Gary,
Thank you for making the changes. I tried to compile the modules, but
the two include statements
/* functions for chi2 and exponential */
#include c_chi2.h
#include exponential.h
are causing problems. If these files have been created with the
relevant function prototypes, they can be
Those additions fixed the problems. The test suite of my checked out
copy now passes.
Edward
On 4/10/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Author: macraild
Date: Mon Apr 10 10:55:59 2006
New Revision: 2460
URL: http://svn.gna.org/viewcvs/relax?rev=2460view=rev
Log:
Adds the
:
+if not global_stats or not combine:
# Skip unselected residues.
if not self.relax.data.res[self.run][instance].select:
return None, None, None
Edward
On 4/11/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
I have a feeling this is a failure of the model
For an email which was accidentally not sent to the mailing lists it
may be better to resend the email rather than forwarding it as your
forwarded post started a new thread in
(https://mail.gna.org/public/relax-devel/2006-04/threads.html). It
may be possible to just remove the forwarding junk in
This exact problem was reported as bug #5698 located at
https://gna.org/bugs/?func=detailitemitem_id=5698 and was fixed by
Chris MacRaild. There are a number of options for fixing the problem.
The first and easiest is to wait for version 1.2.4 to be released.
This may not occur for a few weeks
On 5/5/06, Andrew Perry [EMAIL PROTECTED] wrote:
SSH tunnels is probably not the best option for your system. Do you
know anything about MPI?
I have read about MPI but have not implimented anything __YET__;-). Also
I have compiled some MPI based programs. It seems to a bit of a pig and
I
On 5/24/06, Chris MacRaild [EMAIL PROTECTED] wrote:
On Wed, 2006-05-24 at 13:38 +1000, Edward d'Auvergne wrote:
This is a continuation of my response to the thread started by Chris
at https://mail.gna.org/public/relax-devel/2006-05/msg6.html. I
thought I would start a new thread
Hi,
Yes, this does seem like a difference between the steady-state NOE
(NOE) verses the cross-relaxation rate (sigma NOE). Actually all I
did was simply copy Equation 5 of Zhang, P., Dayie, K. T., and Wagner,
G. (1997) JMB, 272, 443-455 rather than calculate it from the C
matricies of the
Hi,
I've finally put my thesis on a temporary hold and have cleared out a
large number of bugs in relax. A number of new bugs surfaced while
fixing others already in the bug tracker
(https://gna.org/bugs/?group=relax). The fixed bugs include:
Bug #5746
On 8/5/06, Chris MacRaild [EMAIL PROTECTED] wrote:
On Sat, 2006-08-05 at 00:08 +1000, Edward d'Auvergne wrote:
2) there is an external module called fpconst which supplies similar
functionality. This relies on the python struct module to compare the
underlying bit sequence with the IEEE
For 1) I would prefer the NaN catching to be outside of the
'minimise/' directory. It should be safe to assume that that code
will soon not be part of relax. As for handling NaNs within the
minimisation code I know of no other minimisation package that does
this - if the user sends garbage
I've tried to setup a new RelaxError and RelaxWarning system. Chris,
do you think these incomplete changes to the 1.2 line are workable?
These changes shouldn't affect how the program operates and
RelaxErrors can be slowly (or very quickly) migrated to this system.
Edward
On 8/12/06, [EMAIL
I'm not so keen about the 'try:' system. For small programs it works
beautifully. However within relax exceptions can be quite difficult
to handle. For example handling an exception thrown by thread (in
threading mode this is a major headache that I haven't fully solved).
This will come
One more thing, the message argument which will be a string containing
the name of the Warning object can be ignored.
On 8/17/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
relax import warnings
relax def format(message, category, filename, lineno):
relax| return RelaxWarning: %s\n
On 8/17/06, Chris MacRaild wrote:
On Thu, 2006-08-17 at 03:15 +1000, Edward d'Auvergne wrote:
A problem that needs to be solved is how do we implement specific
warnings? For example if two distant areas of relax test for zero
length XH bond vectors, there should be one function
The traceback results look identical to that of the error system.
Once the 'format()' function has been moved into the 'self' namespace
I'm happy for this branch to be merged back into the 1.2 line. The
relax test-suite passes and the code is all good. This implements all
of the ideas discusses
the issue for your data? Also, would you have a different
truncated PDB file I could use for debugging? I may need to do some
testing before closing your bug report.
Thanks,
Edward
On 10/1/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
Alex, do you get the following message when using
/msg00046.html
(Message-id: [EMAIL PROTECTED]).
If anyone has ideas on how to handle multimeric PDB files, it would
be appreciated.
Thanks,
Edward
On 10/1/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
I've attempted to fix bug #7241 (https://gna.org/bugs/?7241). I've
committed the changes
Thank you for accepting the position. If you wish, later on you can
either upgrade to a more intensive position or pass up the job if it
becomes too much work or you move on to other things. If you would
like more information, a brilliant reference for running or
participating in an open source
Hi,
Unfortunately I have been unable to reproduce the bug. I've used the
data that you attached Alex and modified the runner script to use both
my current copy of the 1.2 repository line and relax version 1.2.7 (as
your traceback message suggests that that was the version you were
using). I
problems ... I swear, it
gave me those errors before! This is very odd ...
Alex
On 10/5/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
Hi,
Unfortunately I have been unable to reproduce the bug. I've used the
data that you attached Alex and modified the runner script to use both
my current copy
Is the data you attached exactly the same data that originally caused the error?
On 10/6/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
It may have inadvertently been fixed in one of the many bug fixes that
have gone into the repository lately.
On 10/6/06, Alexandar Hansen [EMAIL PROTECTED
, the bug report can easily be reopened (you may need
to ask for it to be reopened though).
Edward
On 10/6/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
Yes. I haven't changed anything. I merely typed 'svn up' and reran my
script and it worked.
Alex
On 10/5/06, Edward d'Auvergne [EMAIL PROTECTED
This is a message to announce that a new set of web pages have been
added to http://nmr-relax.com. Using the program Epydoc
(http://epydoc.sourceforge.net/) I have created API documentation for
relax (using r1407 of the SVN repository path
https://svn.sourceforge.net/svnroot/epydoc/trunk/epydoc).
+1000, Edward d'Auvergne wrote:
This is a message to announce that a new set of web pages have been
added to http://nmr-relax.com. Using the program Epydoc
(http://epydoc.sourceforge.net/) I have created API documentation for
relax (using r1407 of the SVN repository path
https
On Wed, 2006-10-11 at 17:02 +1000, Edward d'Auvergne wrote:
This post is proposal for the redesign the relax data model. This will
affect how data is input into the program, how data is selected, how
molecular structures are handled, how spin systems are handled, and how
many other parts
On 10/11/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
1.5 The relaxation data
While much of the world is happy to use R1, R2, and NOE exclusively for
studying the motions of a (bio)molecule, it would be nice to have an easy
way to expand the amount, and type, of data to be included. I don't
One thought that occured to me is that sometimes its useful to execute a
command on several runs (or pipes) at once. One way of doing this would
be to retain a 'run' argument for user commands, but to have it
optional. If it is passed, then the command executes in each of the
specified runs, but
Thanks for the offer. Currently relax uses the Scientific Python PDB
reader which is very robust even on RNA X-ray structures with big
chunks missing from it (I tried it on a tRNA molecule I downloaded
from the PDB). Other PDB readers could be added to relax, not as
dependencies but as options.
On 10/11/06, Chris MacRaild [EMAIL PROTECTED] wrote:
On Wed, 2006-10-11 at 18:57 +1000, Edward d'Auvergne wrote:
3.5.3 The 'spin' user function class
This new user function class could contain functions such as:
spin.add()
spin.copy()# Copy the spin info (name and num) from another
This idea, although it is good, unfortunately still suffers from the
problem I described in the second paragraph of section 1.1
(https://mail.gna.org/public/relax-devel/2006-10/msg00054.html,
Message-id: [EMAIL PROTECTED]).
The dense branching of the 'run' argument would simply be replaced
Alex, would you be able to test these new user functions on RNA? Do
they work for you if you use the lines
pdb.read(name, self.alex_pdb)
pdb.vectors(name, heteronuc='N1', proton='H1', res_name='G')
pdb.vectors(name, heteronuc='N3', proton='H3', res_name='U')
in you relax script? These changes
Thanks for fixing the link. It can take between 30 min to 2 hours
before you'll see the changes at http://nmr-relax.com.
Edward
On 10/13/06, Dr Gary S Thompson [EMAIL PROTECTED] wrote:
Commit from varioustoxins 2006-10-13 11:38 CEST
corrected browse link
Diffusion models other than local_tm are not working. My Traceback is:
Traceback (most recent call last):
File relax, line 458, in ?
Relax()
File relax, line 170, in __init__
self.interpreter.run()
File /local/home/viochem/relax/prompt/interpreter.py,
line 213, in run
Gary,
Would you like to have a go porting your revisions to the 'float.py'
file and the subsequent changes to the rest of relax from the 1.2 line
into the 1.3 line? All you have to do is have a checked out copy of
the 1.3 line, use two 'svn merge' commands, then check in the changes.
There will
On 10/16/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
On 10/16/06, Chris MacRaild [EMAIL PROTECTED] wrote:
Edward, at some point you mentioned the idea of high-level testing based
on the extensive back-calculated data you have. How much work would be
involved in getting that going
I've chased this problem down to the MS Windows 2.4.3 version of Python. In
this version, attempting the operation NaN**2 fails with a ValueError. In
the Python 2.4.1 in Linux, NaN**2 = NaN! I'm not sure if this is the Python
version number or the Windows Python version which is
,
Edward
On 10/14/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
On 10/14/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
That's my bad ... I forgot to use pdb.read() instead of pdb( ).
However, Now I'm getting this traceback error for diffusion models not
local_tm:
Traceback (most recent
On 10/20/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
First, I tried the test-suite again, and it failed (new failures this time
though :) )
#
# Results of the test suite #
#
Updated to revision 2654:
The model-free tests:
The BFGS and Newton optimisation tests fail of my machine for this
reason (chi2 as big as 7e-21 in some cases). I'm running Linux on dual
64 bit AMDs. Python is 2.4.1 compiled with gcc.
As long as the difference between the model-free parameters is tiny,
this shouldn't matter.
Testing
The function tolerance between iterations is set to 1e-25 (I'll get to
the importance of this in my next post).
Is this the only termination criterion? If so, why are we seeing
apparently normal optimisations terminating with chi2 1e-25 ?
I guess another possibly related question is why is
So here my thought. What we have here are regression tests so we either
1. define a set of results for each test on each particular platform
(you have a mode there someone can run the tests on a version we believe
works, and then say e-mails them to us for inclusion) We then store them
The failure of the BFGS and Newton tests is likely to be because of
the high level functions (Numeric/LAPACK matrix operations in this
case) mentioned by Gary in his post at
https://mail.gna.org/public/relax-devel/2006-10/msg00117.html
(Message-id: [EMAIL PROTECTED]).
After looking more
Chris, I think you may have accidentally modified the wrong copy of
the code? Is the test suite happy? Do you think it's worth doing a
bit of profiling to see if relax is now faster and, if so, by how
much?
Edward
On 10/21/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Author: macraild
results for both versions of code, but
I've not yet done any profiling or performance tests.
Chris
On Sat, 2006-10-21 at 02:02 +1000, Edward d'Auvergne wrote:
Chris, I think you may have accidentally modified the wrong copy of
the code? Is the test suite happy? Do you think it's worth doing a
bit
On 10/26/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
During discussions with James Horne, James helped with a lot of
debugging of relax back in 2004 prior to relax being publicly
released, a few ideas were raised about how to represent the diffusion
tensor superimposed onto the 3D molecular
I've completed a bit more work for this task and I think I now have
everything functional. This includes revision r2668 which fixed the
missing import of the re 'match' function, r2669 which fixed the names
of the nucleic acids by stripping the letter 'R' prefixed by
Scientific python, and r2670
think there's an easy conversion
from Da to Dratio, is there?
Alex - Mr. RNA problem starter :)
On 10/26/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
I've completed a bit more work for this task and I think I now have
everything functional. This includes revision r2668 which fixed
In the new PDB file, which by default could be called 'tensor.pdb',
the atoms could all be set to a new residue called 'TNS' (an abbrev.
of tensor). The residue could be setup using the HET, HETNAM, and
FORMUL records, each atom could be represented by a HETATM record,
followed by the TER
On 10/26/06, Chris MacRaild [EMAIL PROTECTED] wrote:
I'm still failing on the grid search, both BFGS and the Newton
+backtracking tests (though the reasons for failure are new).
For the grid search I have:
Parameter values: array([ 1., 0., 0.])
Function value: 3.9844117908982244
On 10/27/06, Sebastien Morin [EMAIL PROTECTED] wrote:
Hi all !
I also like the Tensor representation of the diffusion tensor.
If Molmol is a problem for connectivities and heteroatoms, why not change
relax to output script for Pymol instead of Molmol ? This is just a
proposition since I'm
I've now committed all the changes. Does anyone still have a system
in which the relax test suite fails on either the 1.2 or 1.3
repository lines?
Edward
On 10/27/06, Edward d'Auvergne [EMAIL PROTECTED] wrote:
On 10/26/06, Chris MacRaild [EMAIL PROTECTED] wrote:
I'm still failing
Daniel, have you encountered any more problems with the
'grace.write()' user function to plot the reduced spectral density
mapping data? If everything seems okay, I'll close this task (see
https://gna.org/task/?group=relax).
Thanks,
Edward
On 10/22/06, Edward d Auvergne [EMAIL PROTECTED]
That'll be another bug! Could you create another bug report. Thanks.
Edward
On 10/27/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
relax completes without problem (other than not choosing a model for me, but
that's my problem :) ). In the results.bz2, however, all of my nuclei are
On 10/28/06, Sebastien Morin [EMAIL PROTECTED] wrote:
Hi Edward
Well, I'm sorry about my absence of knowledge of the details of the
Pymol licensing... I'm not so much of a developer and obviously often
see things much simpler than they are.
I just wanted to throw the idea about Pymol.
It is
On 10/28/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Hi Edward-
I am able to feed commands into PyMOL from Tcl/Tk scripts through the
use of UNIX pipes. From within the Tcl/Tk script, a pipe is opened
to PyMOL, and the script sends commands to PyMOL. I can tell PyMOL
to open a PDB file,
On 10/28/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Here is the an example of how to do this in Tcl:
set PYMOL [open |pymol -pq w]
puts $PYMOL viewport 400,400
[ snip ]
flush $PYMOL
Here is a page describing the command line options:
and flush.
I could try to figure these out if you would like.
Doug
On Oct 27, 2006, at 11:29 AM, Edward d'Auvergne wrote:
On 10/28/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Hi Edward-
I am able to feed commands into PyMOL from Tcl/Tk scripts through the
use of UNIX pipes. From within
On 10/30/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Actually, the same thing happens on my end in Tcl/Tk, but I only need/
use the pipe while the script is running. Perhaps using a named pipe
will resolve the problem?
http://en.wikipedia.org/wiki/Named_pipe
I haven't played with named
In response to the sub-thread started by Sebastien Morin at
https://mail.gna.org/public/relax-devel/2006-10/msg00147.html
(Message-id: [EMAIL PROTECTED]), I have started to
implement rudimentary support for interfacing between relax and PyMOL
using the '-p' flag information provided by Douglas
Oh, for files such 'specific_fns/model_free.py' which is ~5600 lines
long, it might be better to have multiple unit files corresponding to
the single file.
Edward
On 10/30/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Andrew Perry wrote:
Hopefully not too off topic, but this little article
I would suggest that all the current tests move into the directory
'test_suite/function_tests' (or maybe 'system_tests'). All the unit
tests would go into 'test_suite/unit_tests'. In the base directory
'test_suite', a new file is created to run the unit tests, then run
the function or system
I would suggest to add three directories within the 'test_suite'
directory: 'unit_tests', 'system_tests', and 'regression_tests'.
I would suggest that the unit tests are kept with their Module as it
makes it easier to check what test goes with what, avoids name clashes
and allows you to
the longitude
and latitude. This results in a representation with longitudinal and
latitudinal lines.
Edward
P.S. I will probably soon merge all this new code back into the 1.3
line. It appears to be bug free at the moment.
On Thu, 2006-10-26 at 13:45 +1000, Edward d'Auvergne wrote:
During
results superimposed
onto the structure are not functional. Someone will need to generate
sample macros manually and then code them into relax.
Edward
On Mon, 2006-10-30 at 18:17 +1100, Edward d'Auvergne wrote:
In response to the sub-thread started by Sebastien Morin at
https://mail.gna.org
pymol.cartoon() doesn't work for me. The commands go to pymol (they
appear in the tcl gui at least) but have no apparent effect. Just doing:
hide everything
show cartoon
on the pymol cmd line has the expected effect.
This could be a PyMOL version issue. Which version are you
On 10/31/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Two comments
1. we need to be able to run the unittests woithou the gui sometimes ;-)
(I tend to view qa lot of gui stuff for calculations as 'sugar' command
lines are often quicker easier and more informative)
Good point. The test-suite
On 11/1/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
2. I think the unit_test folder will need to be a mirror of the relax
source tree otherwise there will be name space clashes...
Could the files be named something like
'test_specific_fns_model_free.py
On 11/1/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
It's starting to shape up and it's looking good. The unit tests
framework can now evolve from your 'testfloat' class. Do you think
the unit test code follow the relax convention of the first letter of
the class
That was simple, I didn't know about the 'basename()' and 'splitext()'
os functions. I'll merge all of the changes that have occurred within
the 1.3 line since the creation of the 'tensor_pdb' branch and then
incorporate this function. Another thing for tomorrow (unless you
would like to do it
2. I think the unit_test folder will need to be a mirror of the relax
source tree otherwise there will be name space clashes...
Could the files be named something like
'test_specific_fns_model_free.py'? That would avoid many directories.
I'm not worried about complexity with the test
On 11/1/06, Douglas Kojetin [EMAIL PROTECTED] wrote:
Is there sample data included with relax so we can view this new
feature?
A simple way is to test this is invent stuff - that's what I did when
I was creating this code. I then applied it to real data later. For
example I used the
It wasn't too important to port the floating point code to the
'tensor_pdb' branch yet. I was going to, later on, bulk port all the
revisions applied to the 1.3 line since the branch point (to keep the
branch up to date). I'll need to port every single revision applied
the 1.3 line prior to
An important question is how would you define 'auto'? A number of
algorithms would be required. Would you loop over all atoms of all
residues and pick the atom furthest away from the centre of mass?
Probably the easiest would be to scale relative to the molecular mass,
though a maximum
Yes I can have a go. Time is quite tight here at the moment so if things
are not going fast enough don't be afraid to yank it, back I wont be
embarrased ;-)
Oh well, we'll see what happens.
To round things out
1. are you saying that I should be able to do one big bang merge at
somepoint
On 11/2/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
On 11/2/06, Gary S. Thompson [EMAIL PROTECTED] wrote:
Edward d'Auvergne wrote:
Make sure that your commit contains solely the bug fix (commit early
and often is the open source way). Then just merge
Hi,
Would anyone disapprove of the idea of renaming the user function
class 'pdb' to 'structure' within the 1.3 line? The change would
involve the renaming of the current user functions (including those of
the 'tensor_pdb' branch) from:
pdb.create_tensor_pdb()
pdb.read()
pdb.vectors()
to the
Thank you Gary for the quick response and fix to bug #7641
(http://gna.org/bugs/?7641). Alex, now that Gary has ported the fix
from the 1.2 line into 1.3 line (as well as the 'test_suite' branch),
would you be able to confirm that the bug has been resolved? There
should no longer be a
is unavailible, try compiling
the C modules.
relax repository checkout
Protein dynamics by NMR relaxation data
analysis
Copyright (C) 2001-2006 Edward d'Auvergne
This is free software which you
That's a sneaky way of avoiding the porting of the 1.3 line changes
into the branch and then merging the branch back ;)
Edward
On 11/9/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Author: macraild
Date: Wed Nov 8 17:33:12 2006
New Revision: 2775
URL:
Ta. I'll have a new release out soon.
Edward
On 11/9/06, Alexandar Hansen [EMAIL PROTECTED] wrote:
When I first did 'svn st', float.py had a 'C' in front of it. I went ahead
and did the revert followed by svn up and everything's working fine.
Alex
On 11/8/06, Edward d'Auvergne [EMAIL
that is present after linux complication
Would it be possible to change the
#! /usr/bin/env python
line in relax to
#! /usr/bin/env python
or would that break functionality?
Doug
On Nov 8, 2006, at 11:07 AM, Edward d'Auvergne wrote:
I wonder if it is the file 'maths_fns/relax_fit.dylib
any changes. The modifications you made work well,
and the test in 1.3/test_suite/data/curve_fitting finished as expected.
Thanks,
Doug
On Nov 9, 2006, at 3:46 AM, Edward d'Auvergne wrote:
That's right, I have added the data for running the exponential curve
fitting tests but just haven't
Now that I've finished writing the code in the 'tensor_pdb' branch,
I'll soon merge it back into the 1.3 line. Chris, the work on the
scaling of the diffusion rates to be proportional to mass in the
tensor PDB file can continue within the 1.3 line. Anyway, if you make
any changes to the
This code is starting to shape up. There are a few important points
about 'unit_test_runner.py' though. The unit test runner will
eventually be executed by relax once I write the framework for
integrating the unit and system tests. You have defined the function
'getStartupPath' to use
Yes, I have replicated and confirmed bug #7755
(http://gna.org/bugs/?7755). I'm in the process of working out a
solution. The ZeroDivisionError is another bug I have encountered
whereby all Monte Carlo simulations have failed and have been
eliminated. Hence n, the number of Monte Carlo
Hi,
I've now ported all the changes which have occurred within the 1.3
line into the 'test_suite' branch. See the thread starting at
https://mail.gna.org/public/relax-devel/2006-11/msg00197.html
(Message-id: [EMAIL PROTECTED])
for more details.
I have used the new subversion 1.4.2 which saved
I have also merged the 'test_suite' branch back into the 1.3 line.
Changes can still be made to the 'test_suite' branch but I would
recommend that everything now occurs within the 1.3 line.
I would go ahead and scub the test_suite branch then. Should I go ahead and
make the various other
Actually on
the subject of these functions, the ones not defined as class methods,
they could all be shifted into the classes and accessed by typing
'self.get_module_relative_path()'. Apart from the print statements at
the end of 'unit_test_runner.py', these functions are only
Hi,
You are more than welcome to give it a go. relax has been
specifically designed to make it easy for non-programmers to get
involved.
The first thing to do if you haven't played with Python before would
be to have a read of the Python Tutorial
(http://docs.python.org/tut/). The core of
On 1/8/07, gary thompson [EMAIL PROTECTED] wrote:
mailRedesign of the relax data model: 1. Why change?
On Wed, 2006-10-11 at 17:02 +1000, Edward d'Auvergne wrote:
This post is proposal for the redesign the relax data model. This will
affect how data is input into the program, how
and papers...
I'll let you know when I'm finished with that and feel I can start
writing some simple things...
Thanks for letting me in !
Sébastien :)
Edward d'Auvergne wrote:
Hi,
You are more than welcome to give it a go. relax has been
specifically designed to make it easy for non
On 1/16/07, Chris MacRaild [EMAIL PROTECTED] wrote:
On Mon, 2007-01-15 at 17:44 +1100, Edward d'Auvergne wrote:
[snip]
Some asides
A. I believe the runs that are passed around in relax are strings
which are then used to lookup data in a map. Why not just have
(runs/pipes) as objects
all runs are stored in a dictionary, keyed by run name, but only the
run-selection machinery should access this dictionary. The current run
should be the object self.relax.data.run (or something simiar), and all
relax functions should operate on that object.
I agree, however I would
Hi,
This is just a quick message to say that I've added the --unit-test
command line option to the 1.3 line. This will be useful for the
redesign when multiple unit tests are added for each function.
Edward
___
relax (http://nmr-relax.com)
This is
Hi,
Sorry for the long period of silence, I've been busy holidaying,
trying to find myself a job (postdoc), and been sorting out the relax
papers for publication. Hopefully I will soon have more free time for
coding.
I've been trying to work out a problem with the diffusion tensor data
You shouldn't need to do this path munging on a per test basis just
run unit_test_runner against a particular unit_test.py file or a
directory of unit tests and everyting should work
e.g.
./unit_test_runner.py data/test_diff_tensor.py
or in unit_tests
./unit_test_runner.py .
the
That's not a bad idea incorporating the OptionParser() into the stand
alone unit test operation. It should standardise it's behaviour. I
wonder if we can catch stdout, which isn't caught by the python
unittest framework, and then use arguments to either display or hide
the output when a test
Hi,
Would anyone have an issue with the merging the 'error_import' branch
back into the 1.3 line? The new code implements the ideas from the
'builtins' thread (see
https://mail.gna.org/public/relax-devel/2007-02/threads.html).
Firstly all of the data which was previously placed into __builtin__
]). The design will
need to take into account the user function docstrings, relax help
system, and the relax manual docstring fetching code.
4. Create the spin_loop function (Edward d'Auvergne,
https://mail.gna.org/public/relax-devel/2006-10/msg00057.html,
Message-id: [EMAIL PROTECTED]).
Use a generator
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