r27719 - /trunk/lib/structure/internal/object.py

2015-02-25 Thread edward
Author: bugman Date: Wed Feb 25 13:58:45 2015 New Revision: 27719 URL: http://svn.gna.org/viewcvs/relax?rev=27719&view=rev Log: Implemented the new 'inv' argument for the selection() structural object method. This allows for all atoms not matching the atom ID string to be selected. The unit tes

r27720 - in /branches/frame_order_cleanup: ./ lib/structure/internal/ pipe_control/structure/ test_suite/unit_tests/_pipe_co...

2015-02-25 Thread edward
branches/frame_order_cleanup/test_suite/unit_tests/_pipe_control/_structure/test_internal.py Wed Feb 25 14:00:53 2015 @@ -1,6 +1,6 @@ ### #

r27721 - in /branches/frame_order_cleanup: specific_analyses/frame_order/uf.py user_functions/frame_order.py

2015-02-25 Thread edward
Author: bugman Date: Wed Feb 25 14:16:04 2015 New Revision: 27721 URL: http://svn.gna.org/viewcvs/relax?rev=27721&view=rev Log: Added the new 'atom_id' argument to the frame_order.distribute user function. This uses the new inverse selection functionality recently introduced into the trunk to de

r27722 - /trunk/pipe_control/structure/main.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 11:58:42 2015 New Revision: 27722 URL: http://svn.gna.org/viewcvs/relax?rev=27722&view=rev Log: Improvement for the structure.mean user function. This can now be used to store an averaged structure in an empty data pipe. Previously structural data needed to be pr

r27723 - /trunk/data_store/__init__.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 15:32:59 2015 New Revision: 27723 URL: http://svn.gna.org/viewcvs/relax?rev=27723&view=rev Log: Bug fix for the results.write user function when loading relax state files. The results.write user function can load not only the results file consisting of a single da

r27724 - /trunk/pipe_control/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 15:34:59 2015 New Revision: 27724 URL: http://svn.gna.org/viewcvs/relax?rev=27724&view=rev Log: Fix for the rdc.write user function. The check for the missing rdc_data_types variable in the interatomic containers is now more comprehensive and checks for the presen

r27725 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 16:55:08 2015 New Revision: 27725 URL: http://svn.gna.org/viewcvs/relax?rev=27725&view=rev Log: Created a system test to show a limitation of the rdc.copy user function. Currently, it cannot work when spin systems in two data pipes are different. The system test

r27726 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 17:16:44 2015 New Revision: 27726 URL: http://svn.gna.org/viewcvs/relax?rev=27726&view=rev Log: Simplification of the new Rdc.test_rdc_copy_different_spins system test. This no longer tests the deletion of interatomic data containers by the spin.delete user functi

r27727 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2011-2013 Edward d'Auvergne # +# Copyright (C) 2011-2

r27729 - /trunk/pipe_control/sequence.py

2015-03-02 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2003-2014 Edward d'Auvergne # +# Copyright (C) 2003-2

r27728 - /trunk/pipe_control/sequence.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 17:21:04 2015 New Revision: 27728 URL: http://svn.gna.org/viewcvs/relax?rev=27728&view=rev Log: Added a printout to the sequence.attach_protons user function listing all the newly created spins. Modified: trunk/pipe_control/sequence.py Modified: trunk/pipe_c

r27731 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 17:27:21 2015 New Revision: 27731 URL: http://svn.gna.org/viewcvs/relax?rev=27731&view=rev Log: Another small fix for the new Rdc.test_rdc_copy_different_spins system test. The rdc.copy user function requires the pipe_to argument to be supplied in this case. Mod

r27730 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 17:24:08 2015 New Revision: 27730 URL: http://svn.gna.org/viewcvs/relax?rev=27730&view=rev Log: Some more fixes for the Rdc.test_rdc_copy_different_spins system test. The residue.delete and not spin.delete user function is required to delete the sequence data. M

r27732 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 18:09:12 2015 New Revision: 27732 URL: http://svn.gna.org/viewcvs/relax?rev=27732&view=rev Log: Expansion of the Rdc.test_rdc_copy_different_spins system test. The interatomic data containers are now defined via the interatom.define user function, which requires t

r27733 - /trunk/pipe_control/interatomic.py

2015-03-02 Thread edward
c.py (original) +++ trunk/pipe_control/interatomic.py Mon Mar 2 18:13:09 2015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2012-2014 E

r27735 - /trunk/pipe_control/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 18:22:18 2015 New Revision: 27735 URL: http://svn.gna.org/viewcvs/relax?rev=27735&view=rev Log: Expanded the functionality of the rdc.copy user function. The user function will now operate on two data pipes with different spin sequences. If the interatomic data c

r27734 - /trunk/test_suite/system_tests/rdc.py

2015-03-02 Thread edward
Author: bugman Date: Mon Mar 2 18:19:26 2015 New Revision: 27734 URL: http://svn.gna.org/viewcvs/relax?rev=27734&view=rev Log: Some more modifications for the Rdc.test_rdc_copy_different_spins system test. One of the interatomic data containers does not have RDC data, as it is not present in th

r27736 - /trunk/pipe_control/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 13:43:44 2015 New Revision: 27736 URL: http://svn.gna.org/viewcvs/relax?rev=27736&view=rev Log: Modified the rdc.copy user function to printout all copied RDC values and errors. Modified: trunk/pipe_control/rdc.py Modified: trunk/pipe_control/rdc.py URL: ht

r27737 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 13:51:18 2015 New Revision: 27737 URL: http://svn.gna.org/viewcvs/relax?rev=27737&view=rev Log: Created the Rdc.test_rdc_copy_back_calc system test. This will be used to implement the back_calc Boolean argument for the rdc.copy user function to allow not only meas

r27738 - /trunk/pipe_control/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 13:53:48 2015 New Revision: 27738 URL: http://svn.gna.org/viewcvs/relax?rev=27738&view=rev Log: Modified the rdc.copy printout of RDCs to occur for each alignment ID. Modified: trunk/pipe_control/rdc.py Modified: trunk/pipe_control/rdc.py URL: http://svn.gna

r27739 - in /trunk: pipe_control/rdc.py user_functions/rdc.py

2015-03-03 Thread edward
======= --- trunk/user_functions/rdc.py (original) +++ trunk/user_functions/rdc.py Tue Mar 3 14:01:13 2015 @@ -1,6 +1,6 @@ ### #

r27740 - /trunk/pipe_control/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 14:06:31 2015 New Revision: 27740 URL: http://svn.gna.org/viewcvs/relax?rev=27740&view=rev Log: Small formatting change for the rdc.copy user function printouts. Modified: trunk/pipe_control/rdc.py Modified: trunk/pipe_control/rdc.py URL: http://svn.gna.org/

r27741 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2011-2013 Edward d'Auvergne # +# Copyright (C) 2011-2

r27742 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 14:34:41 2015 New Revision: 27742 URL: http://svn.gna.org/viewcvs/relax?rev=27742&view=rev Log: Fix for the pcs.read user function. The problem was caught by the new Pcs.test_pcs_copy_different_spins system test. If the spin system does not exist in the current d

r27743 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 14:38:33 2015 New Revision: 27743 URL: http://svn.gna.org/viewcvs/relax?rev=27743&view=rev Log: Added a printout of the alignment ID for the pcs.copy user function. This is to match the rdc.copy user function. Modified: trunk/pipe_control/pcs.py Modified: tr

r27744 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 14:43:18 2015 New Revision: 27744 URL: http://svn.gna.org/viewcvs/relax?rev=27744&view=rev Log: Created the Pcs.test_pcs_copy_back_calc system test. This will be used to implement the back_calc Boolean argument for the pcs.copy user function to allow not only meas

r27745 - in /trunk: pipe_control/pcs.py user_functions/pcs.py

2015-03-03 Thread edward
= --- trunk/user_functions/pcs.py (original) +++ trunk/user_functions/pcs.py Tue Mar 3 14:46:20 2015 @@ -1,6 +1,6 @@ ####### # # -# Copyright (C) 2003-2014 Edward d'Auvergne # +# Copyright (C) 2003-2015 Edward d'

r27746 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:04:47 2015 New Revision: 27746 URL: http://svn.gna.org/viewcvs/relax?rev=27746&view=rev Log: Added full per-alignment data printouts to the pcs.copy user function to match rdc.copy. The feedback is important to know what was actually copied. Modified: tru

r27747 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:09:00 2015 New Revision: 27747 URL: http://svn.gna.org/viewcvs/relax?rev=27747&view=rev Log: Modified the pcs.copy user function to handle different spin sequence between data pipes. Modified: trunk/pipe_control/pcs.py Modified: trunk/pipe_control/pcs.py

r27748 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:13:03 2015 New Revision: 27748 URL: http://svn.gna.org/viewcvs/relax?rev=27748&view=rev Log: Fixes for the Pcs.test_pcs_copy_different_spins and Pcs.test_pcs_copy_back_calc system tests. Modified: trunk/test_suite/system_tests/pcs.py Modified: trunk/test_

r27749 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:47:17 2015 New Revision: 27749 URL: http://svn.gna.org/viewcvs/relax?rev=27749&view=rev Log: Fix for the pcs.copy user function for a recently introduced problem (r27747). The data pipe for the spin_loop() function must be supplied. Modified: trunk/pipe_co

r27750 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:48:35 2015 New Revision: 27750 URL: http://svn.gna.org/viewcvs/relax?rev=27750&view=rev Log: The pcs.copy user function now skips deselected spins. Modified: trunk/pipe_control/pcs.py Modified: trunk/pipe_control/pcs.py URL: http://svn.gna.org/viewcvs/rel

r27751 - /trunk/test_suite/system_tests/n_state_model.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 15:59:41 2015 New Revision: 27751 URL: http://svn.gna.org/viewcvs/relax?rev=27751&view=rev Log: Modified the N_state_model.test_data_copying system test to skip deselected spins. Modified: trunk/test_suite/system_tests/n_state_model.py Modified: trunk/test_s

r27752 - in /branches/frame_order_cleanup: ./ data_store/ pipe_control/ pipe_control/structure/ test_suite/system_tests/ use...

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 16:02:51 2015 New Revision: 27752 URL: http://svn.gna.org/viewcvs/relax?rev=27752&view=rev Log: Merged revisions 27722-27751 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27722 | bugman | 2015-03-02 11:58:42 +0100 (Mon, 02 Mar 2015) |

r27754 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 16:33:21 2015 New Revision: 27754 URL: http://svn.gna.org/viewcvs/relax?rev=27754&view=rev Log: Added more checks to the three Rdc.test_rdc_copy* system tests. Modified: trunk/test_suite/system_tests/rdc.py Modified: trunk/test_suite/system_tests/rdc.py URL:

r27753 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 16:30:49 2015 New Revision: 27753 URL: http://svn.gna.org/viewcvs/relax?rev=27753&view=rev Log: Added more checks to the three Pcs.test_pcs_copy* system tests. Modified: trunk/test_suite/system_tests/pcs.py Modified: trunk/test_suite/system_tests/pcs.py URL:

r27755 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 16:46:48 2015 New Revision: 27755 URL: http://svn.gna.org/viewcvs/relax?rev=27755&view=rev Log: Created the Rdc.test_calc_q_factors_no_tensor system test. This is to demonstrate a failure in the rdc.calc_q_factors user function when no alignment tensor is present.

r27756 - /trunk/pipe_control/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 16:49:03 2015 New Revision: 27756 URL: http://svn.gna.org/viewcvs/relax?rev=27756&view=rev Log: Fixes for the rdc.calc_q_factors user function for when no alignment tensor is present. This was caught by the Rdc.test_calc_q_factors_no_tensor system test. Now if n

r27757 - in /branches/frame_order_cleanup: ./ pipe_control/rdc.py test_suite/system_tests/pcs.py test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:03:47 2015 New Revision: 27757 URL: http://svn.gna.org/viewcvs/relax?rev=27757&view=rev Log: Merged revisions 27753-27756 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27753 | bugman | 2015-03-03 16:30:49 +0100 (Tue, 03 Mar 2015) |

r27758 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:10:38 2015 New Revision: 27758 URL: http://svn.gna.org/viewcvs/relax?rev=27758&view=rev Log: The Rdc.test_rdc_copy_* system tests now check for the 'rdc_data_types' data structure. This is in the Rdc.test_rdc_copy_different_spins and Rdc.test_rdc_copy_back_cal

r27765 - /trunk/user_functions/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:42:30 2015 New Revision: 27765 URL: http://svn.gna.org/viewcvs/relax?rev=27765&view=rev Log: Added the 'title' and 'subtitle' arguments to the pcs.corr_plot user function. This problem was detected by the new Pcs.test_corr_plot system test. The pcs.corr_plot u

r27762 - in /branches/frame_order_cleanup: ./ pipe_control/rdc.py test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:22:14 2015 New Revision: 27762 URL: http://svn.gna.org/viewcvs/relax?rev=27762&view=rev Log: Merged revisions 27758-27761 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27758 | bugman | 2015-03-03 17:10:38 +0100 (Tue, 03 Mar 2015) |

r27768 - in /branches/frame_order_cleanup: ./ pipe_control/ test_suite/system_tests/ user_functions/

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:50:29 2015 New Revision: 27768 URL: http://svn.gna.org/viewcvs/relax?rev=27768&view=rev Log: Merged revisions 27763-27767 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27763 | bugman | 2015-03-03 17:34:39 +0100 (Tue, 03 Mar 2015) |

r27760 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:15:33 2015 New Revision: 27760 URL: http://svn.gna.org/viewcvs/relax?rev=27760&view=rev Log: The Rdc.test_rdc_copy_* system tests now check for the 'absolute_rdc' data structure. This is in the Rdc.test_rdc_copy_different_spins and Rdc.test_rdc_copy_back_calc

r27764 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:40:22 2015 New Revision: 27764 URL: http://svn.gna.org/viewcvs/relax?rev=27764&view=rev Log: Created the Pcs.test_corr_plot system test to check the pcs.corr_plot user function. This user function is poorly tested, and this test triggers a series of bugs. Mod

r27763 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:34:39 2015 New Revision: 27763 URL: http://svn.gna.org/viewcvs/relax?rev=27763&view=rev Log: Created the Rdc.test_corr_plot system test to check the rdc.corr_plot user function. This shows that this poorly tested function works correctly. Modified: trunk/

r27761 - /trunk/pipe_control/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:18:14 2015 New Revision: 27761 URL: http://svn.gna.org/viewcvs/relax?rev=27761&view=rev Log: Expanded the rdc.copy user function to copy the RDC data type and absolute RDC flag information. Modified: trunk/pipe_control/rdc.py Modified: trunk/pipe_control/

r27766 - /trunk/pipe_control/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:46:21 2015 New Revision: 27766 URL: http://svn.gna.org/viewcvs/relax?rev=27766&view=rev Log: Fix for the pcs.corr_plot user function when the spin containers have no element information. Modified: trunk/pipe_control/pcs.py Modified: trunk/pipe_control/pcs

r27759 - /trunk/test_suite/system_tests/rdc.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:11:47 2015 New Revision: 27759 URL: http://svn.gna.org/viewcvs/relax?rev=27759&view=rev Log: Removed a debugging printout. Modified: trunk/test_suite/system_tests/rdc.py Modified: trunk/test_suite/system_tests/rdc.py URL: http://svn.gna.org/viewcvs/relax/

r27767 - /trunk/test_suite/system_tests/pcs.py

2015-03-03 Thread edward
Author: bugman Date: Tue Mar 3 17:50:02 2015 New Revision: 27767 URL: http://svn.gna.org/viewcvs/relax?rev=27767&view=rev Log: Completed the Pcs.test_corr_plot system test. The file contents are now known and have been carefully checking in Grace. Modified: trunk/test_suite/system_tests/pc

r27769 - in /trunk: auto_analyses/ data_store/ pipe_control/ test_suite/system_tests/

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 13:33:45 2015 New Revision: 27769 URL: http://svn.gna.org/viewcvs/relax?rev=27769&view=rev Log: Clarification of the RDC and PCS Q factors. This affects the rdc.calc_q_factors and pcs.calc_q_factors user functions, as well as all other operations involving the cal

r27770 - in /branches/frame_order_cleanup: ./ auto_analyses/ data_store/ pipe_control/ test_suite/system_tests/

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 13:46:15 2015 New Revision: 27770 URL: http://svn.gna.org/viewcvs/relax?rev=27770&view=rev Log: Merged revisions 27769 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27769 | bugman | 2015-03-04 13:33:45 +0100 (Wed, 04 Mar 2015) | 12 lin

r27771 - /trunk/test_suite/system_tests/align_tensor.py

2015-03-04 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2006-2013 Edward d'Auvergne # +# Copyright (C) 2006-2015 Edward d'Auvergne # #

r27772 - /trunk/user_functions/align_tensor.py

2015-03-04 Thread edward
14:30:30 2015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2007-2014 Edward d'Auvergne # +# Copyright (C) 2007-2015 Edward d'Auvergne # # # # This file is part

r27773 - /trunk/pipe_control/align_tensor.py

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 14:34:07 2015 New Revision: 27773 URL: http://svn.gna.org/viewcvs/relax?rev=27773&view=rev Log: Modified the pipe_control.align_tensor.align_data_exists() function to handle no tensor IDs. If no tensor ID is supplied, this will then return True if any alignment da

r27774 - /trunk/pipe_control/align_tensor.py

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 14:47:21 2015 New Revision: 27774 URL: http://svn.gna.org/viewcvs/relax?rev=27774&view=rev Log: Improvement for the align_tensor.copy user function. The user function has been modified to allow all alignment tensors to be copied between two data pipes. This allow

r27775 - in /branches/frame_order_cleanup: ./ pipe_control/ test_suite/system_tests/ user_functions/

2015-03-04 Thread edward
t_suite/system_tests/align_tensor.py (original) +++ branches/frame_order_cleanup/test_suite/system_tests/align_tensor.py Wed Mar 4 14:48:39 2015 @@ -1,6 +1,6 @@ ####### #

r27776 - /trunk/test_suite/unit_tests/_prompt/test_align_tensor.py

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 15:10:39 2015 New Revision: 27776 URL: http://svn.gna.org/viewcvs/relax?rev=27776&view=rev Log: Fixes for the align_tensor.copy user function argument unit tests. The tensor_from and tensor_to arguments can now be None. Modified: trunk/test_suite/unit_tests/_

r27780 - /trunk/data_store/align_tensor.py

2015-03-04 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2003-2014 Edward d'Auvergne # +# Copyright (C) 2003-2

r27777 - /trunk/test_suite/system_tests/align_tensor.py

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 15:23:13 2015 New Revision: 2 URL: http://svn.gna.org/viewcvs/relax?rev=2&view=rev Log: Created the Align_tensor.test_copy_pipes_sims system test. This demonstrates a failure of the align_tensor.copy user function when Monte Carlo simulated tensors are pre

r27779 - /trunk/data_store/align_tensor.py

2015-03-04 Thread edward
Author: bugman Date: Wed Mar 4 15:32:53 2015 New Revision: 27779 URL: http://svn.gna.org/viewcvs/relax?rev=27779&view=rev Log: Deleted the data_store.align_tensor.AlignTensorSimList.append() method. This replacement list method was proving fatal when copy.deepcopy() is called on the alignment t

r27778 - /trunk/pipe_control/align_tensor.py

2015-03-04 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2003-2014 Edward d'Auvergne # +# Copyright (C) 2003-2

r27781 - in /branches/frame_order_cleanup: ./ data_store/ pipe_control/ test_suite/system_tests/ test_suite/unit_tests/_prompt/

2015-03-04 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2003-2014 Edward d'Auvergne # +# Copyright (C) 2003-2

r27782 - /trunk/data_store/align_tensor.py

2015-03-05 Thread edward
Author: bugman Date: Thu Mar 5 11:02:08 2015 New Revision: 27782 URL: http://svn.gna.org/viewcvs/relax?rev=27782&view=rev Log: Huge speed up for loading results and state files with Monte Carlo simulation alignment tensors. The reading of the alignment tensor component of XML formatted results

r27783 - /trunk/pipe_control/rdc.py

2015-03-05 Thread edward
Author: bugman Date: Thu Mar 5 14:49:00 2015 New Revision: 27783 URL: http://svn.gna.org/viewcvs/relax?rev=27783&view=rev Log: Added an extra check for the assembly of RDC data. This is in the pipe_control.rdc.return_rdc_data() function and the check is for any unit vectors set to None, which i

r27785 - /trunk/pipe_control/interatomic.py

2015-03-05 Thread edward
Author: bugman Date: Thu Mar 5 15:17:51 2015 New Revision: 27785 URL: http://svn.gna.org/viewcvs/relax?rev=27785&view=rev Log: Added a new warning to the interatom.unit_vectors user function if data is missing. This is to aid in detecting problems earlier before unit vectors of None are encoun

r27784 - /trunk/pipe_control/rdc.py

2015-03-05 Thread edward
Author: bugman Date: Thu Mar 5 15:05:28 2015 New Revision: 27784 URL: http://svn.gna.org/viewcvs/relax?rev=27784&view=rev Log: Improved the RelaxError message from the RDC assembly function when unit vectors are None. Modified: trunk/pipe_control/rdc.py Modified: trunk/pipe_control/rdc.py

r27786 - in /trunk/user_functions: pcs.py rdc.py

2015-03-09 Thread edward
Author: bugman Date: Mon Mar 9 11:48:12 2015 New Revision: 27786 URL: http://svn.gna.org/viewcvs/relax?rev=27786&view=rev Log: Improvements for the rdc.weight and pcs.weight user functions. The spin_id argument can now be set to None to allow all spins or interatomic data containers to be set.

r27787 - /trunk/pipe_control/rdc.py

2015-03-09 Thread edward
Author: bugman Date: Mon Mar 9 16:53:08 2015 New Revision: 27787 URL: http://svn.gna.org/viewcvs/relax?rev=27787&view=rev Log: Modified the rdc.corr_plot user function to skip deselected interatomic data containers. This would normally happen as no back-calculated data is normally present. Ho

r27788 - in /branches/frame_order_cleanup: ./ data_store/ pipe_control/ user_functions/

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:35:38 2015 New Revision: 27788 URL: http://svn.gna.org/viewcvs/relax?rev=27788&view=rev Log: Merged revisions 27782-27787 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27782 | bugman | 2015-03-05 11:02:08 +0100 (Thu, 05 Mar 2015) |

r27789 - in /trunk/test_suite: shared_data/peak_lists/Sam.csv system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:37:20 2015 New Revision: 27789 URL: http://svn.gna.org/viewcvs/relax?rev=27789&view=rev Log: Created the Sequence.test_bug_23372_read_csv system test. This is to catch bug #23372 (https://gna.org/bugs/?23372), the sequence.read failure with CSV files. It uses a

r27790 - in /branches/nmrglue: ./ auto_analyses/ data_store/ lib/structure/internal/ pipe_control/ pipe_control/structure/ t...

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:37:20 2015 New Revision: 27790 URL: http://svn.gna.org/viewcvs/relax?rev=27790&view=rev Log: Merged revisions 27707-27714,27717-27719,27722-27751,27753-27756,27758-27761,27763-27767,27769,27771-27774,27776-27780,27782-27787 via svnmerge from svn+ssh://bug...@s

r27791 - in /branches/nmrglue: ./ test_suite/shared_data/peak_lists/Sam.csv test_suite/system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:39:07 2015 New Revision: 27791 URL: http://svn.gna.org/viewcvs/relax?rev=27791&view=rev Log: Merged revisions 27789 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27789 | bugman | 2015-03-10 09:37:20 +0100 (Tue, 10 Mar 2015) | 7 line

r27792 - in /branches/frame_order_cleanup: ./ test_suite/shared_data/peak_lists/Sam.csv test_suite/system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:39:09 2015 New Revision: 27792 URL: http://svn.gna.org/viewcvs/relax?rev=27792&view=rev Log: Merged revisions 27789 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27789 | bugman | 2015-03-10 09:37:20 +0100 (Tue, 10 Mar 2015) | 7 line

r27793 - /trunk/lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:47:19 2015 New Revision: 27793 URL: http://svn.gna.org/viewcvs/relax?rev=27793&view=rev Log: Converted the lib.sequence.validate_sequence() to the checking function design. This is the checking function design documented at http://wiki.nmr-relax.com/Relax_source

r27794 - /trunk/test_suite/system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:48:39 2015 New Revision: 27794 URL: http://svn.gna.org/viewcvs/relax?rev=27794&view=rev Log: Small typo fix for the Sequence.test_bug_23372_read_csv system test. Modified: trunk/test_suite/system_tests/sequence.py Modified: trunk/test_suite/system_tests/se

r27796 - in /branches/frame_order_cleanup: ./ lib/sequence.py test_suite/system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:50:13 2015 New Revision: 27796 URL: http://svn.gna.org/viewcvs/relax?rev=27796&view=rev Log: Merged revisions 27793-27794 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27793 | bugman | 2015-03-10 09:47:19 +0100 (Tue, 10 Mar 2015) |

r27795 - in /branches/nmrglue: ./ lib/sequence.py test_suite/system_tests/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:50:11 2015 New Revision: 27795 URL: http://svn.gna.org/viewcvs/relax?rev=27795&view=rev Log: Merged revisions 27793-27794 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27793 | bugman | 2015-03-10 09:47:19 +0100 (Tue, 10 Mar 2015) |

r27797 - /trunk/lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:50:16 2015 New Revision: 27797 URL: http://svn.gna.org/viewcvs/relax?rev=27797&view=rev Log: Fix for bug #23372 (https://gna.org/bugs/?23372), the sequence.read failure with CSV files. The problem was that the sep argument was not being passed all the way to th

r27798 - in /branches/nmrglue: ./ lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:52:58 2015 New Revision: 27798 URL: http://svn.gna.org/viewcvs/relax?rev=27798&view=rev Log: Merged revisions 27797 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27797 | bugman | 2015-03-10 09:50:16 +0100 (Tue, 10 Mar 2015) | 6 line

r27799 - in /branches/frame_order_cleanup: ./ lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 09:52:59 2015 New Revision: 27799 URL: http://svn.gna.org/viewcvs/relax?rev=27799&view=rev Log: Merged revisions 27797 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk r27797 | bugman | 2015-03-10 09:50:16 +0100 (Tue, 10 Mar 2015) | 6 line

r27800 - /trunk/lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 10:05:25 2015 New Revision: 27800 URL: http://svn.gna.org/viewcvs/relax?rev=27800&view=rev Log: Fix for the lib.sequence.check_sequence checking object. Although rarely used, the check for the spin number was incorrect and half of the checks were instead for the r

r27801 - /trunk/lib/sequence.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 10:13:33 2015 New Revision: 27801 URL: http://svn.gna.org/viewcvs/relax?rev=27801&view=rev Log: Added the raise_flag argument to the lib.sequence.read_spin_data() function. This is to allow the missing data RelaxError to be deactivated. Modified: trunk/lib/se

r27802 - /trunk/lib/spectrum/peak_list.py

2015-03-10 Thread edward
015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2004-2014 Edward d'Auvergne # +# Copyright (C) 2004-2015 Edward d'Auvergne # # Copyrigh

r27803 - in /trunk/pipe_control: pcs.py rdc.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 18:00:53 2015 New Revision: 27803 URL: http://svn.gna.org/viewcvs/relax?rev=27803&view=rev Log: Python 3 improvement for the rdc.corr_plot and pcs.corr_plot user functions. The world view is now set in floating point numbers. In Python 2, the math.ceil() and math

r27804 - /trunk/pipe_control/pcs.py

2015-03-10 Thread edward
Author: bugman Date: Tue Mar 10 18:36:55 2015 New Revision: 27804 URL: http://svn.gna.org/viewcvs/relax?rev=27804&view=rev Log: Improvements for the pcs.structural_noise user function. The check for the presence of PCS data for points to skip now includes checking for PCS values of None. And th

r27805 - in /trunk: lib/plotting/ test_suite/system_tests/

2015-03-10 Thread edward
= --- trunk/test_suite/system_tests/noe.py(original) +++ trunk/test_suite/system_tests/noe.pyTue Mar 10 18:58:41 2015 @@ -1,6 +1,6 @@ ####### #

r27806 - /branches/frame_order_cleanup/target_functions/frame_order.py

2015-03-12 Thread edward
hu Mar 12 12:38:58 2015 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2009-2014 Edward d'Auvergne # +# Copyright

r27807 - /trunk/lib/structure/pdb_write.py

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 11:39:16 2015 New Revision: 27807 URL: http://svn.gna.org/viewcvs/relax?rev=27807&view=rev Log: Epydoc documentation fix for the lib.structure.pdb_write_handle_atom_name() function. Modified: trunk/lib/structure/pdb_write.py Modified: trunk/lib/structure/pdb

r27808 - /tags/3.3.7/

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 11:39:46 2015 New Revision: 27808 URL: http://svn.gna.org/viewcvs/relax?rev=27808&view=rev Log: relax version 3.3.7. This is a major feature and bugfix release. New features include the statistics.aic and statistics.model user functions, plotting API advancements

r27809 - /tags/3.3.7/version.py

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 11:42:44 2015 New Revision: 27809 URL: http://svn.gna.org/viewcvs/relax?rev=27809&view=rev Log: Updated the version number to relax 3.3.7. Modified: tags/3.3.7/version.py Modified: tags/3.3.7/version.py URL: http://svn.gna.org/viewcvs/relax/tags/3.3.7/versio

r27810 - /tags/3.3.7/docs/relax.pdf

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 11:58:39 2015 New Revision: 27810 URL: http://svn.gna.org/viewcvs/relax?rev=27810&view=rev Log: Added the relax 3.3.7 PDF manual to the repository. Added: tags/3.3.7/docs/relax.pdf (with props) Added: tags/3.3.7/docs/relax.pdf URL: http://svn.gna.org/viewc

r27811 - /tags/3.3.7/docs/CHANGES

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 12:30:20 2015 New Revision: 27811 URL: http://svn.gna.org/viewcvs/relax?rev=27811&view=rev Log: Updated the CHANGES document for relax 3.3.7. Modified: tags/3.3.7/docs/CHANGES [This mail would be too long, it was shortened to contain the URLs only.] Modified

r27812 - /website/download.html

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 15:13:45 2015 New Revision: 27812 URL: http://svn.gna.org/viewcvs/relax?rev=27812&view=rev Log: Changed the download links for relax 3.2.2 and 3.3.0 to 3.3.5. These now point to http://www.nmr-relax.com/download_request.html, as the distribution files have been re

r27813 - /website/manual/

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 15:25:23 2015 New Revision: 27813 URL: http://svn.gna.org/viewcvs/relax?rev=27813&view=rev Log: Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to version 3.3.6. Added: website/manual/office-chart-pie.png (with props) website

r27814 - /website/api/3.3/

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 15:33:07 2015 New Revision: 27814 URL: http://svn.gna.org/viewcvs/relax?rev=27814&view=rev Log: Updated the relax API documentation at http://www.nmr-relax.com/api/3.3/ to version 3.3.7. Added: website/api/3.3/lib.plotting.grace-module.html website/api/3.

r27815 - /website/download.html

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 15:35:24 2015 New Revision: 27815 URL: http://svn.gna.org/viewcvs/relax?rev=27815&view=rev Log: Updated the http://www.nmr-relax.com/download.html webpage for the relax 3.3.7 release. Modified: website/download.html [This mail would be too long, it was short

r27816 - /trunk/docs/CHANGES

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 15:42:37 2015 New Revision: 27816 URL: http://svn.gna.org/viewcvs/relax?rev=27816&view=rev Log: Backported the relax 3.3.7 CHANGES file changes to trunk. The command used was: svn merge -r27810:r27811 svn+ssh://bug...@svn.gna.org/svn/relax/tags/3.3.7 . Modified:

r27817 - /website/api/index.html

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 16:21:48 2015 New Revision: 27817 URL: http://svn.gna.org/viewcvs/relax?rev=27817&view=rev Log: Updated the relax version number to 3.3.7 on the http://www.nmr-relax.com/api/index.html webpage. Modified: website/api/index.html Modified: website/api/index.htm

r27818 - /trunk/docs/CHANGES

2015-03-13 Thread edward
Author: bugman Date: Fri Mar 13 17:55:09 2015 New Revision: 27818 URL: http://svn.gna.org/viewcvs/relax?rev=27818&view=rev Log: Spacing fixes in the CHANGES document. Modified: trunk/docs/CHANGES [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/docs

<    9   10   11   12   13   14   15   16   17   18   >