Author: bugman Date: Mon Nov 17 10:16:29 2014 New Revision: 26587 URL: http://svn.gna.org/viewcvs/relax?rev=26587&view=rev Log: Merged revisions 26577-26578,26583-26586 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk ........ r26577 | bugman | 2014-11-14 10:24:21 +0100 (Fri, 14 Nov 2014) | 3 lines Basic Epydoc fix for the data_store.exp_info module. ........ r26578 | bugman | 2014-11-14 10:26:00 +0100 (Fri, 14 Nov 2014) | 3 lines Epydoc fix for the name_pipe() method of the relaxation dispersion auto-analysis for repeated data. ........ r26583 | bugman | 2014-11-14 11:52:51 +0100 (Fri, 14 Nov 2014) | 6 lines Fixes for the HTML user manual compilation. The index.html file was not being created as the main page has changed from 'relax_user_manual.html' to 'The_relax_user_manual.html'. ........ r26584 | bugman | 2014-11-14 11:55:36 +0100 (Fri, 14 Nov 2014) | 9 lines Added a line to the release checklist document about updating the wiki release links. These are for the combined release notes pages at http://wiki.nmr-relax.com/Relax_releases, http://wiki.nmr-relax.com/Relax_release_descriptions, http://wiki.nmr-relax.com/Relax_release_metadata, http://wiki.nmr-relax.com/Relax_release_features, http://wiki.nmr-relax.com/Relax_release_changes, http://wiki.nmr-relax.com/Relax_release_bugfixes, http://wiki.nmr-relax.com/Relax_release_links. ........ r26585 | bugman | 2014-11-14 16:45:49 +0100 (Fri, 14 Nov 2014) | 3 lines Updates for the release announcement section of the release checklist document. ........ r26586 | bugman | 2014-11-16 14:57:22 +0100 (Sun, 16 Nov 2014) | 3 lines Created a system test to catch a rare relaxation data loading problem. ........ Modified: branches/frame_order_cleanup/ (props changed) branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py branches/frame_order_cleanup/data_store/exp_info.py branches/frame_order_cleanup/docs/devel/Release_Checklist branches/frame_order_cleanup/scons/manuals.py branches/frame_order_cleanup/test_suite/system_tests/model_free.py Propchange: branches/frame_order_cleanup/ ------------------------------------------------------------------------------ --- svnmerge-integrated (original) +++ svnmerge-integrated Mon Nov 17 10:16:29 2014 @@ -1 +1 @@ -/trunk:1-26566 +/trunk:1-26586 Modified: branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py?rev=26587&r1=26586&r2=26587&view=diff ============================================================================== --- branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py (original) +++ branches/frame_order_cleanup/auto_analyses/relax_disp_repeat_cpmg.py Mon Nov 17 10:16:29 2014 @@ -807,11 +807,7 @@ def name_pipe(self, method, model, analysis, glob_ini, clusterid=None): - """Generate a unique name for the data pipe. - - @param prefix: The prefix of the data pipe name. - @type prefix: str - """ + """Generate a unique name for the data pipe.""" # Cluster group is none, set to standard free spins. # cdp.clustering['free spins'] Modified: branches/frame_order_cleanup/data_store/exp_info.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/data_store/exp_info.py?rev=26587&r1=26586&r2=26587&view=diff ============================================================================== --- branches/frame_order_cleanup/data_store/exp_info.py (original) +++ branches/frame_order_cleanup/data_store/exp_info.py Mon Nov 17 10:16:29 2014 @@ -122,8 +122,8 @@ def from_xml(self, exp_info_node, file_version=1): """Recreate the element data structure from the XML element node. - @param super_node: The element XML node. - @type super_node: xml.dom.minicompat.Element instance + @param exp_info_node: The element XML node. + @type exp_info_node: xml.dom.minicompat.Element instance @keyword file_version: The relax XML version of the XML file. @type file_version: int """ Modified: branches/frame_order_cleanup/docs/devel/Release_Checklist URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/devel/Release_Checklist?rev=26587&r1=26586&r2=26587&view=diff ============================================================================== --- branches/frame_order_cleanup/docs/devel/Release_Checklist (original) +++ branches/frame_order_cleanup/docs/devel/Release_Checklist Mon Nov 17 10:16:29 2014 @@ -205,6 +205,8 @@ - Convert all model names to internal wiki links (vi search "\<m[0-9]\>\|\<tm[0-9]\>\|No Rex\|R2eff\|LM63\|LM63 3-site\|CR72\|CR72 full\|IT99\|TSMFK01\|B14\|B14 full\|NS CPMG\|MMQ CR72\|NS MMQ\|M61\|DPL94\|TP02\|TAP03\|MP05\|NS R1rho\|BK13"). - Add as many links as possible to the API documentation (to help users dive into the relax code and to help with search engine indexing). +Update all of the release note links for the new version (http://wiki.nmr-relax.com/Category:Release_Notes). + Mailing list ------------ @@ -224,12 +226,13 @@ - Log into Gna! and go to https://gna.org/news/submit.php?group=relax. - Cut and paste all of the wiki text. Delete the initial lower case title formatting text, the final 'See also' section, and any wiki markup. + - Add a paragraph before the 'Download' paragraph with the text 'For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.1.'. - Use the Savane markup to format the text (recipe #236, https://gna.org/cookbook/?func=detailitem&item_id=236). - - As the Savane markup for sectioning is the same as the wiki, the section titles = Description =, = Download =, and = Full list of changes = do not need to be modified (except changing the text 'CHANGES file' to 'Full list of changes'). The same for the subtitles == Features ==, == Changes ==, and == Bugfixes ==. The leading whitespace from the full list of changes must be stripped, but this should already be done in the wiki text. + - As the Savane markup for sectioning is the same as the wiki, the section titles = Description =, = Download =, and = Full list of changes = do not need to be modified (except changing the text 'CHANGES file' to 'Full list of changes' and deleting the metadata). The same for the subtitles == Features ==, == Changes ==, and == Bugfixes ==. - Convert internal [[xyz]] wiki links into proper [http://wiki.nmr-relax.com/xyz] links. - Item references such as bug #7641, task #3122, etc. are automatically converted into links. Savane will replace the links as formatted for the wiki to these links, so nothing needs to be done. + - Remove all symbol formatting ('&', ';', '<sub>', '<sup>', etc.). - The Gna! news items are often truncated, so start a new thread for the rest of the message, responding to that thread for each block of release notes via the [ Reply ] link at the bottom of the page. - - Remove all symbol formatting ('&', ';', '<sub>', '<sup>', etc.). Cross-linking Modified: branches/frame_order_cleanup/scons/manuals.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/scons/manuals.py?rev=26587&r1=26586&r2=26587&view=diff ============================================================================== --- branches/frame_order_cleanup/scons/manuals.py (original) +++ branches/frame_order_cleanup/scons/manuals.py Mon Nov 17 10:16:29 2014 @@ -389,7 +389,7 @@ system(cmd) # Create the proper index.html file. - cmd = "cp -vp %s%srelax_user_manual.html %s%sindex.html" % (dir, path.sep, dir, path.sep) + cmd = "cp -vp %s%sThe_relax_user_manual.html %s%sindex.html" % (dir, path.sep, dir, path.sep) print("Running the command:\n$ %s\n\n\n" % cmd) system(cmd) Modified: branches/frame_order_cleanup/test_suite/system_tests/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/model_free.py?rev=26587&r1=26586&r2=26587&view=diff ============================================================================== --- branches/frame_order_cleanup/test_suite/system_tests/model_free.py (original) +++ branches/frame_order_cleanup/test_suite/system_tests/model_free.py Mon Nov 17 10:16:29 2014 @@ -488,6 +488,19 @@ # Test the model. self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4') self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te', 'rex']) + + + def test_data_loading_failures(self): + """Catch a failure when loading relaxation data.""" + + # The data directory. + dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'sphere' + + # Set up the spin systems. + self.interpreter.sequence.read(file='noe.500.out', dir=dir, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None) + + # Load the data. + self.interpreter.relax_data.read(ri_id='noe500', ri_type='NOE', frq=500000000.0, file='noe.500.out', dir=dir, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id='@N') def test_dauvergne_protocol(self):