Author: bugman
Date: Mon Nov 17 10:20:46 2014
New Revision: 26589
URL: http://svn.gna.org/viewcvs/relax?rev=26589&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/space_mapping_refactor/ (props changed)
branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
branches/space_mapping_refactor/data_store/exp_info.py
branches/space_mapping_refactor/docs/devel/Release_Checklist
branches/space_mapping_refactor/scons/manuals.py
branches/space_mapping_refactor/test_suite/system_tests/model_free.py
Propchange: branches/space_mapping_refactor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Nov 17 10:20:46 2014
@@ -1 +1 @@
-/trunk:1-26566
+/trunk:1-26586
Modified:
branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py?rev=26589&r1=26588&r2=26589&view=diff
==============================================================================
--- branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
(original)
+++ branches/space_mapping_refactor/auto_analyses/relax_disp_repeat_cpmg.py
Mon Nov 17 10:20:46 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/space_mapping_refactor/data_store/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/data_store/exp_info.py?rev=26589&r1=26588&r2=26589&view=diff
==============================================================================
--- branches/space_mapping_refactor/data_store/exp_info.py (original)
+++ branches/space_mapping_refactor/data_store/exp_info.py Mon Nov 17
10:20:46 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/space_mapping_refactor/docs/devel/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/docs/devel/Release_Checklist?rev=26589&r1=26588&r2=26589&view=diff
==============================================================================
--- branches/space_mapping_refactor/docs/devel/Release_Checklist
(original)
+++ branches/space_mapping_refactor/docs/devel/Release_Checklist Mon
Nov 17 10:20:46 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/space_mapping_refactor/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/scons/manuals.py?rev=26589&r1=26588&r2=26589&view=diff
==============================================================================
--- branches/space_mapping_refactor/scons/manuals.py (original)
+++ branches/space_mapping_refactor/scons/manuals.py Mon Nov 17 10:20:46
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/space_mapping_refactor/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/space_mapping_refactor/test_suite/system_tests/model_free.py?rev=26589&r1=26588&r2=26589&view=diff
==============================================================================
--- branches/space_mapping_refactor/test_suite/system_tests/model_free.py
(original)
+++ branches/space_mapping_refactor/test_suite/system_tests/model_free.py
Mon Nov 17 10:20:46 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):
r26589 - in /branches/space_mapping_refactor: ./ auto_analyses/ data_store/ docs/devel/ scons/ test_suite/system_tests/