Author: tlinnet
Date: Tue Jul 22 12:02:31 2014
New Revision: 24596
URL: http://svn.gna.org/viewcvs/relax?rev=24596&view=rev
Log:
Merged revisions 24521,24526-24528,24535-24536,24543,24549-24550,24562 via
svnmerge from
svn+ssh://tlinnet@xxxxxxxxxxx/svn/relax/trunk
........
r24521 | bugman | 2014-07-11 10:39:52 +0200 (Fri, 11 Jul 2014) | 6 lines
Updated the minfx version in the release checklist document to 1.0.8.
This version has not been released yet, but it will include important fixes
and additions for
constrained parallelised grid searches.
........
r24526 | bugman | 2014-07-11 16:19:49 +0200 (Fri, 11 Jul 2014) | 3 lines
Fix for a broken link in the development chapter of the relax manual.
........
r24527 | bugman | 2014-07-11 16:25:35 +0200 (Fri, 11 Jul 2014) | 6 lines
Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax
manual.
The B14 model links to
http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken
as the B in B14 was capitalised.
........
r24528 | bugman | 2014-07-11 16:43:26 +0200 (Fri, 11 Jul 2014) | 6 lines
Sent in the verbosity argument value to the minfx.grid.grid_split()
function.
The minfx function in the next release (1.0.8) will now be more verbose, so
this will help with user
feedback when running the model-free analysis on a cluster or multi-core
system using MPI.
........
r24535 | bugman | 2014-07-15 12:36:47 +0200 (Tue, 15 Jul 2014) | 5 lines
Created the time user function.
This is just a shortcut for printing out the output of the time.asctime()
function.
........
r24536 | bugman | 2014-07-15 12:38:40 +0200 (Tue, 15 Jul 2014) | 3 lines
The time user function now uses the chronometer Oxygen icon in the GUI.
........
r24543 | bugman | 2014-07-16 20:34:10 +0200 (Wed, 16 Jul 2014) | 3 lines
Added the missing timing module to the relax library package __all__ list.
........
r24549 | bugman | 2014-07-17 14:56:24 +0200 (Thu, 17 Jul 2014) | 5 lines
Removed the line wrapping in the epydoc parameter section of the
optimisation function docstrings.
This is for the pipe_control.minimise module.
........
r24550 | bugman | 2014-07-17 14:57:01 +0200 (Thu, 17 Jul 2014) | 3 lines
More docstring line wrapping removal from pipe_control.minimise.
........
r24562 | bugman | 2014-07-18 10:58:56 +0200 (Fri, 18 Jul 2014) | 7 lines
Bug fix for the parameter units descriptions.
This only affects a few rare parameters. The specific analysis API
parameter object units() method
was incorrectly checking if the units value is a function - it was checking
the parameter conversion
factor instead.
........
Added:
branches/disp_spin_speed/lib/timing.py
- copied unchanged from r24562, trunk/lib/timing.py
Modified:
branches/disp_spin_speed/ (props changed)
branches/disp_spin_speed/docs/Release_Checklist
branches/disp_spin_speed/docs/latex/develop.tex
branches/disp_spin_speed/docs/latex/dispersion.tex
branches/disp_spin_speed/lib/__init__.py
branches/disp_spin_speed/pipe_control/minimise.py
branches/disp_spin_speed/specific_analyses/model_free/api.py
branches/disp_spin_speed/specific_analyses/parameter_object.py
branches/disp_spin_speed/user_functions/sys_info.py
Propchange: branches/disp_spin_speed/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jul 22 12:02:31 2014
@@ -1 +1 @@
-/trunk:1-24511
+/trunk:1-24595
Modified: branches/disp_spin_speed/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/Release_Checklist?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/docs/Release_Checklist (original)
+++ branches/disp_spin_speed/docs/Release_Checklist Tue Jul 22 12:02:31
2014
@@ -70,7 +70,7 @@
Bundle minfx and bmrblib by checking out the latest stable release tags, for
example:
-$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/minfx/tags/1.0.7/minfx
+$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/minfx/tags/1.0.8/minfx
$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/bmrblib/tags/1.0.3/bmrblib
@@ -107,7 +107,7 @@
$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/2.0.1
$ cd 2.0.1
-$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/minfx/tags/1.0.7/minfx
+$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/minfx/tags/1.0.8/minfx
$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/bmrblib/tags/1.0.3/bmrblib
$ scons binary_dist key=xxxxx
@@ -115,7 +115,7 @@
$ svn co http://svn.gna.org/svn/relax/tags/2.0.1
$ cd 2.0.1
-$ svn co http://svn.gna.org/svn/minfx/tags/1.0.7/minfx
+$ svn co http://svn.gna.org/svn/minfx/tags/1.0.8/minfx
$ svn co http://svn.gna.org/svn/bmrblib/tags/1.0.3/bmrblib
$ scons binary_dist
Modified: branches/disp_spin_speed/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/latex/develop.tex?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/docs/latex/develop.tex (original)
+++ branches/disp_spin_speed/docs/latex/develop.tex Tue Jul 22 12:02:31
2014
@@ -918,7 +918,7 @@
Having a large web of links across relax's infrastructure aids in the search
engine indexing of the mailing list archives and the
\href{http://www.nmr-relax.com}{http://www.nmr-relax.com} web site.
The web of links is useful for catching those Google bots.
-That way the Google searching of the mailing list archives located on the
\href{http://www.nmr-relax.com/\-communication.html}{communication web page}
will be more up to date.
+That way the Google searching of the mailing list archives located on the
\href{http://www.nmr-relax.com/communication.html}{communication web page}
will be more up to date.
However to increase the search engine ranking of the web site, links to
\href{http://www.nmr-relax.com}{http://www.nmr-relax.com} from external sites
is required.
This is one reason why relax can be found at a number of sites across the
web:
\begin{description}
Modified: branches/disp_spin_speed/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/latex/dispersion.tex?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/docs/latex/dispersion.tex (original)
+++ branches/disp_spin_speed/docs/latex/dispersion.tex Tue Jul 22 12:02:31
2014
@@ -653,7 +653,7 @@
More information about the B14 full model is available from:
\begin{itemize}
\item the relax wiki at \url{http://wiki.nmr-relax.com/B14\_full},
- \item the API documentation at
\url{http://www.nmr-relax.com/api/3.2/lib.dispersion.B14-module.html},
+ \item the API documentation at
\url{http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html},
\item the relaxation dispersion page of the relax website at
\url{http://www.nmr-relax.com/analyses/relaxation\_dispersion.html#B14\_full}.
\end{itemize}
@@ -672,7 +672,7 @@
More information about the B14 model is available from:
\begin{itemize}
\item the relax wiki at \url{http://wiki.nmr-relax.com/B14},
- \item the API documentation at
\url{http://www.nmr-relax.com/api/3.2/lib.dispersion.B14-module.html},
+ \item the API documentation at
\url{http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html},
\item the relaxation dispersion page of the relax website at
\url{http://www.nmr-relax.com/analyses/relaxation\_dispersion.html#B14}.
\end{itemize}
Modified: branches/disp_spin_speed/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/__init__.py?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/__init__.py (original)
+++ branches/disp_spin_speed/lib/__init__.py Tue Jul 22 12:02:31 2014
@@ -56,6 +56,7 @@
'statistics',
'structure',
'text',
+ 'timing',
'warnings',
'xml'
]
Modified: branches/disp_spin_speed/pipe_control/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/pipe_control/minimise.py?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/pipe_control/minimise.py (original)
+++ branches/disp_spin_speed/pipe_control/minimise.py Tue Jul 22 12:02:31
2014
@@ -34,8 +34,7 @@
def calc(verbosity=1):
"""Function for calculating the function value.
- @param verbosity: The amount of information to print. The higher the
value, the greater
- the verbosity.
+ @param verbosity: The amount of information to print. The higher the
value, the greater the verbosity.
@type verbosity: int
"""
@@ -86,21 +85,15 @@
def grid_search(lower=None, upper=None, inc=None, constraints=True,
verbosity=1):
"""The grid search function.
- @param lower: The lower bounds of the grid search which must be
equal to the number of
- parameters in the model.
+ @param lower: The lower bounds of the grid search which must be
equal to the number of parameters in the model.
@type lower: array of numbers
- @param upper: The upper bounds of the grid search which must be
equal to the number of
- parameters in the model.
+ @param upper: The upper bounds of the grid search which must be
equal to the number of parameters in the model.
@type upper: array of numbers
- @param inc: The increments for each dimension of the space for
the grid search. The
- number of elements in the array must equal to the
number of parameters in
- the model.
+ @param inc: The increments for each dimension of the space for
the grid search. The number of elements in the array must equal to the
number of parameters in the model.
@type inc: array of int
- @param constraints: If True, constraints are applied during the grid
search (elinating parts of
- the grid). If False, no constraints are used.
+ @param constraints: If True, constraints are applied during the grid
search (elinating parts of the grid). If False, no constraints are used.
@type constraints: bool
- @param verbosity: The amount of information to print. The higher the
value, the greater
- the verbosity.
+ @param verbosity: The amount of information to print. The higher the
value, the greater the verbosity.
@type verbosity: int
"""
@@ -241,8 +234,7 @@
def reset_min_stats(data_pipe=None, spin=None):
"""Function for resetting the minimisation statistics.
- @param data_pipe: The name of the data pipe to reset the minimisation
statisics of. This
- defaults to the current data pipe.
+ @param data_pipe: The name of the data pipe to reset the minimisation
statisics of. This defaults to the current data pipe.
@type data_pipe: str
@param spin: The spin data container if spin specific data is to
be reset.
@type spin: SpinContainer
Modified: branches/disp_spin_speed/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/model_free/api.py?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/specific_analyses/model_free/api.py
(original)
+++ branches/disp_spin_speed/specific_analyses/model_free/api.py Tue
Jul 22 12:02:31 2014
@@ -1366,7 +1366,7 @@
print("Parallelised diffusion tensor grid search.")
# Loop over each grid subdivision.
- for subdivision in
grid_split(divisions=processor.processor_size(), lower=opt_params.lower,
upper=opt_params.upper, inc=opt_params.inc):
+ for subdivision in
grid_split(divisions=processor.processor_size(), lower=opt_params.lower,
upper=opt_params.upper, inc=opt_params.inc, verbosity=verbosity):
# Set the points.
opt_params.subdivision = subdivision
Modified: branches/disp_spin_speed/specific_analyses/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/parameter_object.py?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/specific_analyses/parameter_object.py
(original)
+++ branches/disp_spin_speed/specific_analyses/parameter_object.py Tue
Jul 22 12:02:31 2014
@@ -703,7 +703,7 @@
self.check_param(name)
# Function.
- if isinstance(self._conv_factor[name], FunctionType) or
isinstance(self._conv_factor[name], MethodType):
+ if isinstance(self._units[name], FunctionType) or
isinstance(self._units[name], MethodType):
return self._units[name]()
# Return the value.
Modified: branches/disp_spin_speed/user_functions/sys_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/user_functions/sys_info.py?rev=24596&r1=24595&r2=24596&view=diff
==============================================================================
--- branches/disp_spin_speed/user_functions/sys_info.py (original)
+++ branches/disp_spin_speed/user_functions/sys_info.py Tue Jul 22 12:02:31
2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2011-2013 Edward d'Auvergne
#
+# Copyright (C) 2011-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -24,6 +24,7 @@
# relax module imports.
from info import print_sys_info
+from lib.timing import print_time
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -41,3 +42,18 @@
uf.gui_icon = "oxygen.actions.help-about"
uf.wizard_size = (700, 400)
uf.wizard_apply_button = False
+
+
+# The time user function.
+uf = uf_info.add_uf('time')
+uf.title = "Display the current time."
+uf.title_short = "Current time."
+uf.display = True
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This user function will display the current time
which can be useful for timing long calculations by having time information
in any saved log files.")
+uf.backend = print_time
+uf.menu_text = "&time"
+uf.gui_icon = "oxygen.actions.chronometer"
+uf.wizard_size = (700, 400)
+uf.wizard_apply_button = False
r24596 - in /branches/disp_spin_speed: ./ docs/ docs/latex/ lib/ pipe_control/ specific_analyses/ specific_analyses/model_fr...