Blocked revisions 2506,2579,2582,2594,2596,2598,2601-2604,2606-2610,2613-2615,2617,2633,2645,2649-2655,2657,2659,2661,2663,2668-2670,2673,2675-2676,2707,2717,2719,2724,2732-2733,2737,2739,2743,2769,2775,2779,2781,2785,2790-2792,2798-2799,2829,2831-2833,2838,2844,2847-2853,2856-2857,2859,2864-2872,2874,2878-2879,2881-2882,2884,2886,2888,2891,2893-2897,2910-2912,2914-2928,2931,2933-2936,2939,2949,2993-3011,3013-3022,3025,3033-3034 via svnmerge
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r2506 | bugman | 2006-07-06 15:25:51 +1000 (Thu, 06 Jul 2006) | 3 lines
Creation of the 1.3 developmental branch for the MPI and any other destabilising changes.
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r2579 | bugman | 2006-09-20 18:21:09 +1000 (Wed, 20 Sep 2006) | 6 lines
Merged r2506 to r2578 of the 1.2 line into the untouched 1.3 line.
The command used was:
svn merge -r2506:2578 svn+ssh://bugman@.../svn/relax/1.2
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r2582 | bugman | 2006-09-30 14:20:04 +1000 (Sat, 30 Sep 2006) | 8 lines
Merged r2579 to r2581 of the 1.2 line into the 1.3 line.
The command used was:
svn merge -r2578:2581 svn+ssh://bugman@.../svn/relax/1.2
This includes a fix for bug #7192 and a few other superficial changes.
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r2594 | bugman | 2006-10-01 15:19:37 +1000 (Sun, 01 Oct 2006) | 15 lines
Merged r2581 to r2593 of the 1.2 line into the 1.3 line.
The command used was:
svn merge -r2581:2593 svn+ssh://bugman@.../svn/relax/1.2
This merges a number of bug fixes: bug #7192 (https://gna.org/bugs/index.php?7192), bug #7224
(https://gna.org/bugs/?7224), bug #7225 (https://gna.org/bugs/index.php?7225), bug #7226
(https://gna.org/bugs/?7226), and bug #7241 (https://gna.org/bugs/?7241).
In addition, task #3781 (https://gna.org/task/?3781) has been completed, the sample script CSA values
have been changed from -160 ppm to -170 ppm, a regression test for catching bug #7224
(https://gna.org/bugs/?7224) has been added, and the Modelfree4 exit status is caught in all
situations.
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r2596 | bugman | 2006-10-01 15:32:19 +1000 (Sun, 01 Oct 2006) | 8 lines
Ported the changes of r2595 of the 1.2 line into the 1.3 line.
The command used was:
$ svn merge -r2594:2595 svn+ssh://bugman@.../svn/relax/1.2
This changes the CSA value in the sample scripts to -172 ppm.
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r2598 | bugman | 2006-10-01 18:20:53 +1000 (Sun, 01 Oct 2006) | 7 lines
Completion of task #3630 (https://gna.org/task/?3630).
The unmodified Hessian and turning the line search off are no longer both specified by the string
'None'. Now they are specified by the regular expressions '^[Nn]o [Ll]ine [Ss]earch$' and
'^[Nn]o [Hh]essian [Mm]od' respecively.
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r2601 | bugman | 2006-10-06 16:55:01 +1000 (Fri, 06 Oct 2006) | 10 lines
Splitting of the 'pdb()' user function into 'pdb.read()' and 'pdb.vectors()' (task #3838).
These changes complete task #3838 (https://gna.org/task/?3838). The details of the changes were
discussed at https://mail.gna.org/public/relax-users/2006-10/msg00002.html (Message-id:
<7f080ed10610032153o4571935bq138d2739f55ca3bd@...>).
The only difference between the post proposing the changes and the actual changes is that the
proposed user function 'pdb.set_vectors()' is actually now called 'pdb.vectors()'.
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r2602 | bugman | 2006-10-07 18:49:58 +1000 (Sat, 07 Oct 2006) | 8 lines
Ported r2599 from the 1.2 line.
The command used was:
$ svn merge -r2598:2599 svn+ssh://bugman@.../svn/relax/1.2
This changes 'Sconstruct' to 'SCons' in the relax manual.
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r2603 | bugman | 2006-10-07 18:52:57 +1000 (Sat, 07 Oct 2006) | 8 lines
Ported r2600 from the 1.2 line.
The command used was:
svn merge -r2599:2600 svn+ssh://bugman@.../svn/relax/1.2
This fixes bug #7297 (https://gna.org/bugs/index.php?7297).
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r2604 | bugman | 2006-10-07 21:28:39 +1000 (Sat, 07 Oct 2006) | 3 lines
Created the JOBS file. This file describes the roles of the relax manager positions.
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r2606 | bugman | 2006-10-08 01:35:24 +1000 (Sun, 08 Oct 2006) | 8 lines
Ported r2605 from the 1.2 line.
The command used was:
$ svn merge -r2604:2605 svn+ssh://bugman@.../svn/relax/1.2
This fixes bug #7277 (https://gna.org/bugs/?7277).
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r2607 | bugman | 2006-10-08 03:13:42 +1000 (Sun, 08 Oct 2006) | 7 lines
Fix for bug #7333 (https://gna.org/bugs/index.php?7333).
The three tests of the test-suite have been modified to use the correct PDB functions. A few calls
to the user function 'pdb.vectors()' needed to be added and the 'heteronuc' and 'proton' argments
to the 'pdb.read()' funtion had to be removed.
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r2608 | bugman | 2006-10-08 03:24:08 +1000 (Sun, 08 Oct 2006) | 6 lines
Fix for bug #7334 (https://gna.org/bugs/index.php?7334).
The problem was that the relax base class in the PDB class of 'prompt/pdb.py' was set to
'self.__relax__'. However two lines were attempting to use 'self.relax'.
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r2609 | bugman | 2006-10-08 03:37:56 +1000 (Sun, 08 Oct 2006) | 8 lines
Fix for bug #7335 (https://gna.org/bugs/index.php?7335).
The code which tests that the proton and heteronucleus have not been set to the same atom name has
been moved from the 'self.read()' function to the 'self.vectors()' function. Two more lines of
code, which were placing the atom names into the 'self.relax.data.pdb' data structure were also
identified to cause similar problems and were shifted from the read to the vectors function.
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r2610 | bugman | 2006-10-08 03:46:37 +1000 (Sun, 08 Oct 2006) | 7 lines
Fix for bug #7336 (https://gna.org/bugs/index.php?7336).
The user function 'pdb.vectors()' was not set up properly. It was expecting the residue number to
be an integer and the residue name to be a string. However the default is that both are set to
None. This was causing a RelaxError.
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r2613 | bugman | 2006-10-12 13:20:26 +1000 (Thu, 12 Oct 2006) | 8 lines
Ported r2611 from the 1.2 line.
The command used was:
$ svn merge -r2610:2611 svn+ssh://bugman@.../svn/relax/1.2
This adds the directory for Scons Python modules for the Builder functions.
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r2614 | bugman | 2006-10-12 13:23:22 +1000 (Thu, 12 Oct 2006) | 8 lines
Ported r2612 from the 1.2 line.
The command used was:
$ svn merge -r2611:2612 svn+ssh://bugman@.../svn/relax/1.2
This completes the fixing of bug #7241 (https://gna.org/bugs/?7241).
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r2615 | bugman | 2006-10-12 13:29:26 +1000 (Thu, 12 Oct 2006) | 5 lines
The user function 'pdb.read()' still was accepting the arguements heteronuc='N' and proton='H'.
The code of the user function was not using these or passing them on. They have now been removed.
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r2617 | bugman | 2006-10-12 13:46:16 +1000 (Thu, 12 Oct 2006) | 8 lines
Ported r2616 from the 1.2 line.
The command used was:
$ svn merge -r2615:2616 svn+ssh://bugman@.../svn/relax/1.2
This removes the ancient unused file 'maths_fns/test.c_chi.py'.
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r2633 | bugman | 2006-10-12 17:43:25 +1000 (Thu, 12 Oct 2006) | 10 lines
Ported r2618 to r2632 from the 1.2 line.
The command used was:
$ svn merge -r2617:2632 svn+ssh://bugman@.../svn/relax/1.2
These changes all relate to the Scons system. The Scons scripts have been completely overhauled.
Bugs have been removed. The help system has been redone. A target for creating the API
documentation using Epydoc has been added.
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r2645 | bugman | 2006-10-17 14:41:14 +1000 (Tue, 17 Oct 2006) | 24 lines
Fixes for a number of bugs caused by the changes for task #3838.
Task #3838 is located at https://gna.org/task/?3838 and more information is given at
https://mail.gna.org/public/relax-users/2006-10/msg00002.html (Message-id:
<7f080ed10610032153o4571935bq138d2739f55ca3bd@...>).
Part of the problem, the failure of two of the tests of the test suite was reported by Alex Hansen
(viochemist _at_ gmail _dot_ com) in the post located at
https://mail.gna.org/public/relax-devel/2006-10/msg00095.html (Message-id:
<481156b20610130720u39a93e30k6d4603efd8730c96@...>). Another failure was reported by
Alex at https://mail.gna.org/public/relax-devel/2006-10/msg00096.html (Message-id:
<481156b20610130728jb6aa76ag3d9487a20397391b@...).
The first fix, which was a missing run argument, is described at
https://mail.gna.org/public/relax-devel/2006-10/msg00099.html (Message-id:
<7f080ed10610130741j146721c8w512ba61bac3644c7@...>).
The second problem was that the residue number and residue name was being referred to as 'num' and
'name' when they should have been 'res_num' and 'res_name'.
The third problem was an index for selecting the residue. Rather than using the real index 'i', the
index 'j' was being used.
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r2649 | bugman | 2006-10-17 15:09:57 +1000 (Tue, 17 Oct 2006) | 8 lines
Ported r2635 from the 1.2 line.
The command used was:
$ svn merge -r2634:2635 svn+ssh://bugman@.../svn/relax/1.2
This involves a few functions moving to the new Scons module file 'scons/distrib.py'.
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r2650 | bugman | 2006-10-17 15:13:09 +1000 (Tue, 17 Oct 2006) | 10 lines
Ported r2637 to r2640 from the 1.2 line.
The command used was:
$ svn merge -r2636:2640 svn+ssh://bugman@.../svn/relax/1.2
This includes a number of changes to the Scons system including fixes for the distribution target
functions, the creation of the new module 'scons.install', and a restructure of the base
'sconstruct' file.
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r2651 | bugman | 2006-10-17 15:14:48 +1000 (Tue, 17 Oct 2006) | 8 lines
Ported r2641 from the 1.2 line.
The command used was:
$ svn merge -r2640:2641 svn+ssh://bugman@.../svn/relax/1.2
This fixes documentation bug #7402 (https://gna.org/bugs/?7402).
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r2652 | bugman | 2006-10-17 15:20:48 +1000 (Tue, 17 Oct 2006) | 10 lines
Ported r2642 and r2644 of the 1.2 line (r2643 is not included).
The commands used were:
$ svn merge -r2641:2642 svn+ssh://bugman@.../svn/relax/1.2
$ svn merge -r2643:2644 svn+ssh://bugman@.../svn/relax/1.2
These changes include improvements to the infrastructure chapter of the relax user manual, and a
large expansion of the relax development chapter.
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r2653 | bugman | 2006-10-17 15:22:34 +1000 (Tue, 17 Oct 2006) | 8 lines
Ported r2643 from the 1.2 line.
The command used was:
$ svn merge -r2642:2643 svn+ssh://bugman@.../svn/relax/1.2
This includes a few small formatting changes to the model-free file.
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r2654 | bugman | 2006-10-17 15:33:14 +1000 (Tue, 17 Oct 2006) | 8 lines
Ported r2646 to r2647 from the 1.2 line.
The command used was:
$ svn merge -r2645:2647 svn+ssh://bugman@.../svn/relax/1.2
This adds a number of model-free optimisation tests to the test suite.
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r2655 | bugman | 2006-10-20 21:57:49 +1000 (Fri, 20 Oct 2006) | 8 lines
This fixes a bug in the compile re function.
The bug was reported by Alex Hansen at https://mail.gna.org/public/relax-devel/2006-10/msg00112.html
(Message-id: <481156b20610190725ud6bab67w1f8fbbdf849da52c@...>). The simple fix is
described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html (Message-id:
<7f080ed10610190738g7df6566fl13b74d9217071924@...>).
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r2657 | macraild | 2006-10-21 01:21:10 +1000 (Sat, 21 Oct 2006) | 6 lines
Removal of apply(func, args) calls from the minimisation code
As discussed at relax-devel:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html
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r2659 | bugman | 2006-10-22 19:51:57 +1000 (Sun, 22 Oct 2006) | 9 lines
Ported r2658 from the 1.2 line.
The command used was:
$ svn merge -r2657:2658 svn+ssh://bugman@.../svn/relax/1.2
These changes complete task #4002 (https://gna.org/task/index.php?4002), the implementation of the
'grace.write()' user function for reduced spectral density mapping.
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r2661 | bugman | 2006-10-23 18:28:26 +1000 (Mon, 23 Oct 2006) | 9 lines
Ported r2660 from the 1.2 line.
The command used was:
$ svn merge -r2659:2660 svn+ssh://bugman@.../svn/relax/1.2
This fixes an error when trying to plot the MC simulation data in reduced spectral density mapping
using the 'grace.write()' user function.
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r2663 | macraild | 2006-10-23 19:09:37 +1000 (Mon, 23 Oct 2006) | 8 lines
Roll-back of revision 2656 from 1.3 line:
svn merge -r 2657:2656 svn+ssh://macraild@.../svn/relax/1.3
see: https://mail.gna.org/public/relax-devel/2006-10/msg00103.html
r2656 was accidentally applied to the 1.3 line (intended for the apply
branch). r2662 merged the changes into the apply branch
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r2668 | bugman | 2006-10-26 17:52:51 +1000 (Thu, 26 Oct 2006) | 3 lines
Fixed a bug whereby the match re function had not been imported.
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r2669 | bugman | 2006-10-26 18:09:12 +1000 (Thu, 26 Oct 2006) | 7 lines
Fixed the nucleic acid residue names.
These names were being prefixed by 'R' by Scientific python, so residue 'G' would be labelled as
residue 'RG'! This was causing the user function 'pdb.vectors()' to fail as the residue was
expected to be called 'G'. The prefix 'R' is now stripped from the residue name.
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r2670 | bugman | 2006-10-26 18:17:45 +1000 (Thu, 26 Oct 2006) | 6 lines
Fixed the overwriting of the residue specific xh_vect data structure.
If the user function 'pdb.vectors()' was called twice, the vectors calculated from the first
function call were being overwriten by the empty structure '[]'. This is now fixed.
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r2673 | bugman | 2006-10-26 19:16:54 +1000 (Thu, 26 Oct 2006) | 9 lines
Ported r2671 and r2672 from the 1.2 line.
The command used was:
$ svn merge -r2670:2672 svn+ssh://bugman@.../svn/relax/1.2
This improves the optimisation tests and makes them a little more lenient to allow for machine
precision and round-off error artifacts on different architectures, operating systems, etc.
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r2675 | bugman | 2006-10-27 18:38:40 +1000 (Fri, 27 Oct 2006) | 10 lines
Ported r2674 from the 1.2 line.
The command used was:
$ svn merge -r2673:2674 svn+ssh://bugman@.../svn/relax/1.2
This includes a number of improvements to the optimisation tests of the test suite. See the post at
https://mail.gna.org/public/relax-devel/2006-10/msg00145.html (Message-id:
<7f080ed10610260854p3d7d0a45w32c731345ed244d3@...>) for the exact details.
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r2676 | bugman | 2006-10-27 18:50:44 +1000 (Fri, 27 Oct 2006) | 8 lines
Fix for bug #7540 (https://gna.org/bugs/index.php?7540).
This bug was reported by Alex Hansen (viochemist at gmail dot com). The problem was that the
function 'self.relax.generic.pdb.load()' had been renamed to 'self.relax.generic.pdb.read()'. The
correct function is now being called and the heteronucleus and proton name arguments, as well as the
'calc_vectors' argument have been removed.
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r2707 | bugman | 2006-10-31 18:31:08 +1100 (Tue, 31 Oct 2006) | 9 lines
Ported r2705 and r2706 from the 1.2 line.
The command used was:
$ svn merge -r2704:2706 svn+ssh://bugman@.../svn/relax/1.2
This fixes bug #7583 (https://gna.org/bugs/?7583) and fixes a problem with one of the comments in
'specific_fns/model_free.py'.
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r2717 | varioustoxins | 2006-10-31 23:02:39 +1100 (Tue, 31 Oct 2006) | 9 lines
ported r2634,r2636 & r2716 to the 1.3 line
commands used
svn merge -r2633:2634 svn+ssh://varioustoxins@.../svn/relax/1.2
svn merge -r2635:2636 svn+ssh://varioustoxins@.../svn/relax/1.2
svn merge -r2715:2716 svn+ssh://varioustoxins@.../svn/relax/1.2
these changes add the ieee-754 nan/inf code and and add nan catching
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r2719 | macraild | 2006-11-01 03:49:36 +1100 (Wed, 01 Nov 2006) | 5 lines
Impliments the io.file_root() function.
As suggested:
https://mail.gna.org/public/relax-devel/2006-10/msg00218.html
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r2724 | bugman | 2006-11-02 15:23:44 +1100 (Thu, 02 Nov 2006) | 3 lines
Changed the comment of the 'RelaxNoPdbChainError' class to the correct explanation.
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r2732 | bugman | 2006-11-04 16:12:26 +1100 (Sat, 04 Nov 2006) | 6 lines
Creation of a planning document for the relax data model redesign.
This is still in draft form and will need a lot of work, including the addition of URLs to the
mailing list archives.
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r2733 | bugman | 2006-11-04 16:18:05 +1100 (Sat, 04 Nov 2006) | 9 lines
Ported r2731 from the 1.2 line.
The command used was:
svn merge -r2730:2731 svn+ssh://bugman@.../svn/relax/1.2
This updates the release checklist file. The freshmeat announcment has been added and the point
about the changes file has been moved.
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r2737 | bugman | 2006-11-04 16:52:05 +1100 (Sat, 04 Nov 2006) | 6 lines
Ported r2736 from the 1.2 line to fix bug #7587 (https://gna.org/bugs/index.php?7587).
The command used was:
svn merge -r2735:2736 svn+ssh://bugman@.../svn/relax/1.2
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r2739 | bugman | 2006-11-04 18:08:14 +1100 (Sat, 04 Nov 2006) | 10 lines
Ported r2738 from the 1.2 line.
The command used was:
svn merge -r2737:2738 svn+ssh://bugman@.../svn/relax/1.2
This fixes the massively important bug #7616 (https://gna.org/bugs/index.php?7616) which is the
failure of the model selection between the global diffusion models when the local tm models are
included.
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r2743 | bugman | 2006-11-04 19:31:37 +1100 (Sat, 04 Nov 2006) | 6 lines
Ported r2741 from the 1.2.8 tag (the CHANGES file details for 1.2.8).
The command used was:
svn merge -r2740:2741 svn+ssh://bugman@.../svn/relax/tags/1.2.8
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r2769 | varioustoxins | 2006-11-08 10:35:18 +1100 (Wed, 08 Nov 2006) | 5 lines
ported r2768 (fix to bug #7641)
commands used
svn merge -r2767:2768 svn+ssh://varioustoxins@.../svn/relax/1.2
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r2775 | macraild | 2006-11-09 03:33:12 +1100 (Thu, 09 Nov 2006) | 7 lines
Restoring revision 2656. This removes usage of apply() from minimisation
code.
svn merge -r 2656:2657 svn+ssh://macraild@.../svn/relax/1.3
This introduces the changes made and tested in the apply branch.
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r2779 | bugman | 2006-11-09 14:31:34 +1100 (Thu, 09 Nov 2006) | 10 lines
Ported r2745, r2746, and r2778 from the 1.2 line.
The commands used were:
svn merge -r2744:2746 svn+ssh://bugman@.../svn/relax/1.2
svn merge -r2777:2778 svn+ssh://bugman@.../svn/relax/1.2
This includes editing of the release checklist file, a spell check of the CHANGES file, and the fix
to bug #7677 (https://gna.org/bugs/index.php?7677).
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r2781 | bugman | 2006-11-09 14:44:49 +1100 (Thu, 09 Nov 2006) | 8 lines
Ported r2780 from the 1.2 line.
The command used was:
svn merge -r2779:2780 svn+ssh://bugman@.../svn/relax/1.2
This changes the interpreter from '/usr/bin/python' to '/usr/bin/env python'.
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r2785 | bugman | 2006-11-09 16:23:18 +1100 (Thu, 09 Nov 2006) | 6 lines
Ported r2783 from the 1.2.9 tag (the CHANGES file details for relax version 1.2.9).
The command used was:
svn merge -r2782:2783 svn+ssh://bugman@.../svn/relax/tags/1.2.9
................
r2790 | bugman | 2006-11-09 19:11:43 +1100 (Thu, 09 Nov 2006) | 16 lines
An attempt at removing the '-dynamiclib' gcc option when compiling the C modules on Mac OS X.
This problem was reported by Douglas Kojetin <douglas dot kojetin at gmail dot com> at
https://mail.gna.org/public/relax-users/2006-11/msg00002.html (Message-id:
<AD17DD2D-A37B-44D4-B1B8-1A2349EC7EC5@...>) and as bug #7670 (https://gna.org/bugs/?7670).
To remove the '-dynamiclib' option, I replicated what Doug had done in his post at
https://mail.gna.org/public/relax-devel/2006-11/msg00098.html (Message-id:
<0E180DBB-896A-45F6-B19D-D6A02FD2BA4A@...>). Rather than changing the line:
env['SHLINKFLAGS'] = SCons.Util.CLVar('$LINKFLAGS -dynamiclib')
in the SCons sources, I have replicated Doug's modification within the relax 'sconstruct' script.
This change needs to be tested.
................
r2791 | bugman | 2006-11-09 19:17:36 +1100 (Thu, 09 Nov 2006) | 10 lines
An attempt to change the shared library suffix from '.dylib' to '.so' on Mac OS X.
This problem was reported by Douglas Kojetin <douglas dot kojetin at gmail dot com> at
https://mail.gna.org/public/relax-users/2006-11/msg00002.html (Message-id:
<AD17DD2D-A37B-44D4-B1B8-1A2349EC7EC5@...>) and as bug #7670 (https://gna.org/bugs/?7670).
To use a different suffix, I have explicitly set the 'SHLIBSUFFIX' environmental variable to '.so'.
This should overwrite the SCons default of '.dylib'.
................
r2792 | bugman | 2006-11-09 20:12:19 +1100 (Thu, 09 Nov 2006) | 7 lines
Modified 'self.vectors()' to place the proton and heteronucleus name in 'self.relax.data.res[run]'.
Previously the names were being placed into 'self.relax.data.pdb[run]' which is problematic for
task #3838 (https://gna.org/task/?3838). This is also preventing the resolution of bug #7544
(https://gna.org/bugs/?7544).
................
r2798 | bugman | 2006-11-10 17:48:15 +1100 (Fri, 10 Nov 2006) | 8 lines
The intensity reading function now counts the number of header lines in the Sparky or XEasy file.
The function 'self.number_of_header_lines()' has been added. This attempts to execute the intensity
reading functions 'self.intensity_sparky()' or 'self.intensity_xeasy()' and if these fail with
either a RelaxError or an IndexError, then the line is considered a header line. The function will
then return the number of header lines.
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r2799 | bugman | 2006-11-10 18:18:32 +1100 (Fri, 10 Nov 2006) | 13 lines
Fix for bug #7676 (https://gna.org/bugs/?7676).
This bug was reported by Stephen Headey <s dot j dot headey at massey dot ac dot nz>. The issue was
originally reported at https://mail.gna.org/public/relax-users/2006-11/msg00003.html (Message-id:
<59ADAF5CA6A8FC4C889BD4097D912BB1072D330D@...>). Together with r2798
(https://mail.gna.org/public/relax-commits/2006-11/msg00096.html) which fixed the issue of not
having 2 header lines, this gives more flexibility in reading XEasy text files.
The function 'self.det_dimensions()' has been added to determine which of w1 or w2 is the proton
dimension. The intensity reading function 'self.intensity_xeasy()' then uses this info to return
the correct proton and heteronucleus names for the given data line.
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r2829 | bugman | 2006-11-13 14:28:58 +1100 (Mon, 13 Nov 2006) | 7 lines
Updated the release checklist.
The HTML user manual construction has been separated from the download page and the compilation of
the API HTML documentation has been added. Detailed instructions on how to announce a relax release
have also been added.
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r2831 | bugman | 2006-11-13 15:09:48 +1100 (Mon, 13 Nov 2006) | 6 lines
Updated the relax core design diagram in the development chapter of the manual.
The user functions were being referred to as macros. The change of name from user function to macro
occurred years ago.
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r2832 | bugman | 2006-11-13 15:17:18 +1100 (Mon, 13 Nov 2006) | 13 lines
Added three flow diagrams to the relax manual describing the steps of model-free analysis.
The first diagram details the steps of the model-free optimisation protocol introduced by Mandel et
al., 1995.
The second presents the changes which occurred with the introduction of AIC model selection,
model elimination of failed models, and the use of all diffusion tensor types.
The last diagram presents the new model-free optimisation protocol encoded into the
'full_analysis.py' sample script (which is described in a manuscript which has been submitted for
publication).
................
r2833 | bugman | 2006-11-13 15:53:11 +1100 (Mon, 13 Nov 2006) | 5 lines
Changes to the model-free optimisation protocol diagrams (relax manual).
Arrows have been added to indicate where to start with the analysis.
................
r2838 | bugman | 2006-11-13 17:24:10 +1100 (Mon, 13 Nov 2006) | 8 lines
Ported r2837 from the 1.2 line.
The command used was:
svn merge -r2836:2837 svn+ssh://bugman@.../svn/relax/1.2
This fixes a bug in the Sparky peak intensity code.
................
r2844 | bugman | 2006-11-15 16:48:15 +1100 (Wed, 15 Nov 2006) | 6 lines
Included the Eufrak font in the model-free optimisation protocol diagrams of the relax manual.
The Eufrak font, which was converted from the font used in the LaTeX eufrak package, was missing
when the images were converted from the SVG files.
................
r2847 | bugman | 2006-11-15 18:24:38 +1100 (Wed, 15 Nov 2006) | 10 lines
Merged the 'tensor_pdb' branch back into the 1.3 line.
The command used was:
svn merge -r2664:2846 svn+ssh://bugman@.../svn/relax/branches/tensor_pdb
This branch arose from the discussions starting with post located at
https://mail.gna.org/public/relax-devel/2006-10/msg00136.html (Message-id:
<7f080ed10610252045r3dcbba38q58aa53142af96e5a@...>).
................
r2848 | bugman | 2006-11-15 19:20:34 +1100 (Wed, 15 Nov 2006) | 6 lines
Renamed the 'pdb' user function class to 'structure'.
For full details, see the post at https://mail.gna.org/public/relax-devel/2006-11/msg00081.html
(Message-id: <7f080ed10611062354i6c4c8601y825585c2c021b9ab@...>).
................
r2849 | bugman | 2006-11-15 19:31:50 +1100 (Wed, 15 Nov 2006) | 10 lines
Because of the previous commit (renaming 'pdb' to 'structure'), much code needed updating.
All calls to the functions of 'self.relax.generic.pdb' were replaced with the equivalent function in
'self.relax.generic.structure'. For example all calls to 'self.relax.generic.pdb.read()' are now
'self.relax.generic.structure.read_pdb'.
All instances of 'self.relax.interpreter._PDB' in the test suite were replaced with
'self.relax.interpreter._Structure'.
................
r2850 | bugman | 2006-11-15 19:35:31 +1100 (Wed, 15 Nov 2006) | 3 lines
Updated the '__init__.py' files for the 'pdb' to 'structure' rename.
................
r2851 | bugman | 2006-11-15 19:41:37 +1100 (Wed, 15 Nov 2006) | 6 lines
Renaming of the user function 'init_data()' to 'reset()'.
For more details see https://mail.gna.org/public/relax-devel/2006-11/msg00145.html (Message-id:
<7f080ed10611102042q55068c56l42aa691764f18d66@...>).
................
r2852 | bugman | 2006-11-15 19:49:05 +1100 (Wed, 15 Nov 2006) | 3 lines
Updated all the sample scripts to use the new PDB reading user function name 'structure.read_pdb()'.
................
r2853 | bugman | 2006-11-15 19:51:57 +1100 (Wed, 15 Nov 2006) | 3 lines
Updated the test suite to call 'reset()' rather than its old name of 'init_data()'.
................
r2856 | bugman | 2006-11-20 14:19:04 +1100 (Mon, 20 Nov 2006) | 10 lines
Partial fix for bug #7787 (https://gna.org/bugs/?7787).
This bug was reported by Stephen Headey (https://gna.org/users/sjheadey).
The issue is that if the 'full_analysis.py' script is improperly used, the error messages don't tell
you what the real issue is. In the bug report, the problem was that only a single round of
optimisation of the sphere, spheroids, and ellipsoid was being run. The 'full_analysis.py' script
has therefore been modified to catch this and throw a RelaxError describing the issue.
................
r2857 | bugman | 2006-11-20 14:35:14 +1100 (Mon, 20 Nov 2006) | 8 lines
Completed the fix for bug #7787 (https://gna.org/bugs/?7787).
This bug was reported by Stephen Headey (https://gna.org/users/sjheadey).
These changes to the 'full_analysis.py' script fixes the problem of fixing the diffusion tensor when
the local_tm model has been selected. Also the relax namespace is now passed into the main class.
................
r2859 | bugman | 2006-11-20 15:26:27 +1100 (Mon, 20 Nov 2006) | 3 lines
Updated the data model redesign planning document to include links to the posts.
................
r2864 | bugman | 2006-11-23 14:58:12 +1100 (Thu, 23 Nov 2006) | 12 lines
Added a function to test for convergence after each round in the 'full_analysis.py' script.
This is in response to the convergence question asked by Sebastien Morin in the post located at
https://mail.gna.org/public/relax-users/2006-11/msg00015.html (Message-id:
<456515E5.6020908@...>).
There are three convergence tests:
Identical chi-squared values.
Identical model-free models.
Identical model-free parameter values.
................
r2865 | bugman | 2006-11-23 15:09:52 +1100 (Thu, 23 Nov 2006) | 3 lines
Added a convergence test for the diffusion parameter values to the 'full_analysis.py' script.
................
r2866 | bugman | 2006-11-23 15:32:24 +1100 (Thu, 23 Nov 2006) | 3 lines
Changed all the references to the old user function class 'pdb' to 'structure'.
................
r2867 | bugman | 2006-11-23 15:34:13 +1100 (Thu, 23 Nov 2006) | 3 lines
Bug fix. 'self.relax.generic.structure.read()' was being called when 'read_pdb()' should be.
................
r2868 | bugman | 2006-11-23 15:38:02 +1100 (Thu, 23 Nov 2006) | 3 lines
Fixed the parameter convergence test in 'full_analysis.py'.
................
r2869 | bugman | 2006-11-23 16:05:49 +1100 (Thu, 23 Nov 2006) | 6 lines
Bug fix.
This fixes a bug introduced by the changes for task #3838 (https://gna.org/task/?3838). It is also
a partial fix for bug #7544 (https://gna.org/bugs/?7544).
................
r2870 | bugman | 2006-11-23 16:21:31 +1100 (Thu, 23 Nov 2006) | 3 lines
Removed some whitespace.
................
r2871 | bugman | 2006-11-23 16:23:22 +1100 (Thu, 23 Nov 2006) | 7 lines
Fixed a bug in the 'full_analysis.py' script for the 1.3 line.
The problem was that task #3838 (https://gna.org/task/?3838) had split the PDB reading user function
from the user function to calculate the unit vector parallel to the XH bond. However the script had
not been updated to call 'structure.vectors()' and hence was not working.
................
r2872 | bugman | 2006-11-23 16:25:01 +1100 (Thu, 23 Nov 2006) | 5 lines
Fixed a bug in the 'full_analysis.py' script whereby 'run.delete()' was being called.
This was destroying the data required for the convergence tests.
................
r2874 | bugman | 2006-11-23 16:39:20 +1100 (Thu, 23 Nov 2006) | 8 lines
Ported r2873 from the 1.2 line.
The command used was:
svn merge -r2872:2873 svn+ssh://bugman@.../svn/relax/1.2
This improves the release checklist.
................
r2878 | bugman | 2006-11-23 16:59:15 +1100 (Thu, 23 Nov 2006) | 7 lines
Bug fix for the failure of model selection in the 'full_analysis.py' script.
Because the 'run.delete()' user function had been removed the 'previous' run, which is a global
model, was being included in the list of runs (m0, m1, m2, etc.) for model selection cause a
failure.
................
r2879 | bugman | 2006-11-23 17:13:06 +1100 (Thu, 23 Nov 2006) | 3 lines
Fixed a bug in the convergence tests where a float was being printed as a string.
................
r2881 | bugman | 2006-11-23 19:01:11 +1100 (Thu, 23 Nov 2006) | 3 lines
Fixed two misspellings of the 'params_converged' flag.
................
r2882 | bugman | 2006-11-23 19:07:41 +1100 (Thu, 23 Nov 2006) | 3 lines
Improvements to the printed out convergence test messages.
................
r2884 | bugman | 2006-11-25 13:49:40 +1100 (Sat, 25 Nov 2006) | 7 lines
Fix for bug #7845 (https://gna.org/bugs/?7845).
This bug was reported by Sébastien Morin (https://gna.org/users/semor).
The fix was to increase the precision of the chi-squared value in the model-free results file.
................
r2886 | bugman | 2006-11-25 18:09:36 +1100 (Sat, 25 Nov 2006) | 7 lines
Removed the PDF user manual from the repository.
As the file is a large (2.6 Mb) binary file and changes often, it has been removed from the
repository. This should stop the relax Subversion repository getting too bign. The manual can
easily be compiled from the sources using Scons.
................
r2888 | bugman | 2006-11-28 14:33:40 +1100 (Tue, 28 Nov 2006) | 8 lines
Fix for bug #7863 (https://gna.org/bugs/index.php?7863).
This bug was reported by Sebastien Morin (https://gna.org/users/semor).
The fix was simply to set 'self.runs' to all the global diffusion models to be used by the AIC model
selection step.
................
r2891 | bugman | 2006-11-30 19:01:16 +1100 (Thu, 30 Nov 2006) | 12 lines
Fix for bug #7875 (https://gna.org/bugs/index.php?7875).
This bug was reported by Sebastien Morin (https://gna.org/users/semor).
The problem was that the 'model_selection()' user function was incorrectly copying the data into the
model selection run when the local tm global diffusion model was selected over the sphere, spheroid,
ellipsoid, etc. The local tm global diffusion model was being treated as a single spin system model
by the 'self.duplicate_data()' function of 'specific_fns/model_free.py' and hence only the data from
the first spin was being duplicated. By passing the 'global_data' flag in from the model selection
code, the data duplication function is now acting correctly.
................
r2893 | bugman | 2006-11-30 19:08:06 +1100 (Thu, 30 Nov 2006) | 3 lines
Added print out messages for when spin systems are being eliminated.
................
r2894 | bugman | 2006-11-30 19:59:47 +1100 (Thu, 30 Nov 2006) | 16 lines
Fix for bug #7755 (https://gna.org/bugs/?7755).
This bug was reported by Stephen Headey (https://gna.org/users/sjheadey).
The problem was that the select_sim array created by the columnar results reading function
'self.read_columnar_results()' in 'specific_fns/model_free.py' was one massive single array
containing all the selected simulation data of all spin systems of all simulations. Subsequently
this was then not being split up for each spin system. Hence the total number of simulations was
being set to the number of spin systems times the number of simulations. The select_sim array for
each spin system was also of the same length and contained the data for all spins.
The fix was to convert the 'select_sim' array being created by 'self.read_columnar_results()' into
a Numeric matrix. The first dimension corresponds to the simulation and the second corresponds to
the instance.
................
r2895 | bugman | 2006-11-30 20:37:25 +1100 (Thu, 30 Nov 2006) | 7 lines
Renamed the Numeric matrix 'select_sim' to 'all_select_sim'.
This matrix contains the Monte Carlo simulation selection status of all spin systems of all
simulations. Hence the name 'all_select_sim' has been chosen to differentiate it from the array
'select_sim' stored at 'self.relax.data.res[run]'.
................
r2896 | bugman | 2006-11-30 20:40:23 +1100 (Thu, 30 Nov 2006) | 6 lines
Fix for bug #7890 (https://gna.org/bugs/index.php?7890).
The columnar results file reading function now turns the Monte Carlo simulation state off after
executing the 'self.relax.generic.monte_carlo.setup()' function.
................
r2897 | bugman | 2006-11-30 21:05:08 +1100 (Thu, 30 Nov 2006) | 6 lines
Fix for bug #7891 (https://gna.org/bugs/index.php?7891).
The fix was to create the 'self.relax.data.res[run][i].heteronuc' and
'self.relax.data.res[run][i].proton' data structures when reading in the model-free results file.
................
r2910 | bugman | 2006-12-02 16:46:28 +1100 (Sat, 02 Dec 2006) | 6 lines
Merged the 'test_suite' branch back into the 1.3 line.
The command used was:
svn merge -r2715:2908 svn+ssh://bugman@.../svn/relax/branches/test_suite
................
r2911 | bugman | 2006-12-03 19:02:05 +1100 (Sun, 03 Dec 2006) | 3 lines
Fixed the running of the test suite through the --test-suite command line flag.
................
r2912 | bugman | 2006-12-03 19:30:33 +1100 (Sun, 03 Dec 2006) | 3 lines
Improvements to the model-free optimisation protocol flow diagrams.
................
r2914 | bugman | 2006-12-07 11:18:22 +1100 (Thu, 07 Dec 2006) | 3 lines
Added a sample script for the creation of the PDB representation of the diffusion tensor.
................
r2915 | bugman | 2006-12-07 11:28:29 +1100 (Thu, 07 Dec 2006) | 3 lines
Fixes for the script for creating the PDB representation of the diffusion tensor.
................
r2916 | bugman | 2006-12-07 11:39:30 +1100 (Thu, 07 Dec 2006) | 3 lines
Renamed all instances of 'create_tensor_pdb' to 'create_diff_tensor_pdb'.
................
r2917 | bugman | 2006-12-07 14:15:12 +1100 (Thu, 07 Dec 2006) | 3 lines
Spun out the XH bond vector calculation code into its own function 'self.xh_vector()'.
................
r2918 | bugman | 2006-12-07 14:28:24 +1100 (Thu, 07 Dec 2006) | 6 lines
Started to created the 'structure.create_vector_dist()' user function.
This function will, when completed, create a PDB representation of the XH bond vectors from the
structure.
................
r2919 | bugman | 2006-12-07 14:33:48 +1100 (Thu, 07 Dec 2006) | 8 lines
Added the method 'self.create_vector_dist()' to 'generic_fns/structure.py'.
This function currently calculates and adds the centre of mass to the PDB file, adds the XH vectors
as protons to the 'self.atomic_data' data structure, and creates the PDB file. The code is
incomplete as each vector is being set to the true residue name and number and ATM record support
still needs to be added.
................
r2920 | bugman | 2006-12-07 14:41:40 +1100 (Thu, 07 Dec 2006) | 6 lines
Changed the format of the PDB representation of the XH vector distribution.
Each XH pair is being created as a proper vector with two atoms rather than all protons connecting
back to a single centre of mass.
................
r2921 | bugman | 2006-12-07 14:53:27 +1100 (Thu, 07 Dec 2006) | 3 lines
Added the ability to create ATOM PDB records within the 'self.write_pdb_file()' method.
................
r2922 | bugman | 2006-12-07 15:34:34 +1100 (Thu, 07 Dec 2006) | 3 lines
Created a symmetric chain 'B' in the PDB representation of the XH vector distribution.
................
r2923 | bugman | 2006-12-07 16:43:09 +1100 (Thu, 07 Dec 2006) | 6 lines
Addition of the user function 'structure.vector_dist()'.
This function will display the PDB representation of the XH vector distribution overlain over the
macromolecular structure within PyMOL.
................
r2924 | bugman | 2006-12-07 17:17:29 +1100 (Thu, 07 Dec 2006) | 5 lines
You can now specify a different column for residue numbers in the selection user functions.
This affects both the 'select.read()' and 'unselect.read()' user functions.
................
r2925 | bugman | 2006-12-07 17:20:05 +1100 (Thu, 07 Dec 2006) | 3 lines
Bug fix, the 'self.sel_read()' function was not expecting the 'column' argment.
................
r2926 | bugman | 2006-12-07 17:33:51 +1100 (Thu, 07 Dec 2006) | 3 lines
The selection user functions which read data from a file now take header lines into account.
................
r2927 | bugman | 2006-12-08 13:21:49 +1100 (Fri, 08 Dec 2006) | 7 lines
Spin systems can now be selected using boolean operators.
The user functions 'select.res()' and 'select.read()' now accept the boolean keyword option which
can be set to 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. The default, and previous behaviour, is
'OR'.
................
r2928 | bugman | 2006-12-08 17:50:44 +1100 (Fri, 08 Dec 2006) | 3 lines
Added a sample script to create a LaTeX longtable of the model-free results.
................
r2931 | bugman | 2006-12-09 12:07:50 +1100 (Sat, 09 Dec 2006) | 7 lines
Bug fix for the plotting of model-free results within Molmol macros.
The fast correlation time macro (te < 100 ps and tf) was setting bond lengths to zero when there
was no parameter. This has been changed so that the bond is now set to a width of 0.3 and is
coloured white.
................
r2933 | bugman | 2006-12-10 13:22:00 +1100 (Sun, 10 Dec 2006) | 3 lines
Changed the model-free Molmol cutoff for fast and slow motions from 100 to 200 ps.
................
r2934 | bugman | 2006-12-10 14:47:56 +1100 (Sun, 10 Dec 2006) | 3 lines
Small fix for the docstring of the 'self._update_object()' function.
................
r2935 | bugman | 2006-12-10 17:59:55 +1100 (Sun, 10 Dec 2006) | 3 lines
A few fixes to the 'structure.create_vector_dist()' user function docstring.
................
r2936 | bugman | 2006-12-22 14:37:08 +1100 (Fri, 22 Dec 2006) | 8 lines
A small change to clarify the error message produced by bug #8059 (https://gna.org/bugs/?8059).
See the post at https://mail.gna.org/public/relax-devel/2006-12/msg00027.html (Message-id:
<7f080ed10612210231l17934be5k7b614ab38f1b09d@...>) for more details.
Instead of returning None when no diffusion tensor data is present, a RelaxNoTensorError is raised.
................
r2939 | bugman | 2007-01-06 14:37:49 +1100 (Sat, 06 Jan 2007) | 6 lines
Fix for bug #8182 (https://gna.org/bugs/index.php?8182).
The fix was to change the class string 'boolean_doc' of the selection prompt class into a private
variable.
................
r2949 | bugman | 2007-01-06 21:06:52 +1100 (Sat, 06 Jan 2007) | 7 lines
Fix for bug #8187 (https://gna.org/bugs/?8187).
The model-free results writing function was expecting the spin system specific data structures
'heteronuc' and 'proton' to exist however they only exist if the user function 'structure.vectors()'
has been called. Now None is supplied to the line writing function if they're not there.
................
r2993 | bugman | 2007-01-12 16:02:08 +1100 (Fri, 12 Jan 2007) | 12 lines
Ported r2982 from the 1.2.10 tag using the command:
svn merge -r2981:2982 svn+ssh://bugman@.../svn/relax/tags/1.2.10
........
r2982 | bugman | 2007-01-12 13:54:15 +1100 (Fri, 12 Jan 2007) | 3 lines
Changed paths:
M /tags/1.2.10/docs/CHANGES
Updated the CHANGES file for relax version 1.2.10.
........
................
r2994 | bugman | 2007-01-13 15:11:00 +1100 (Sat, 13 Jan 2007) | 10 lines
Rearrangement of the diffusion tensor parameter calculation functions.
These changes are part of the solution for bug #7979 (https://gna.org/bugs/?7979).
The 'self._calc_x()' methods of the DiffTensorElement class, where x is a diffusion tensor
parameter, vector, or matrix, have been shifted from the 'data' directory to the diffusion tensor
code of the 'generic_fns' directory. The methods have also been converted into module functions.
The 'self._update_object()' method calls in the 'self.__setattr__()' method have been modified so
that the type of diffusion is passed into the necessary 'calc_x()' functions.
................
r2995 | bugman | 2007-01-13 15:20:50 +1100 (Sat, 13 Jan 2007) | 7 lines
Changed the diffusion tensor MC sim objects from lists to the ListType 'DiffTensorSimList'.
These changes are part of the solution for bug #7979 (https://gna.org/bugs/?7979).
The 'append()' and '__setattr__()' methods of 'DiffTensorSimList' have been set to dummy functions.
................
r2996 | bugman | 2007-01-13 16:51:55 +1100 (Sat, 13 Jan 2007) | 3 lines
Added an initial unit test framework for testing of the diffusion tensor objects.
................
r2997 | bugman | 2007-01-13 17:03:35 +1100 (Sat, 13 Jan 2007) | 3 lines
Set the executable bit on the diffusion tensor data structure test module.
................
r2998 | bugman | 2007-01-13 17:39:38 +1100 (Sat, 13 Jan 2007) | 3 lines
Spell check of the 'unit_test_runner' module.
................
r2999 | bugman | 2007-01-13 17:46:48 +1100 (Sat, 13 Jan 2007) | 6 lines
Modified the system/functional + unit test running code so that only the true unit tests are run.
The current setup was looking for unit tests throughout the relax source tree and accidentally
running the code in the file 'minimise/line_search/test_functions.py'.
................
r3000 | bugman | 2007-01-13 18:09:15 +1100 (Sat, 13 Jan 2007) | 3 lines
Completed the 'test_set_Diso()' and 'test_set_tm()' unit tests.
................
r3001 | bugman | 2007-01-13 18:26:12 +1100 (Sat, 13 Jan 2007) | 3 lines
Modified the 'test_set_Diso' and 'test_set_tm' unit tests to use the proper assert functions.
................
r3002 | bugman | 2007-01-13 18:32:59 +1100 (Sat, 13 Jan 2007) | 6 lines
Modified the 'test_set_Diso' unit test.
Rather than testing the RelaxError message string, the 'self.assertRaises()' function is called to
assert that a RelaxError must occur.
................
r3003 | bugman | 2007-01-13 18:37:06 +1100 (Sat, 13 Jan 2007) | 6 lines
Modification of the 'test_set_tm' diffusion tensor data structure unit test.
After setting the tm parameter, the automatically generated Diso parameter is tested to see if it is
correctly set.
................
r3004 | bugman | 2007-01-13 21:00:17 +1100 (Sat, 13 Jan 2007) | 7 lines
Changes to the output formatting functions of the test suite.
The methods 'self.heading()' and 'self.summary_line()' have been converted to functions and have
been shifted from the file 'test_suite/system_tests/main.py' into the new file
'test_suite/formatting.py'. The final printout by 'test_suite/runner.py' now used these functions.
................
r3005 | bugman | 2007-01-13 21:21:47 +1100 (Sat, 13 Jan 2007) | 5 lines
Added the '--unit-test' command line argument.
Supplying this argument to relax will cause solely the unit tests of the test suite to be run.
................
r3006 | bugman | 2007-01-13 23:20:29 +1100 (Sat, 13 Jan 2007) | 6 lines
Added the diffusion tensor data structure unit test 'test_set_prolate_params'.
This test checks that all the parameters, vectors, and matrices associated with the prolate
spheroidal diffusion tensor are set up correctly.
................
r3007 | bugman | 2007-01-13 23:23:37 +1100 (Sat, 13 Jan 2007) | 3 lines
Renamed the unit test 'test_set_prolate_params' to 'test_set_spheroid_params'.
................
r3008 | bugman | 2007-01-13 23:31:39 +1100 (Sat, 13 Jan 2007) | 6 lines
Shifted the calculation of the diffusion objects from the 'test_set_spheroid_params' unit test.
These are now calculated by the method 'self.calc_spheroid_objects()' so that it can be used by
unit tests for the setting of spheroidal errors and simulation values.
................
r3009 | bugman | 2007-01-13 23:40:07 +1100 (Sat, 13 Jan 2007) | 3 lines
Added the diffusion tensor object unit test 'test_set_spheroid_errors'.
................
r3010 | bugman | 2007-01-13 23:52:49 +1100 (Sat, 13 Jan 2007) | 6 lines
Added the unit test 'test_append_spheroid_sim'.
This test checks that the appending of Monte Carlo simulation spheroidal diffusion tensor parameters
works OK.
................
r3011 | bugman | 2007-01-14 00:03:07 +1100 (Sun, 14 Jan 2007) | 7 lines
Added the unit test 'test_set_spheroid_sim'.
This test checks the setting of Monte Carlo simulation spheroidal diffusion tensor parameters making
sure that the diffusion tensor objects are correctly created and that the previous values have been
properly overwritten.
................
r3013 | bugman | 2007-02-17 20:43:57 +1100 (Sat, 17 Feb 2007) | 3 lines
Renamed the object 'base_name' to 'param_name'.
................
r3014 | bugman | 2007-02-17 20:58:58 +1100 (Sat, 17 Feb 2007) | 3 lines
Small changes to the 'DiffTensorSimList' object.
................
r3015 | bugman | 2007-02-18 10:36:48 +1100 (Sun, 18 Feb 2007) | 5 lines
Modified the diffusion tensor data structure unit test for setting the tm parameter.
Now the spherical diffusion tensor type is initially set.
................
r3016 | bugman | 2007-02-18 10:48:21 +1100 (Sun, 18 Feb 2007) | 7 lines
Created the generator function 'dependency_generator()'.
This generator is for looping over the list of target parameters to update when a parameter is set.
It replaces all the self._update_object() calls and simplifies the code. It will also be used for
updating the Monte Carlo simulation data structures.
................
r3017 | bugman | 2007-02-18 11:25:05 +1100 (Sun, 18 Feb 2007) | 6 lines
Modifications to the DiffTensorSimList object.
The self.__setitem__() function now sets the value and the parent DiffTensorElement is now passed
into the DiffTensorSimList object.
................
r3018 | bugman | 2007-02-18 16:40:36 +1100 (Sun, 18 Feb 2007) | 13 lines
Fix for bug #7979 (https://gna.org/bugs/?7979).
A large number of changes were required. Two private functions 'self.__update_sim_append()' and
'self.__update_sim_set()' have been added to the DiffTensorElement class. These are used to
automatically update the Monte Carlo simulation parameter lists.
The name 'dependencies' is now properly spelt.
The unused Monte Carlo simulation code in the function 'self._update_object()' has been deleted.
The object DiffTensorSimList has been modifed to handle the two new private functions.
................
r3019 | bugman | 2007-02-18 16:41:37 +1100 (Sun, 18 Feb 2007) | 3 lines
Renamed the function 'self._update_object()' to the private function 'self.__update_object()'.
................
r3020 | bugman | 2007-02-18 16:50:07 +1100 (Sun, 18 Feb 2007) | 3 lines
Bug fix. Fixed a typo committed in the last revision.
................
r3021 | bugman | 2007-02-18 17:06:24 +1100 (Sun, 18 Feb 2007) | 3 lines
Removed Gary's dummy functions to allow the unit test and test suite to pass.
................
r3022 | bugman | 2007-02-18 18:01:39 +1100 (Sun, 18 Feb 2007) | 3 lines
Modified the unit test runner to return True if the tests pass and Fail if they fail.
................
r3025 | bugman | 2007-02-19 19:22:14 +1100 (Mon, 19 Feb 2007) | 12 lines
Ported r3024 from the 1.3.0 tag using the command:
svn merge -r3023:3024 svn+ssh://bugman@.../svn/relax/tags/1.3.0
........
r3024 | bugman | 2007-02-19 19:17:37 +1100 (Mon, 19 Feb 2007) | 3 lines
Changed paths:
M /tags/1.3.0/docs/CHANGES
Updated the changes file for relax version 1.3.0.
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r3033 | varioustoxins | 2007-02-20 21:02:10 +1100 (Tue, 20 Feb 2007) | 2 lines
changes to allow command line unit tests to run
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r3034 | bugman | 2007-02-27 14:20:57 +1100 (Tue, 27 Feb 2007) | 3 lines
Fixed the relax_path variable in the diffusion tensor data structure unit tests.
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