct 2008) | 3 lines
Changed an MC simulation te value to 200 ns to trigger MC sim failure
detection by eliminate().
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r7531 | bugman | 2008-10-06 22:18:03 +0200 (Mon, 06 Oct 2008) | 3 lines
Added some checks to the test_omp_analysis() system test.
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r7532 | bugman | 2008-10-06 22:26:18 +0200 (Mon, 06 Oct 2008) | 3 lines
Fix for the tests added at r7531.
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r7533 | bugman | 2008-10-06 22:30:06 +0200 (Mon, 06 Oct 2008) | 3 lines
Changed the checks in test_omp_analysis() for the 'select_sim' arrays to
lists of Booleans.
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r7534 | bugman | 2008-10-06 22:33:38 +0200 (Mon, 06 Oct 2008) | 3 lines
Converted the 'select_sim' variable to a list of bools.
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r7535 | bugman | 2008-10-06 22:50:26 +0200 (Mon, 06 Oct 2008) | 5 lines
Fix for the loading of a version 1.2 model-free results file.
The 'select_sim' array was not being set as a list of booleans but rather
an numpy array of bools.
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r7536 | bugman | 2008-10-06 22:52:15 +0200 (Mon, 06 Oct 2008) | 5 lines
Modified the test_omp_analysis() system test to add more MC sim failures.
This adds a second failure to the second residue.
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r7537 | bugman | 2008-10-06 23:05:04 +0200 (Mon, 06 Oct 2008) | 3 lines
Docstring fix for setup().
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r7538 | bugman | 2008-10-06 23:13:50 +0200 (Mon, 06 Oct 2008) | 6 lines
Fix for the 'select_sim' list setting methods.
The copy.deepcopy() function is now used to set 'select_sim' so that the
lists from different spins
are no longer actually exactly the same list.
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r7539 | bugman | 2008-10-06 23:28:44 +0200 (Mon, 06 Oct 2008) | 3 lines
Removed the sconstruct file from the API manual.
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r7540 | bugman | 2008-10-06 23:40:47 +0200 (Mon, 06 Oct 2008) | 3 lines
Converted the linear_gradient() docstring to epytxt format and added a
module docstring.
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r7541 | bugman | 2008-10-06 23:56:07 +0200 (Mon, 06 Oct 2008) | 7 lines
Epydoc fixes for the docstrings appended to molmol.write() and
pymol.write().
The text appended to the user functions have been shifted to the global
variables
__molmol_colours_prompt_doc__ and __x11_colours_prompt_doc__. Proper
docstrings have been added to
the functions of the colour module.
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r7542 | bugman | 2008-10-06 23:59:57 +0200 (Mon, 06 Oct 2008) | 3 lines
Epydoc fixes for the module docstring.
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r7543 | bugman | 2008-10-07 00:09:47 +0200 (Tue, 07 Oct 2008) | 3 lines
Shifted the prompt documentation from docstrings into global variables.
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r7544 | bugman | 2008-10-07 00:17:25 +0200 (Tue, 07 Oct 2008) | 3 lines
Shifted the prompt documentation from docstrings into global variables.
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r7545 | bugman | 2008-10-07 00:22:39 +0200 (Tue, 07 Oct 2008) | 3 lines
Many epydoc docstring fixes.
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r7546 | bugman | 2008-10-07 00:57:18 +0200 (Tue, 07 Oct 2008) | 3 lines
Many eypdoc docstring fixes for the unit test runner.
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r7547 | bugman | 2008-10-07 01:03:06 +0200 (Tue, 07 Oct 2008) | 3 lines
Removed the system tests from the API documentation.
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r7548 | bugman | 2008-10-07 01:15:04 +0200 (Tue, 07 Oct 2008) | 3 lines
A number of epydoc docstring fixes.
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r7549 | bugman | 2008-10-07 21:14:37 +0200 (Tue, 07 Oct 2008) | 3 lines
Fixed the indentation of the prompt interface documentation.
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r7550 | bugman | 2008-10-07 21:17:27 +0200 (Tue, 07 Oct 2008) | 7 lines
Added example Sparky peak lists to the NOE and relaxation curve fitting
chapter.
This documentation improvement was suggested by Tyler Reddy at
https://mail.gna.org/public/relax-users/2008-10/msg00011.html (Message-id:
<20081007144810.ab985qup4408wokg@xxxxxxxxxx>).
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r7551 | bugman | 2008-10-07 21:25:09 +0200 (Tue, 07 Oct 2008) | 3 lines
Added a user script for adding a new system test of an NOE analysis.
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r7552 | bugman | 2008-10-07 21:34:11 +0200 (Tue, 07 Oct 2008) | 3 lines
Fixes for the system test NOE analysis script.
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r7553 | bugman | 2008-10-07 21:37:06 +0200 (Tue, 07 Oct 2008) | 3 lines
Added some truncated Sparky peak lists from an NOE analysis.
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r7554 | bugman | 2008-10-07 21:37:24 +0200 (Tue, 07 Oct 2008) | 3 lines
Activated the NOE analysis system test.
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r7555 | bugman | 2008-10-07 21:39:58 +0200 (Tue, 07 Oct 2008) | 3 lines
Shifted the last of the system test data into the test suite common data
directory.
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r7556 | bugman | 2008-10-07 21:41:02 +0200 (Tue, 07 Oct 2008) | 3 lines
Removed the empty system test data directory.
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r7557 | bugman | 2008-10-07 21:44:00 +0200 (Tue, 07 Oct 2008) | 3 lines
Fixed all the references to the shifted system test data.
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r7559 | bugman | 2008-10-07 22:46:59 +0200 (Tue, 07 Oct 2008) | 3 lines
Fixed the noe.read() user function.
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r7560 | bugman | 2008-10-07 22:49:53 +0200 (Tue, 07 Oct 2008) | 5 lines
Fix for the noe.py system test script.
The spin names needed to be set to 'N'.
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r7561 | bugman | 2008-10-07 22:52:59 +0200 (Tue, 07 Oct 2008) | 3 lines
Converted the assign_function() method to the new design.
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r7562 | bugman | 2008-10-07 22:54:17 +0200 (Tue, 07 Oct 2008) | 3 lines
Added a check to assign_function() for when the spectrum_type arg is
incorrect.
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r7563 | bugman | 2008-10-07 22:57:05 +0200 (Tue, 07 Oct 2008) | 3 lines
The spectrum_type arg is now propagated all the way to where it's needed.
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r7564 | bugman | 2008-10-07 22:58:04 +0200 (Tue, 07 Oct 2008) | 3 lines
Added some missing imports.
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r7565 | bugman | 2008-10-07 23:04:49 +0200 (Tue, 07 Oct 2008) | 3 lines
Converted the noe.error() user function front and back-end to the new
design.
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r7566 | bugman | 2008-10-07 23:06:41 +0200 (Tue, 07 Oct 2008) | 5 lines
Fixed the calls to noe.error().
The sample script and system test script now use the spin_id arg rather
than residue number.
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r7567 | bugman | 2008-10-07 23:09:05 +0200 (Tue, 07 Oct 2008) | 3 lines
Converted the overfit_deselect() method to the new design.
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r7568 | bugman | 2008-10-07 23:09:57 +0200 (Tue, 07 Oct 2008) | 3 lines
Modified overfit_deselect() to set the spin container select flag to False
rather than 0.
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r7569 | bugman | 2008-10-07 23:12:08 +0200 (Tue, 07 Oct 2008) | 5 lines
Fixes for the spin container select flag.
Now the flag is always set to the bools True or False rather than 1 and 0.
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r7570 | bugman | 2008-10-07 23:14:41 +0200 (Tue, 07 Oct 2008) | 3 lines
Converted the calculate() method to the new design.
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r7571 | bugman | 2008-10-07 23:16:40 +0200 (Tue, 07 Oct 2008) | 8 lines
Deletion of a number of methods no longer used in the 1.3 line.
These are:
read_columnar_results()
write_columnar_line()
write_columnar_results()
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r7572 | bugman | 2008-10-07 23:17:46 +0200 (Tue, 07 Oct 2008) | 3 lines
Deleted the write() method as it has never been used!!!
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r7573 | bugman | 2008-10-07 23:21:13 +0200 (Tue, 07 Oct 2008) | 3 lines
Updated the value.write() user function interface to the new design.
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r7574 | bugman | 2008-10-07 23:25:23 +0200 (Tue, 07 Oct 2008) | 6 lines
Fix for the write_data() function.
The file arg was missing from the write_header() call, and the docstring
has been converted to
epydoc format.
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r7575 | bugman | 2008-10-07 23:28:57 +0200 (Tue, 07 Oct 2008) | 3 lines
Set the specific_fns.base_class.Common_functions as the base class of the
Noe class.
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r7576 | bugman | 2008-10-07 23:29:38 +0200 (Tue, 07 Oct 2008) | 3 lines
Deleted the return_value() method as the base class method is sufficient.
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r7577 | bugman | 2008-10-07 23:53:40 +0200 (Tue, 07 Oct 2008) | 3 lines
Added the removal of temporary manual file to the 'clean' scons target.
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r7578 | bugman | 2008-10-08 00:00:08 +0200 (Wed, 08 Oct 2008) | 3 lines
Fix for assign_function(), the spectrum_type arg is sent into it!
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r7579 | bugman | 2008-10-08 00:00:51 +0200 (Wed, 08 Oct 2008) | 5 lines
Another fix for assign_function().
The last commit incorrectly set up the function args.
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r7582 | bugman | 2008-10-08 22:29:23 +0200 (Wed, 08 Oct 2008) | 14 lines
Ported the modifications to the CHANGES file from the 1.3.2 tag.
The command used was:
svn merge -r7580:7581 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.2
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r7581 | bugman | 2008-10-08 22:27:25 +0200 (Wed, 08 Oct 2008) | 3 lines
Changed paths:
M /tags/1.3.2/docs/CHANGES
Updated the CHANGES file for relax version 1.3.2.
.....
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r7592 | semor | 2008-10-09 19:37:20 +0200 (Thu, 09 Oct 2008) | 3 lines
Continued the implementation for the reading of a Nmrview peak list.
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r7593 | semor | 2008-10-10 04:23:03 +0200 (Fri, 10 Oct 2008) | 10 lines
Added more for the reading of intensities from a nmrview peak list.
There is still a need to fix the reading of the assignments which are of
the format number.nucleus
(e.g. 22.HN).
Moreover, a functionality to chose whether the intensity or volume column
is read could be added as
proposed in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00026.html
(Message-id: <48EE7028.6060409@xxxxxxxxx>).
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r7595 | bugman | 2008-10-11 18:15:19 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted all the Dasha class methods into module functions.
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r7596 | bugman | 2008-10-11 18:18:08 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the Dasha user function class prompt interface to the new design.
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r7597 | bugman | 2008-10-11 18:40:20 +0200 (Sat, 11 Oct 2008) | 3 lines
Created 7 arg unit tests for all fns of the dasha user function class.
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r7598 | bugman | 2008-10-11 18:41:47 +0200 (Sat, 11 Oct 2008) | 5 lines
Missing import bug fix.
This was identified by the arg unit tests of 7597.
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r7599 | bugman | 2008-10-11 18:43:02 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixes for the Dasha user function print outs.
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r7600 | bugman | 2008-10-11 20:45:03 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create() function to the new design.
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r7601 | bugman | 2008-10-11 21:09:54 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create_script() function to the new design.
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r7602 | bugman | 2008-10-11 21:16:30 +0200 (Sat, 11 Oct 2008) | 3 lines
Created the 2 new API functions: first_residue_num() and last_residue_num().
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r7603 | bugman | 2008-10-11 21:20:18 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the execute() function to the new design.
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r7604 | bugman | 2008-10-11 21:25:49 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the extract() function to the new design.
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r7605 | bugman | 2008-10-11 22:03:02 +0200 (Sat, 11 Oct 2008) | 6 lines
Fixes for the copy() and read() functions.
The specific set() function was destroyed at r4822, well at least shifted to
generic_fns.value.set_spin_params().
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r7606 | bugman | 2008-10-11 22:16:08 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixed the creation of the Dasha script.
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r7607 | bugman | 2008-10-11 22:17:22 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the extract() method. The current data pipe was missing.
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r7608 | bugman | 2008-10-11 22:18:42 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the extract() docstring.
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r7609 | bugman | 2008-10-11 22:35:06 +0200 (Sat, 11 Oct 2008) | 6 lines
Switched to using os.popen3 for executing Dasha.
This allows STDOUT and STDERR to be caught and sent to relax's STDOUT and
STDERR. Hence Dasha's
output is caught by the system tests, etc.
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r7610 | bugman | 2008-10-11 22:36:49 +0200 (Sat, 11 Oct 2008) | 5 lines
Bug fix for the minimisation set() function.
The variable 'index' no longer exists as it is replace by the SpinContainer
instance.
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r7611 | bugman | 2008-10-11 22:42:51 +0200 (Sat, 11 Oct 2008) | 3 lines
Modified the Dasha system test script to use the temporary directory.
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r7612 | bugman | 2008-10-11 22:46:23 +0200 (Sat, 11 Oct 2008) | 3 lines
The Dasha system test script can now run outside of the system test
framework.
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r7613 | bugman | 2008-10-11 22:47:48 +0200 (Sat, 11 Oct 2008) | 3 lines
Fixed the call to results.write() in the Dasha system test script.
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r7614 | bugman | 2008-10-11 22:49:03 +0200 (Sat, 11 Oct 2008) | 3 lines
Comment fix.
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r7615 | bugman | 2008-10-11 23:04:16 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create() args to keyword args and the docstring to epydoc
format.
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r7616 | bugman | 2008-10-11 23:04:36 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the constraints flag to a bool.
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r7617 | bugman | 2008-10-11 23:06:13 +0200 (Sat, 11 Oct 2008) | 3 lines
The Modelfree4 execution system test script can now be run outside of the
test suite framework.
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r7618 | bugman | 2008-10-11 23:07:00 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the palmer.create() print out.
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r7619 | bugman | 2008-10-11 23:07:51 +0200 (Sat, 11 Oct 2008) | 3 lines
Fix for the check of the constraints arg in palmer.create().
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r7620 | bugman | 2008-10-11 23:14:16 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the last pieces of create() to the new design.
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r7621 | bugman | 2008-10-11 23:21:05 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_mfin() to the new design.
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r7622 | bugman | 2008-10-11 23:34:53 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_mfdata() to the new design.
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r7623 | bugman | 2008-10-11 23:47:44 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted the create_mfmodel() and create_mfpar() functions to the new
design.
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r7624 | bugman | 2008-10-11 23:51:37 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted create_run() to the new design.
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r7625 | bugman | 2008-10-11 23:55:21 +0200 (Sat, 11 Oct 2008) | 3 lines
Converted execute() to the new design.
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r7626 | bugman | 2008-10-12 00:03:01 +0200 (Sun, 12 Oct 2008) | 5 lines
Bug fix for the palmer.py sample script.
The model_selection() user function args were wrong.
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r7627 | bugman | 2008-10-12 00:11:52 +0200 (Sun, 12 Oct 2008) | 3 lines
Many fixes for the Modelfree4 execution system test script.
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r7628 | bugman | 2008-10-12 00:51:36 +0200 (Sun, 12 Oct 2008) | 6 lines
Switched from os.spawnlp to os.popen3 for proper IO redirection.
This allows the system tests to capture Modelfree4's STDOUT and STDERR
streams, as they are fused
into relax's.
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r7629 | bugman | 2008-10-12 00:54:20 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the palmer.py sample script.
The model selection data pipe is created by the user function so it
shouldn't be created beforehand.
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r7630 | bugman | 2008-10-12 01:33:29 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the reset() user function - the generic_fns.reset module was
not properly imported.
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r7631 | bugman | 2008-10-12 11:23:07 +0200 (Sun, 12 Oct 2008) | 3 lines
Shifted the pipe creation from setUp() to the script to allow for stand
alone execution.
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r7632 | bugman | 2008-10-12 11:40:43 +0200 (Sun, 12 Oct 2008) | 3 lines
Created a system test for the saving, loading, saving, and loading again of
the system state.
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r7633 | bugman | 2008-10-12 11:47:14 +0200 (Sun, 12 Oct 2008) | 5 lines
Removed the state loadings which was uncovering a pickling issue.
This bug is now caught by its own system test.
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r7634 | bugman | 2008-10-12 11:48:16 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the call to the fix() user function.
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r7635 | bugman | 2008-10-12 11:57:44 +0200 (Sun, 12 Oct 2008) | 3 lines
Updated the ancient palmer.py sample script to the new design.
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r7636 | bugman | 2008-10-12 12:07:28 +0200 (Sun, 12 Oct 2008) | 3 lines
Removed all references to 'run' and removed some useless comments.
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r7637 | bugman | 2008-10-12 12:26:47 +0200 (Sun, 12 Oct 2008) | 5 lines
Created the new specific method model_desc() for returning a human readable
model description.
This will be used in the model selection printouts.
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r7638 | bugman | 2008-10-12 12:27:23 +0200 (Sun, 12 Oct 2008) | 3 lines
Shifted to the use of the model_loop().
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r7639 | bugman | 2008-10-12 12:38:48 +0200 (Sun, 12 Oct 2008) | 8 lines
Converted the rest of the model selection to the model_loop() design.
The following model-free methods have been converted to using the
model_loop():
duplicate_data()
model_statistics()
skip_function()
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r7640 | bugman | 2008-10-12 12:42:09 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the determination of the global_stats flag in model_statistics().
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r7641 | bugman | 2008-10-12 12:48:17 +0200 (Sun, 12 Oct 2008) | 3 lines
Renamed the duplicate_data() arg model_info to model_index.
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r7642 | bugman | 2008-10-12 13:00:50 +0200 (Sun, 12 Oct 2008) | 3 lines
Created the model_type() method to determine whether the model is local or
global.
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r7643 | bugman | 2008-10-12 13:02:29 +0200 (Sun, 12 Oct 2008) | 3 lines
Activated the specific model_type() method.
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r7644 | bugman | 2008-10-12 13:04:07 +0200 (Sun, 12 Oct 2008) | 3 lines
Removed the model_index arg from model_type().
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r7645 | bugman | 2008-10-12 13:05:50 +0200 (Sun, 12 Oct 2008) | 3 lines
Used the new model_type() specific method to differentiate between global
and local models.
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r7646 | bugman | 2008-10-12 13:24:48 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the setUp() method. The 'palmer' data pipe shouldn't be created!
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r7647 | bugman | 2008-10-12 15:17:44 +0200 (Sun, 12 Oct 2008) | 3 lines
Changes to the model selection print out.
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r7648 | bugman | 2008-10-12 16:09:04 +0200 (Sun, 12 Oct 2008) | 3 lines
Added checks to the Modelfree4 system test.
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r7649 | bugman | 2008-10-12 16:12:49 +0200 (Sun, 12 Oct 2008) | 3 lines
Bug fix for the extract() function.
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r7650 | bugman | 2008-10-12 16:30:32 +0200 (Sun, 12 Oct 2008) | 5 lines
Removed the 'format' arg from results.write() and results.display().
This is no longer used as the only supported format is now XML.
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r7651 | bugman | 2008-10-12 17:05:21 +0200 (Sun, 12 Oct 2008) | 7 lines
Fixes for the relax data store singleton 'add()', 'to_xml()', and
'from_xml()' methods.
These were referring to the contents of the singleton as self, whereas in
reality with the current
temporary implementation it is stored in self.instance. Hence the
singleton wasn't operating on
itself.
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r7652 | bugman | 2008-10-12 17:07:57 +0200 (Sun, 12 Oct 2008) | 3 lines
Fix for the extraction of mfout file data in the Modelfree4 system test.
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r7653 | bugman | 2008-10-12 17:09:00 +0200 (Sun, 12 Oct 2008) | 5 lines
Fix for the Modelfree4 controlling sample script.
This matches the fixes of r7652.
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r7654 | bugman | 2008-10-12 17:22:45 +0200 (Sun, 12 Oct 2008) | 3 lines
Fixes for the checks of the test_palmer() system test.
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r7655 | bugman | 2008-10-12 17:30:11 +0200 (Sun, 12 Oct 2008) | 3 lines
[... 582 lines stripped ...]
r7708 - in /branches/multi_processor_merge: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx...