Author: bugman
Date: Mon Jun 2 13:38:51 2008
New Revision: 6305
URL: http://svn.gna.org/viewcvs/relax?rev=6305&view=rev
Log:
Blocked revisions
2506,2579,2582,2594,2596,2598,2601-2604,2606-2610,2613-2615,2617,2633,2645,2649-2655,2657,2659,2661,2663,2668-2670,2673,2675-2676,2707,2717,2719,2724,2732-2733,2737,2739,2743,2769,2775,2779,2781,2785,2790-2792,2798-2799,2829,2831-2833,2838,2844,2847-2853,2856-2857,2859,2864-2872,2874,2878-2879,2881-2882,2884,2886,2888,2891,2893-2897,2910-2912,2914-2928,2931,2933-2936,2939,2949,2993-3011,3013-3022,3025,3033-3034,3058,3074-3075,3077,3080-3081,3086,3088-3096,3098,3100-3116,3121-3171,3173-3194,3196-3197,3200-3207,3209,3211-3234,3240,3245,3247,3255-3258,3260,3286,3290,3297,3303-3308,3333,3339-3340,3342,3346,3352,3355,3359,3369,3379,3382-3524,3528-3529,3540-3691,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757,3773-3807,3809-3833,3836-3838,3840-3869,3872-3905,3907-3974,3976-3986,4004,4014-4015,4018-4021,4027-4031,4061-4102,4104-4114,4137-4139,4141,4144,4146-4175,4223,4241-4253,4255-4262,4264-4270,4272-4274,4276-4291,4293-4295,4297-4298,4300,4302-4305,4307-4335,4338-4372,4374-4398,4402-4419,4424,4426-4428,4430-4433,4440,4447,4449-4450,4452-4458,4461,4481-4493,4523-4527,4529-4547,4549-4551,4567,4569,4571-4572,4575-4577,4579,4585-4586,4618,4621-4623,4659,4662-4671,4673-4693,4698-4701,4712-4717,4745,4748,4759,4778-4780,4785,4787,4792,4796,4799,4802,4804,4815-4819,4821-4834,4839,4841-4850,4854-4856,4858-4860,4886-4888,4898-4936,4970-4971,5003,5005-5006,5008-5010,5013,5015-5023,5033-5037,5040-5045,5047,5056,5058-5060,5063,5065,5067,5069,5071,5074,5076,5079,5081,5085,5087,5089,5091-5115,5136-5233,5236,5238,5240,5247-5248,5250-5253,5258-5272,5274,5276-5394,5400-5461,5466-5501,5506-5603,5605-5610,5615-5621,5625-5627,5629-5662,5664-5707,5709,5721-5725,5727-5728,5730-5791,5793,5795-5814,5825-5968,5973-6012,6015-6016,6018,6026-6032,6036-6040,6043,6046-6055,6101-6103,6110-6248,6257-6259,6261-6304
via svnmerge
................
r2506 | bugman | 2006-07-06 07:25:51 +0200 (Thu, 06 Jul 2006) | 3 lines
Creation of the 1.3 developmental branch for the MPI and any other
destabilising changes.
................
r2579 | bugman | 2006-09-20 10:21:09 +0200 (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@xxxxxxxxxxx/svn/relax/1.2
................
r2582 | bugman | 2006-09-30 06:20:04 +0200 (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@xxxxxxxxxxx/svn/relax/1.2
This includes a fix for bug #7192 and a few other superficial changes.
................
r2594 | bugman | 2006-10-01 07:19:37 +0200 (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@xxxxxxxxxxx/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.
................
r2596 | bugman | 2006-10-01 07:32:19 +0200 (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@xxxxxxxxxxx/svn/relax/1.2
This changes the CSA value in the sample scripts to -172 ppm.
................
r2598 | bugman | 2006-10-01 10:20:53 +0200 (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.
................
r2601 | bugman | 2006-10-06 08:55:01 +0200 (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@xxxxxxxxxxxxxx>).
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()'.
................
r2602 | bugman | 2006-10-07 10:49:58 +0200 (Sat, 07 Oct 2006) | 8 lines
Ported r2599 from the 1.2 line.
The command used was:
$ svn merge -r2598:2599 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This changes 'Sconstruct' to 'SCons' in the relax manual.
................
r2603 | bugman | 2006-10-07 10:52:57 +0200 (Sat, 07 Oct 2006) | 8 lines
Ported r2600 from the 1.2 line.
The command used was:
svn merge -r2599:2600 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This fixes bug #7297 (https://gna.org/bugs/index.php?7297).
................
r2604 | bugman | 2006-10-07 13:28:39 +0200 (Sat, 07 Oct 2006) | 3 lines
Created the JOBS file. This file describes the roles of the relax manager
positions.
................
r2606 | bugman | 2006-10-07 17:35:24 +0200 (Sat, 07 Oct 2006) | 8 lines
Ported r2605 from the 1.2 line.
The command used was:
$ svn merge -r2604:2605 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This fixes bug #7277 (https://gna.org/bugs/?7277).
................
r2607 | bugman | 2006-10-07 19:13:42 +0200 (Sat, 07 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.
................
r2608 | bugman | 2006-10-07 19:24:08 +0200 (Sat, 07 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'.
................
r2609 | bugman | 2006-10-07 19:37:56 +0200 (Sat, 07 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.
................
r2610 | bugman | 2006-10-07 19:46:37 +0200 (Sat, 07 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.
................
r2613 | bugman | 2006-10-12 05:20:26 +0200 (Thu, 12 Oct 2006) | 8 lines
Ported r2611 from the 1.2 line.
The command used was:
$ svn merge -r2610:2611 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This adds the directory for Scons Python modules for the Builder functions.
................
r2614 | bugman | 2006-10-12 05:23:22 +0200 (Thu, 12 Oct 2006) | 8 lines
Ported r2612 from the 1.2 line.
The command used was:
$ svn merge -r2611:2612 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This completes the fixing of bug #7241 (https://gna.org/bugs/?7241).
................
r2615 | bugman | 2006-10-12 05:29:26 +0200 (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.
................
r2617 | bugman | 2006-10-12 05:46:16 +0200 (Thu, 12 Oct 2006) | 8 lines
Ported r2616 from the 1.2 line.
The command used was:
$ svn merge -r2615:2616 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This removes the ancient unused file 'maths_fns/test.c_chi.py'.
................
r2633 | bugman | 2006-10-12 09:43:25 +0200 (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@xxxxxxxxxxx/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.
................
r2645 | bugman | 2006-10-17 06:41:14 +0200 (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@xxxxxxxxxxxxxx>).
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@xxxxxxxxxxxxxx>). Another
failure was reported by
Alex at https://mail.gna.org/public/relax-devel/2006-10/msg00096.html
(Message-id:
<481156b20610130728jb6aa76ag3d9487a20397391b@xxxxxxxxxxxxxx).
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@xxxxxxxxxxxxxx>).
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.
................
r2649 | bugman | 2006-10-17 07:09:57 +0200 (Tue, 17 Oct 2006) | 8 lines
Ported r2635 from the 1.2 line.
The command used was:
$ svn merge -r2634:2635 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This involves a few functions moving to the new Scons module file
'scons/distrib.py'.
................
r2650 | bugman | 2006-10-17 07:13:09 +0200 (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@xxxxxxxxxxx/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.
................
r2651 | bugman | 2006-10-17 07:14:48 +0200 (Tue, 17 Oct 2006) | 8 lines
Ported r2641 from the 1.2 line.
The command used was:
$ svn merge -r2640:2641 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This fixes documentation bug #7402 (https://gna.org/bugs/?7402).
................
r2652 | bugman | 2006-10-17 07:20:48 +0200 (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@xxxxxxxxxxx/svn/relax/1.2
$ svn merge -r2643:2644 svn+ssh://bugman@xxxxxxxxxxx/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.
................
r2653 | bugman | 2006-10-17 07:22:34 +0200 (Tue, 17 Oct 2006) | 8 lines
Ported r2643 from the 1.2 line.
The command used was:
$ svn merge -r2642:2643 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
This includes a few small formatting changes to the model-free file.
................
r2654 | bugman | 2006-10-17 07:33:14 +0200 (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@xxxxxxxxxxx/svn/relax/1.2
This adds a number of model-free optimisation tests to the test suite.
................
r2655 | bugman | 2006-10-20 13:57:49 +0200 (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@xxxxxxxxxxxxxx>).
The simple fix is
described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html
(Message-id:
<7f080ed10610190738g7df6566fl13b74d9217071924@xxxxxxxxxxxxxx>).
................
r2657 | macraild | 2006-10-20 17:21:10 +0200 (Fri, 20 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
................
r2659 | bugman | 2006-10-22 11:51:57 +0200 (Sun, 22 Oct 2006) | 9 lines
Ported r2658 from the 1.2 line.
The command used was:
$ svn merge -r2657:2658 svn+ssh://bugman@xxxxxxxxxxx/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.
................
r2661 | bugman | 2006-10-23 10:28:26 +0200 (Mon, 23 Oct 2006) | 9 lines
Ported r2660 from the 1.2 line.
The command used was:
$ svn merge -r2659:2660 svn+ssh://bugman@xxxxxxxxxxx/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.
................
r2663 | macraild | 2006-10-23 11:09:37 +0200 (Mon, 23 Oct 2006) | 8 lines
Roll-back of revision 2656 from 1.3 line:
svn merge -r 2657:2656 svn+ssh://macraild@xxxxxxxxxxx/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
................
r2668 | bugman | 2006-10-26 09:52:51 +0200 (Thu, 26 Oct 2006) | 3 lines
Fixed a bug whereby the match re function had not been imported.
................
r2669 | bugman | 2006-10-26 10:09:12 +0200 (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.
................
r2670 | bugman | 2006-10-26 10:17:45 +0200 (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.
................
r2673 | bugman | 2006-10-26 11:16:54 +0200 (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@xxxxxxxxxxx/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.
................
r2675 | bugman | 2006-10-27 10:38:40 +0200 (Fri, 27 Oct 2006) | 10 lines
Ported r2674 from the 1.2 line.
The command used was:
$ svn merge -r2673:2674 svn+ssh://bugman@xxxxxxxxxxx/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@xxxxxxxxxxxxxx>) for the
exact details.
................
r2676 | bugman | 2006-10-27 10:50:44 +0200 (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.
................
r2707 | bugman | 2006-10-31 08:31:08 +0100 (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@xxxxxxxxxxx/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'.
................
r2717 | varioustoxins | 2006-10-31 13:02:39 +0100 (Tue, 31 Oct 2006) | 9
lines
ported r2634,r2636 & r2716 to the 1.3 line
commands used
svn merge -r2633:2634 svn+ssh://varioustoxins@xxxxxxxxxxx/svn/relax/1.2
svn merge -r2635:2636 svn+ssh://varioustoxins@xxxxxxxxxxx/svn/relax/1.2
svn merge -r2715:2716 svn+ssh://varioustoxins@xxxxxxxxxxx/svn/relax/1.2
these changes add the ieee-754 nan/inf code and and add nan catching
................
r2719 | macraild | 2006-10-31 17:49:36 +0100 (Tue, 31 Oct 2006) | 5 lines
Impliments the io.file_root() function.
As suggested:
https://mail.gna.org/public/relax-devel/2006-10/msg00218.html
................
r2724 | bugman | 2006-11-02 05:23:44 +0100 (Thu, 02 Nov 2006) | 3 lines
Changed the comment of the 'RelaxNoPdbChainError' class to the correct
explanation.
................
r2732 | bugman | 2006-11-04 06:12:26 +0100 (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.
................
r2733 | bugman | 2006-11-04 06:18:05 +0100 (Sat, 04 Nov 2006) | 9 lines
Ported r2731 from the 1.2 line.
The command used was:
svn merge -r2730:2731 svn+ssh://bugman@xxxxxxxxxxx/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.
................
r2737 | bugman | 2006-11-04 06:52:05 +0100 (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@xxxxxxxxxxx/svn/relax/1.2
................
r2739 | bugman | 2006-11-04 08:08:14 +0100 (Sat, 04 Nov 2006) | 10 lines
Ported r2738 from the 1.2 line.
The command used was:
svn merge -r2737:2738 svn+ssh://bugman@xxxxxxxxxxx/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.
................
r2743 | bugman | 2006-11-04 09:31:37 +0100 (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@xxxxxxxxxxx/svn/relax/tags/1.2.8
................
[... 12082 lines stripped ...]
r6305 - /1.2/