Author: bugman Date: Fri Feb 18 17:51:38 2011 New Revision: 12574 URL: http://svn.gna.org/viewcvs/relax?rev=12574&view=rev Log: Merged revisions 12423-12429,12431-12448,12450,12453,12460,12517-12520,12550-12552,12554-12563,12566 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ r12423 | bugman | 2011-01-21 18:53:04 +0100 (Fri, 21 Jan 2011) | 3 lines *.old files are now removed by the HTML user manual cleaning script. ................ r12424 | bugman | 2011-01-21 18:54:25 +0100 (Fri, 21 Jan 2011) | 6 lines The relax website http://nmr-relax.com is now referenced in the HTML version of the user manual. A new button in the navigation bar has been added for this. See http://www.nmr-relax.com/manual/1.3/relax.html (once the new 1.3.9 version of relax is released). ................ r12425 | bugman | 2011-01-21 18:55:09 +0100 (Fri, 21 Jan 2011) | 6 lines Big improvements to the HTML user manual generation. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html once relax version 1.3.9 is released. ................ r12426 | bugman | 2011-01-22 17:59:44 +0100 (Sat, 22 Jan 2011) | 3 lines The HTML user manual cleaning script now removes all *.css files. ................ r12427 | bugman | 2011-01-22 21:12:14 +0100 (Sat, 22 Jan 2011) | 3 lines Created an init file for latex2html so that the figures not in this directory are included. ................ r12428 | bugman | 2011-01-22 21:47:08 +0100 (Sat, 22 Jan 2011) | 3 lines Added custom icons for the HTML user manual navigation bar. ................ r12429 | bugman | 2011-01-22 21:47:48 +0100 (Sat, 22 Jan 2011) | 3 lines Added the relax title and custom icon path to the latex2html config file. ................ r12431 | bugman | 2011-01-22 21:55:44 +0100 (Sat, 22 Jan 2011) | 3 lines The grey icons are now properly named. ................ r12432 | bugman | 2011-01-22 22:15:37 +0100 (Sat, 22 Jan 2011) | 5 lines Fixes for the navigation icons sizes in the HTML user manual. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html. ................ r12433 | bugman | 2011-01-22 22:17:10 +0100 (Sat, 22 Jan 2011) | 5 lines Increased the splitting level by one. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12434 | bugman | 2011-01-22 22:19:51 +0100 (Sat, 22 Jan 2011) | 7 lines The PDF version of the user manual is being partly compiled before the HTML version. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. The aim is to have the aux and bbl files made so latex2html can use them. ................ r12435 | bugman | 2011-01-22 22:20:22 +0100 (Sat, 22 Jan 2011) | 3 lines Created the dir var for storing the target directory. ................ r12436 | bugman | 2011-01-22 22:21:07 +0100 (Sat, 22 Jan 2011) | 5 lines Removed the -no-math option to hopefully decrease the number of images in the HTML user manual. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12437 | bugman | 2011-01-22 22:40:31 +0100 (Sat, 22 Jan 2011) | 5 lines Improved the quality of the maths equation images in the HTML user manual. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12438 | bugman | 2011-01-22 22:56:16 +0100 (Sat, 22 Jan 2011) | 5 lines Added footnote and crossref icons to the HTML user manual. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12439 | bugman | 2011-01-22 23:11:18 +0100 (Sat, 22 Jan 2011) | 5 lines Set the font size to 12pt in the HTML user manual. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12440 | bugman | 2011-01-22 23:12:08 +0100 (Sat, 22 Jan 2011) | 5 lines The sections numbers from the PDF manual are now shown. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12441 | bugman | 2011-01-24 16:34:34 +0100 (Mon, 24 Jan 2011) | 7 lines Removed http://nmr-relax.com from the bottom of all the HTML user manual pages. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. http://nmr-relax.com is redundant due to all the http://nmr-relax.com links in the navigation bar. ................ r12442 | bugman | 2011-01-24 16:37:45 +0100 (Mon, 24 Jan 2011) | 5 lines Shifted the -local_icons commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12443 | bugman | 2011-01-24 16:39:12 +0100 (Mon, 24 Jan 2011) | 5 lines Shifted the -html_version commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12444 | bugman | 2011-01-24 16:41:33 +0100 (Mon, 24 Jan 2011) | 5 lines hifted the -split commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12445 | bugman | 2011-01-24 16:42:55 +0100 (Mon, 24 Jan 2011) | 5 lines Shifted the -auto_navigation commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12446 | bugman | 2011-01-24 16:44:41 +0100 (Mon, 24 Jan 2011) | 5 lines Shifted the -external_file commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12447 | bugman | 2011-01-24 16:46:00 +0100 (Mon, 24 Jan 2011) | 5 lines Shifted the -antialias commmand line arg into the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12448 | bugman | 2011-01-24 16:46:50 +0100 (Mon, 24 Jan 2011) | 5 lines The antialiasing is now actually in the latex2html init file. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. ................ r12450 | bugman | 2011-01-25 09:30:32 +0100 (Tue, 25 Jan 2011) | 7 lines Forced titles into the navigation bar images in the HTML user manual by tricking latex2html. This will be visible at http://www.nmr-relax.com/manual/1.3/relax.html with a new relax release. The titles were added to the image size strings. ................ r12453 | bugman | 2011-01-26 21:01:43 +0100 (Wed, 26 Jan 2011) | 14 lines Merged the changes to the CHANGES file from the 1.3.9 tag. The command used was: svn merge -r12451:12452 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.9 ..... r12452 | bugman | 2011-01-26 20:59:51 +0100 (Wed, 26 Jan 2011) | 3 lines Changed paths: M /tags/1.3.9/docs/CHANGES Updated the CHANGES file for relax version 1.3.9 (see http://www.nmr-relax.com/download.html). ..... ................ r12460 | bugman | 2011-01-28 18:47:24 +0100 (Fri, 28 Jan 2011) | 7 lines Fixes for 2 model-free system tests for a new system which again shows optimisation differences :S The results are from Tiago Pais <tpais att itqb dott unl dott pt> (Message-id: <BA08C06336CE4466990EBAFB59D7DFCF@Mercurio>, https://mail.gna.org/public/relax-users/2011-01/msg00029.html. ................ r12517 | bugman | 2011-02-07 19:00:09 +0100 (Mon, 07 Feb 2011) | 5 lines Fix for the N-state model error returning method for when errors are not present. The spin_id variable was not defined. ................ r12518 | bugman | 2011-02-07 19:07:19 +0100 (Mon, 07 Feb 2011) | 3 lines Fix for the calls to RelaxError in the N-state model return_error() method. ................ r12519 | bugman | 2011-02-09 13:20:35 +0100 (Wed, 09 Feb 2011) | 3 lines Added checks showing that Monte Carlo simulations in the N-state model modify the Q factors. ................ r12520 | bugman | 2011-02-09 13:23:19 +0100 (Wed, 09 Feb 2011) | 7 lines The optimisation of Monte Carlo simulations no longer changes the Q factors and back calculated data. There was a bug in which the back calculated RDCs and PCSs, as well as the Q factors were being calculated for each Monte Carlo simulation but stored in the non-MC sim data structures. Therefore after MC sims, the Q factor and back calculated data would be that of the last simulation!!! ................ r12550 | bugman | 2011-02-18 11:31:46 +0100 (Fri, 18 Feb 2011) | 3 lines Initialized merge tracking via "svnmerge" with revisions "1-11635" from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import ................ r12551 | bugman | 2011-02-18 11:33:18 +0100 (Fri, 18 Feb 2011) | 79 lines Merged revisions 11636-11637,12535-12547,12549 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import ........ r11636 | michaelbieri | 2010-10-11 00:25:46 +0200 (Mon, 11 Oct 2010) | 2 lines Example outputfiles of BRUKER Protein Dynamic Center (PDC) were added. ........ r11637 | michaelbieri | 2010-10-11 03:42:10 +0200 (Mon, 11 Oct 2010) | 4 lines Function to import BRUKER Protein Dynamic Center project is added. The import will be converted to a relax formatted parameter file, either as a dummy file or saved at a specified location. ........ r12535 | bugman | 2011-02-17 16:14:49 +0100 (Thu, 17 Feb 2011) | 7 lines Updated the PDC R1 data file to version 1.1.5. This file was sent by Klaus-Peter Neidig <peter dot neidig att bruker-biospin dot de> in the message https://mail.gna.org/public/relax-devel/2011-01/msg00043.html (Message-id: <4D3ED3AC.20107@xxxxxxxxxxxxxxxxx>). ........ r12536 | bugman | 2011-02-17 16:22:15 +0100 (Thu, 17 Feb 2011) | 3 lines Created the prompt/script interface to the pdc.read() user function. ........ r12537 | bugman | 2011-02-17 16:25:56 +0100 (Thu, 17 Feb 2011) | 3 lines Create a stub of a back-end for the pdc.read() user function. ........ r12538 | bugman | 2011-02-17 16:42:14 +0100 (Thu, 17 Feb 2011) | 3 lines Added a sequence file for the data in these test PDC files. ........ r12539 | bugman | 2011-02-17 16:59:31 +0100 (Thu, 17 Feb 2011) | 3 lines Added a basic system test for the loading of a PDC file. ........ r12540 | bugman | 2011-02-17 17:00:44 +0100 (Thu, 17 Feb 2011) | 3 lines Added some missing imports. ........ r12541 | bugman | 2011-02-17 17:01:25 +0100 (Thu, 17 Feb 2011) | 3 lines Typo fix for the PDC reading system test. ........ r12542 | bugman | 2011-02-17 17:30:24 +0100 (Thu, 17 Feb 2011) | 3 lines Implemented the reading of relaxation data from the PDC file. ........ r12543 | bugman | 2011-02-17 17:31:45 +0100 (Thu, 17 Feb 2011) | 3 lines The PDC system test has been loosened - the precision is not perfect. ........ r12544 | bugman | 2011-02-17 17:34:53 +0100 (Thu, 17 Feb 2011) | 3 lines Added some checks for the current data pipe relaxation data structures to the PDC reading system test. ........ r12545 | bugman | 2011-02-18 10:23:00 +0100 (Fri, 18 Feb 2011) | 3 lines The temperature from the PDC file is now being read, although it isn't used yet. ........ r12546 | bugman | 2011-02-18 10:23:37 +0100 (Fri, 18 Feb 2011) | 3 lines The 'Labelling' line from the PDC file is now used to set the heteronucleus type and spin name. ........ r12547 | bugman | 2011-02-18 10:41:25 +0100 (Fri, 18 Feb 2011) | 5 lines Implemented the code for reading the peak intensity type. This is not active yet as it can only be used in the BMRB branch. ........ r12549 | bugman | 2011-02-18 11:25:45 +0100 (Fri, 18 Feb 2011) | 5 lines Fix for the integration method block in the pdc.read() back end. The commented out code requires at least some code in the block. ........ ................ r12552 | bugman | 2011-02-18 11:35:40 +0100 (Fri, 18 Feb 2011) | 3 lines Removed merge tracking for "svnmerge" for svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bruker_import ................ r12554 | bugman | 2011-02-18 12:41:55 +0100 (Fri, 18 Feb 2011) | 3 lines Added some data files and scripts for checking the consistency of the PDC data verse relax's data. ................ r12555 | bugman | 2011-02-18 12:45:09 +0100 (Fri, 18 Feb 2011) | 3 lines Some cosmetic changes to the PDC data conversion test script. ................ r12556 | bugman | 2011-02-18 14:20:06 +0100 (Fri, 18 Feb 2011) | 3 lines Added a relax script and R1 data file for relax's optimisation and MC sims using the PDC file errors. ................ r12557 | bugman | 2011-02-18 14:24:01 +0100 (Fri, 18 Feb 2011) | 3 lines Created the peak height error file errors_R1.txt from testT1.txt. ................ r12558 | bugman | 2011-02-18 14:24:52 +0100 (Fri, 18 Feb 2011) | 3 lines Added residue name and number info to the print out of the convert_data.py PDC file script. ................ r12559 | bugman | 2011-02-18 14:32:10 +0100 (Fri, 18 Feb 2011) | 3 lines Added a script for converting the PDC NOE data into Python lists. ................ r12560 | bugman | 2011-02-18 14:37:50 +0100 (Fri, 18 Feb 2011) | 3 lines Added a system test for the reading of a PDC NOE file. ................ r12561 | bugman | 2011-02-18 14:49:43 +0100 (Fri, 18 Feb 2011) | 3 lines Fix for the NOE PDC data conversion script. ................ r12562 | bugman | 2011-02-18 14:50:37 +0100 (Fri, 18 Feb 2011) | 5 lines Fix for the test_pdc_read_noe() PDC file reading system test. The NOE values were actually the errors. ................ r12563 | bugman | 2011-02-18 14:51:49 +0100 (Fri, 18 Feb 2011) | 3 lines Some fixes for the pdc.read() back end so that PDC NOE data files can be read properly. ................ r12566 | bugman | 2011-02-18 15:19:21 +0100 (Fri, 18 Feb 2011) | 13 lines Merged the changes to the CHANGES file from the 1.3.10 tag. The command used was: svn merge -r12564:12565 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.10 ..... r12565 | bugman | 2011-02-18 15:18:06 +0100 (Fri, 18 Feb 2011) | 3 lines Changed paths: M /tags/1.3.10/docs/CHANGES Updated the CHANGES file for relax version 1.3.10 (see http://www.nmr-relax.com/download.html). ..... ................ Added: branches/relax_disp/docs/html/icons/ - copied from r12566, 1.3/docs/html/icons/ branches/relax_disp/docs/latex/.latex2html-init - copied unchanged from r12566, 1.3/docs/latex/.latex2html-init branches/relax_disp/generic_fns/pdc.py - copied unchanged from r12566, 1.3/generic_fns/pdc.py branches/relax_disp/prompt/pdc.py - copied unchanged from r12566, 1.3/prompt/pdc.py branches/relax_disp/test_suite/shared_data/pdc_files/ - copied from r12566, 1.3/test_suite/shared_data/pdc_files/ branches/relax_disp/test_suite/system_tests/pdc.py - copied unchanged from r12566, 1.3/test_suite/system_tests/pdc.py Modified: branches/relax_disp/ (props changed) branches/relax_disp/docs/CHANGES branches/relax_disp/docs/html/clean branches/relax_disp/docs/latex/relax.tex branches/relax_disp/generic_fns/__init__.py branches/relax_disp/generic_fns/spectrum.py branches/relax_disp/prompt/__init__.py branches/relax_disp/prompt/interpreter.py branches/relax_disp/scons/manuals.py branches/relax_disp/specific_fns/n_state_model.py branches/relax_disp/test_suite/system_tests/__init__.py branches/relax_disp/test_suite/system_tests/model_free.py branches/relax_disp/test_suite/system_tests/n_state_model.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/relax_disp/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/CHANGES?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/docs/html/clean URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/html/clean?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/docs/latex/relax.tex URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax.tex?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/generic_fns/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/__init__.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/generic_fns/spectrum.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/spectrum.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/prompt/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/__init__.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/prompt/interpreter.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/interpreter.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/scons/manuals.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/scons/manuals.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/specific_fns/n_state_model.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/n_state_model.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/test_suite/system_tests/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/__init__.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/test_suite/system_tests/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/model_free.py?rev=12574&r1=12573&r2=12574&view=diff Modified: branches/relax_disp/test_suite/system_tests/n_state_model.py URL: http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/n_state_model.py?rev=12574&r1=12573&r2=12574&view=diff