Author: bugman Date: Tue Feb 23 02:45:46 2010 New Revision: 10839 URL: http://svn.gna.org/viewcvs/relax?rev=10839&view=rev Log: Merged revisions 10766-10789,10794-10829 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r10766 | bugman | 2010-02-19 11:09:06 +0100 (Fri, 19 Feb 2010) | 3 lines Converted write_multi_header() to write_xy_header() and simplified the args by expecting [X, Y] pairs. ........ r10767 | bugman | 2010-02-19 11:43:22 +0100 (Fri, 19 Feb 2010) | 6 lines Clean up of write_xy_header(). Labels are now not overwritten if supplied, all file.write() operations are collected together, and the X and Y-axis settings have been merged. ........ r10768 | bugman | 2010-02-19 11:46:25 +0100 (Fri, 19 Feb 2010) | 3 lines write_xy_header() now has a sets arg for specifying the number of data sets in the graph G0. ........ r10769 | bugman | 2010-02-19 14:11:57 +0100 (Fri, 19 Feb 2010) | 7 lines More changes to write_xy_header(). The return_units() and return_grace_string() analysis specific methods are no longer passed in as args but are set up in the method itself. Many simplifications have been made. And now spin data has been made axis independent - it can be X or Y data. ........ r10770 | bugman | 2010-02-19 14:43:19 +0100 (Fri, 19 Feb 2010) | 3 lines Bug fix for write_xy_header(), a statement typo was stopping relax from running. ........ r10771 | bugman | 2010-02-19 14:46:26 +0100 (Fri, 19 Feb 2010) | 3 lines Added symbol formatting to the individual graph sets in write_xy_header(). ........ r10772 | bugman | 2010-02-19 14:47:42 +0100 (Fri, 19 Feb 2010) | 5 lines Deletion of the write_header() function. This is now redundant due to the improvements in write_xy_header(). ........ r10773 | bugman | 2010-02-19 14:51:15 +0100 (Fri, 19 Feb 2010) | 5 lines Fix for the call to write_xy_header(). This is now independent of the number of data sets, and is called correctly. ........ r10774 | bugman | 2010-02-19 14:54:39 +0100 (Fri, 19 Feb 2010) | 3 lines Added the axis_min and axis_max args to write_xy_header() for specifying the graph ranges. ........ r10775 | bugman | 2010-02-19 14:56:10 +0100 (Fri, 19 Feb 2010) | 5 lines Typo fix in write_xy_header(). axis_label should have been axis_labels! ........ r10776 | bugman | 2010-02-19 15:09:10 +0100 (Fri, 19 Feb 2010) | 5 lines Spin ids are no longer passed into write_xy_header(). Instead the new args seq_type and set_names are passed in. ........ r10777 | bugman | 2010-02-19 15:13:32 +0100 (Fri, 19 Feb 2010) | 3 lines Fix for the counting of the number of graph sets. ........ r10778 | bugman | 2010-02-19 15:33:40 +0100 (Fri, 19 Feb 2010) | 5 lines Shifted to using write_xy_data(). This was the write_multi_data() function, and write_data() function has been deleted. ........ r10779 | bugman | 2010-02-19 15:52:28 +0100 (Fri, 19 Feb 2010) | 7 lines Changed the format of the data arg to write_xy_data(). This is a huge simplification and makes the function more usable for any type of data thrown at it. The structure is now expected to be a 4D list/array corresponding to Gx, Sx, data point, data point info. ........ r10780 | bugman | 2010-02-19 17:03:42 +0100 (Fri, 19 Feb 2010) | 7 lines Redesign of get_data() and deletion of determine_graph_type(). get_data() determines the graph type in a few lines of code, so determine_graph_type() is not necessary. get_data() now returns the 4D grace graph data structure, the labels for the data sets, and the graph_type. ........ r10781 | bugman | 2010-02-19 17:08:23 +0100 (Fri, 19 Feb 2010) | 3 lines Clean up of the write() function for the new get_data() design. ........ r10782 | bugman | 2010-02-19 18:18:44 +0100 (Fri, 19 Feb 2010) | 3 lines Fixes for get_data() for when the analysis specific return_value() fn returns a list of values! ........ r10783 | bugman | 2010-02-19 18:22:23 +0100 (Fri, 19 Feb 2010) | 3 lines Fix for the graph type determination in get_data(). ........ r10784 | bugman | 2010-02-19 18:23:34 +0100 (Fri, 19 Feb 2010) | 3 lines Removed the linestyle setting in write_xy_header() that made the line invisible. ........ r10785 | bugman | 2010-02-19 18:35:57 +0100 (Fri, 19 Feb 2010) | 5 lines Fix for the write_xy_header() method. The args are now explicitly reset as they are lists and are persistent! ........ r10786 | bugman | 2010-02-19 18:37:59 +0100 (Fri, 19 Feb 2010) | 5 lines Another fix for write_xy_header(). The "world xmax" and "world xmax" were being set as the minimums! ........ r10787 | bugman | 2010-02-19 18:40:42 +0100 (Fri, 19 Feb 2010) | 5 lines Another fix for write_xy_header(). This time, "(normalised)" is not added to the X-axis label for normalised plots. ........ r10788 | bugman | 2010-02-19 19:00:30 +0100 (Fri, 19 Feb 2010) | 5 lines Fix for the test_bug_12670_12679() system test. The Grace file lines are now not hardcoded!!! ........ r10789 | bugman | 2010-02-21 15:44:45 +0100 (Sun, 21 Feb 2010) | 5 lines Bug fix for the test_R_to_axis_angle_180_complex() for MS Windows. self.assertAlmostEquals() has to be used do to precision issues. ........ r10794 | bugman | 2010-02-22 10:13:04 +0100 (Mon, 22 Feb 2010) | 3 lines Args after the flags -x, -u, -s are now considered to be the tests performed and not a script. ........ r10795 | bugman | 2010-02-22 10:14:15 +0100 (Mon, 22 Feb 2010) | 3 lines Test_suite_runner now has an __init__() method and stores the list of tests. ........ r10796 | bugman | 2010-02-22 10:20:14 +0100 (Mon, 22 Feb 2010) | 3 lines Finished the __init__() docstring and passed the tests arg into the system tests. ........ r10797 | bugman | 2010-02-22 10:22:27 +0100 (Mon, 22 Feb 2010) | 3 lines Passed self.tests into the run() method instead of the class __init__() method. ........ r10798 | bugman | 2010-02-22 10:32:27 +0100 (Mon, 22 Feb 2010) | 3 lines Individual system tests can now be executed through the relax test suite. ........ r10799 | bugman | 2010-02-22 10:33:34 +0100 (Mon, 22 Feb 2010) | 3 lines The tests list is now optional. ........ r10800 | bugman | 2010-02-22 10:39:03 +0100 (Mon, 22 Feb 2010) | 3 lines The paper size of A4 can now be set in write_xy_header(). ........ r10801 | bugman | 2010-02-22 10:43:28 +0100 (Mon, 22 Feb 2010) | 5 lines Changed the handling of the [None, None] format args. These now default to None and are converted to [None, None] inside the function. ........ r10802 | bugman | 2010-02-22 10:47:27 +0100 (Mon, 22 Feb 2010) | 3 lines In write_xy_header(), the legend box can be now turned on or off and can have its position set. ........ r10803 | bugman | 2010-02-22 10:50:42 +0100 (Mon, 22 Feb 2010) | 3 lines Set colours can now be specified in write_xy_header(). ........ r10804 | bugman | 2010-02-22 10:52:36 +0100 (Mon, 22 Feb 2010) | 3 lines The symbols are now also coloured in write_xy_header(). ........ r10805 | bugman | 2010-02-22 11:00:12 +0100 (Mon, 22 Feb 2010) | 5 lines Much finer control of the set appearance in write_xy_header(). The symbol style, sizes, and line linestyle can now all be specified. ........ r10806 | bugman | 2010-02-22 11:10:18 +0100 (Mon, 22 Feb 2010) | 5 lines Fix for the colour setting in write_xy_header(). The arg is called set_colours, not colours! ........ r10807 | bugman | 2010-02-22 11:15:09 +0100 (Mon, 22 Feb 2010) | 3 lines The graph title and subtitle can be specified in write_xy_header(). ........ r10808 | bugman | 2010-02-22 11:18:28 +0100 (Mon, 22 Feb 2010) | 3 lines Fix for write_xy_header(), axis limits are now set when the value is 0. ........ r10809 | bugman | 2010-02-22 11:21:03 +0100 (Mon, 22 Feb 2010) | 3 lines The 'Spin ' text is now prepended to the legend only in get_data(), and not write_xy_header(). ........ r10810 | bugman | 2010-02-22 11:23:04 +0100 (Mon, 22 Feb 2010) | 3 lines The grace version of the write_xy_header() header is not output. ........ r10811 | bugman | 2010-02-22 13:07:36 +0100 (Mon, 22 Feb 2010) | 3 lines The graph view port size can now be changes and defaults to a larger value. ........ r10812 | bugman | 2010-02-22 13:21:51 +0100 (Mon, 22 Feb 2010) | 3 lines The symbol fill style can now be specified in write_xy_header(). ........ r10813 | bugman | 2010-02-22 13:26:50 +0100 (Mon, 22 Feb 2010) | 3 lines The linewidth for all graph elements can now be set in write_xy_header(). ........ r10814 | bugman | 2010-02-22 13:38:09 +0100 (Mon, 22 Feb 2010) | 3 lines The line type for each set can now be specified in write_xy_header(). ........ r10815 | bugman | 2010-02-22 13:39:46 +0100 (Mon, 22 Feb 2010) | 3 lines Stereochem_analysis.grace_plots() now uses the new write_xy_header() & write_xy_data() fns. ........ r10816 | bugman | 2010-02-22 14:31:21 +0100 (Mon, 22 Feb 2010) | 5 lines The number of ensembles string is now more nicely formatted in the subtitle. This is in Stereochem_analysis.grace_plots(). ........ r10817 | bugman | 2010-02-22 15:10:11 +0100 (Mon, 22 Feb 2010) | 3 lines Fix for the write_xy_header() function for when the data_type arg is not supplied. ........ r10818 | bugman | 2010-02-22 16:13:55 +0100 (Mon, 22 Feb 2010) | 3 lines Added an NOE normalisation variable to the stereochem_analysis.py sample script. ........ r10819 | bugman | 2010-02-22 16:19:10 +0100 (Mon, 22 Feb 2010) | 3 lines Scaled NOE violation correlation plots (RDC Q vs. NOE Q) are now being created. ........ r10820 | bugman | 2010-02-22 16:20:45 +0100 (Mon, 22 Feb 2010) | 3 lines The noe_norm arg is now accepted by the Stereochem_analysis class. ........ r10821 | bugman | 2010-02-22 16:21:22 +0100 (Mon, 22 Feb 2010) | 3 lines Whitespace fixes for the storage of all the Stereochem_analysis args. ........ r10822 | bugman | 2010-02-22 16:36:13 +0100 (Mon, 22 Feb 2010) | 3 lines Completed the Stereochem_analysis.__init__() docstring, adding all the epydoc tags. ........ r10823 | bugman | 2010-02-22 16:45:27 +0100 (Mon, 22 Feb 2010) | 3 lines Fixed the x-axis label for the scaled Q-factor vs. Q-factor correlation plot. ........ r10824 | bugman | 2010-02-22 17:03:21 +0100 (Mon, 22 Feb 2010) | 3 lines Changed the axis ranges for the RDC Q-factor vs. NOE Q-factor correlation plot. ........ r10825 | bugman | 2010-02-22 18:04:14 +0100 (Mon, 22 Feb 2010) | 6 lines Added the -i or --info option to relax. This causes all of the information about relax and Python to be printed by calling Info_box.print_sys_info(). This option will be useful for determining issues with relax installs! ........ r10826 | bugman | 2010-02-22 18:10:52 +0100 (Mon, 22 Feb 2010) | 3 lines Shifted the relax intro string (written to STDOUT) from the interpreter module to the Info_box. ........ r10827 | bugman | 2010-02-22 18:17:12 +0100 (Mon, 22 Feb 2010) | 5 lines Renamed Info_box.print_sys_info() to Info_box.sys_info(). The method now returns the info string, and this is printed later. ........ r10828 | bugman | 2010-02-22 18:19:09 +0100 (Mon, 22 Feb 2010) | 3 lines Replaced the relax version line with the full relax intro when using the -i cmdline flag. ........ r10829 | bugman | 2010-02-22 19:59:57 +0100 (Mon, 22 Feb 2010) | 14 lines The Info_box.package_info() has been added to provide package information. This is show with the -i cmdline option. The following packages are currently reported: minfx bmrblib numpy Numeric ScientificPython wxPython mpi4py scons epydoc ........ Modified: branches/multi_processor_merge/ (props changed) branches/multi_processor_merge/auto_analyses/stereochem_analysis.py branches/multi_processor_merge/generic_fns/grace.py branches/multi_processor_merge/info.py branches/multi_processor_merge/prompt/interpreter.py branches/multi_processor_merge/relax branches/multi_processor_merge/sample_scripts/stereochem_analysis.py branches/multi_processor_merge/test_suite/system_tests/__init__.py branches/multi_processor_merge/test_suite/system_tests/relax_fit.py branches/multi_processor_merge/test_suite/test_suite_runner.py branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/multi_processor_merge/auto_analyses/stereochem_analysis.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/auto_analyses/stereochem_analysis.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/generic_fns/grace.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/grace.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/info.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/info.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/prompt/interpreter.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/interpreter.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/relax URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/relax?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/sample_scripts/stereochem_analysis.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/sample_scripts/stereochem_analysis.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/test_suite/system_tests/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/__init__.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/test_suite/system_tests/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/relax_fit.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/test_suite/test_suite_runner.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/test_suite_runner.py?rev=10839&r1=10838&r2=10839&view=diff Modified: branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py?rev=10839&r1=10838&r2=10839&view=diff