Author: bugman
Date: Fri Feb 1 22:13:00 2013
New Revision: 18378
URL: http://svn.gna.org/viewcvs/relax?rev=18378&view=rev
Log:
Merged revisions 18362-18364,18367-18368,18374 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18362 | bugman | 2013-02-01 17:06:40 +0100 (Fri, 01 Feb 2013) | 5 lines
Fix for the Bmrb.test_bug_20471_structure_present system test.
The bmrb.read user function call should and does raise a RelaxError.
........
r18363 | bugman | 2013-02-01 17:10:35 +0100 (Fri, 01 Feb 2013) | 3 lines
Modified the bmrb.read documentation to make it clearer that the data pipe
must be empty.
........
r18364 | bugman | 2013-02-01 17:27:13 +0100 (Fri, 01 Feb 2013) | 3 lines
Another fix for the new Bmrb.test_bug_20471_structure_present system test.
........
r18367 | bugman | 2013-02-01 18:15:38 +0100 (Fri, 01 Feb 2013) | 6 lines
Merged the relax version 2.2.1 CHANGES file back to trunk.
The command used was:
svn merge -r18365:18366 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.2.1 .
........
r18368 | bugman | 2013-02-01 18:16:04 +0100 (Fri, 01 Feb 2013) | 3 lines
Updated the release checklist to include the devel_scripts/log_converter.py
script usage.
........
r18374 | bugman | 2013-02-01 20:32:35 +0100 (Fri, 01 Feb 2013) | 3 lines
Modified the relax manual subtitle as this is no longer only for relaxation
analysis.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/docs/CHANGES
branches/frame_order_testing/docs/Release_Checklist
branches/frame_order_testing/docs/latex/relax.tex
branches/frame_order_testing/test_suite/system_tests/bmrb.py
branches/frame_order_testing/user_functions/bmrb.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Feb 1 22:13:00 2013
@@ -1,1 +1,1 @@
-/trunk:1-18360
+/trunk:1-18377
Modified: branches/frame_order_testing/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/CHANGES?rev=18378&r1=18377&r2=18378&view=diff
==============================================================================
--- branches/frame_order_testing/docs/CHANGES (original)
+++ branches/frame_order_testing/docs/CHANGES Fri Feb 1 22:13:00 2013
@@ -1,3 +1,36 @@
+Version 2.2.1
+(01 February 2013, from /trunk)
+http://svn.gna.org/svn/relax/tags/2.2.1
+
+ Features:
+ N/A
+
+
+ Changes:
+ * Replaced a reference to freshmeat with Freecode in the Release
checklist document. Freshmeat no longer exists and is now called Freecode
(http://freecode.com/projects/nmr-relax).
+ * Created the Mf.test_bug_20464_missing_ri_data system test to catch
bug #20464. The data comes from the bug report submitted by Stanislava
Panova (stpanova att gmail dot com) at https://gna.org/bugs/?20464.
+ * Created the Structure.test_bug_sr_2998_broken_conect_records
system test. This is to catch the bug reported as service request #2998
(https://gna.org/support/?2998) and is for corrupted PDB files with broken
CONECT records.
+ * Created the
Structure.test_bug_20469_scientific_parser_xray_records system test. This is
to catch bug #20469 (https://gna.org/bugs/?20469).
+ * Created the Structure.test_bug_20470_alternate_location_indicator
system test to catch bug #20470. This report is at
https://gna.org/bugs/?20470.
+ * Created the Structure.test_alt_loc_missing system test. This is
to test that the internal relax PDB reader raises an error when a PDB file is
encountered with alternate location indicators but the alt_loc argument has
not been specified.
+ * Created the Bmrb.test_bug_20471_structure_present to catch bug
#20471 (https://gna.org/bugs/?20471).
+ * Modified the bmrb.read documentation to make it clearer that the
data pipe must be empty.
+
+
+ Bugfixes:
+ * Python 3 fix for a print statement in the metal_pos_opt.py N-state
model system test script.
+ * Python 3 fix for the part of ScientificPython distributed with
relax (for the PDB parser).
+ * Python 3 import fixes for the GUI.
+ * Python 3 fixes for the list sort() method - this has been replaced
by the builtin sorted() function.
+ * Fix for bug #20464 (https://gna.org/bugs/?20464) - the model-free
analysis failure with missing relaxation data. The problem was the
previously missing data had a value of None whereas now the dictionary
element can be missing. Checks have been added to make sure the spin
specific relaxation data structures have the key corresponding to the data.
+ * Fix for the N_state_model.test_monte_carlo_sims system test. On
certain systems, the chi2 check is too stringent.
+ * Fix for the bug reported as the support request #2998
(https://gna.org/support/?2998). CONECT records pointing to non-existent
atoms can now be handled.
+ * Fix for bug #20469 (https://gna.org/bugs/?20469). This is the
Failure in reading X-ray PDB files using the ScientificPython parser. The
ScientificPython Geometry.Transformation module is now distributed with
relax. Some linear algebra imports in the Geometry.TensorModule in newly
used code paths have been fixed as well.
+ * Fix for bug #20470 (https://gna.org/bugs/?20470). The
structure.read_pdb user function now accepts the alt_loc argument for
specifying the alternate location indicator to read. This is used by the
internal PDB reader. The bug was caught by the
Structure.test_bug_20470_alternate_location_indicator system test.
+ * Fix for bug #20471 (https://gna.org/bugs/?20471) - the is_empty()
AttributeError when reading BMRB files. The problem was that the data pipe
is_empty() method was not handling structural data correctly. The is_empty()
method now belongs to the MolContainer objects rather than cdp.structure, and
the object cdp.structure is not always present.
+
+
+
Version 2.2.0
(27 January 2013, from /trunk)
http://svn.gna.org/svn/relax/tags/2.2.0
Modified: branches/frame_order_testing/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/Release_Checklist?rev=18378&r1=18377&r2=18378&view=diff
==============================================================================
--- branches/frame_order_testing/docs/Release_Checklist (original)
+++ branches/frame_order_testing/docs/Release_Checklist Fri Feb 1 22:13:00
2013
@@ -20,7 +20,10 @@
-* Review the SVN logs and add an entry into the CHANGES file (in the 'docs/'
directory) for the current release. Create three sections titled 'Features',
'Changes', and 'Bugfixes'. Commit the changes and then port the revision
back into the main line.
+* Review the SVN logs and add an entry into the CHANGES file (in the 'docs/'
directory) for the current release. Create three sections titled 'Features',
'Changes', and 'Bugfixes'. Commit the changes and then port the revision
back into the main line. The 'devel_scripts/log_converter.py' script can be
used to generate the documentation, which will need major editing (the
starting revision is from the CHANGES merge of the previous release):
+
+$ svn log -v -r18314:HEAD > log
+$ devel_scripts/log_converter.py log
Modified: branches/frame_order_testing/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/relax.tex?rev=18378&r1=18377&r2=18378&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/relax.tex (original)
+++ branches/frame_order_testing/docs/latex/relax.tex Fri Feb 1 22:13:00 2013
@@ -140,10 +140,10 @@
\vspace{\stretch{2}}
% Subtitle.
-{\huge \textbf{A program for NMR relaxation}}
+{\huge \textbf{Molecular dynamics by}}
\vspace{\stretch{0.5}}
-{\huge \textbf{data analysis}}
+{\huge \textbf{NMR data analysis}}
\vspace{\stretch{1}}
% Date.
Modified: branches/frame_order_testing/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/bmrb.py?rev=18378&r1=18377&r2=18378&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/bmrb.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/bmrb.py Fri Feb 1
22:13:00 2013
@@ -30,6 +30,7 @@
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
import dep_check
+from relax_errors import RelaxError
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -249,7 +250,7 @@
# Load the relaxation data.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bmrb'
- self.interpreter.bmrb.read(file='17226.txt', dir=path, version=None,
sample_conditions=None)
+ self.assertRaises(RelaxError, self.interpreter.bmrb.read,
file='17226.txt', dir=path, version=None, sample_conditions=None)
def test_rw_bmrb_3_0_model_free(self):
Modified: branches/frame_order_testing/user_functions/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/bmrb.py?rev=18378&r1=18377&r2=18378&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/bmrb.py (original)
+++ branches/frame_order_testing/user_functions/bmrb.py Fri Feb 1 22:13:00
2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
+# Copyright (C) 2003-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -246,7 +246,7 @@
)
# Description.
uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This will allow most of the data from a BMRB
NMR-STAR formatted file to be loaded into the relax data store. Note that a
data pipe should be created for storing the data, and that currently only
model-free data pipes can be used. Also, only one sample condition can be
read per relax data pipe. Therefore if one of the sample conditions is not
specified and multiple conditions exist in the NMR-STAR file, an error will
be raised.")
+uf.desc[-1].add_paragraph("This will allow most of the data from a BMRB
NMR-STAR formatted file to be loaded into the relax data store. Note that an
empty data pipe should be created for storing the data, and that currently
only model-free data pipes can be used. Also, only one sample condition can
be read per relax data pipe. Therefore if one of the sample conditions is
not specified and multiple conditions exist in the NMR-STAR file, an error
will be raised.")
uf.backend = bmrb.read
uf.menu_text = "&read"
uf.gui_icon = "oxygen.actions.document-open"
r18378 - in /branches/frame_order_testing: ./ docs/ docs/latex/ test_suite/system_tests/ user_functions/