Done. Thank for the detailed bug report (https://gna.org/bugs/index.php?12582). That really speeds things up, as you can see! And now that there is a system test for this bug, it can never come back.
Cheers, Edward On Mon, Nov 10, 2008 at 10:02 PM, Edward d'Auvergne <[EMAIL PROTECTED]> wrote: > Hi, > > If this is still a problem, would you be able to create a bug report > for this? The quick link for bug submission is > https://gna.org/bugs/?func=additem&group=relax. Could you possibly > also attach the script to the bug report as well? I'm not sure what > is happening but relax is trying to access relaxation data from a spin > which has no relaxation data associated with it. It is a strange one > as spins with no relaxation data are automatically deselected in the > second last user function - minimise(). Maybe this is triggered by > the new XML results file saving all contents of the spin. > > This is a problem with relax that I cannot currently reproduce (hence > makes my debugging very difficult). Would you be able to include in > the bug report everything you did with your test of the data in > /test_suite/shared_data/model_free/S2_0….0.149/? This would include > all scripts, modifications, etc. needed to reproduce the bug exactly. > I'll then add this to the relax test suite which will allow me to very > quickly kill this bug. > > Cheers, > > Edward > > > > On Mon, Nov 10, 2008 at 5:41 PM, Brosey, Chris A > <[EMAIL PROTECTED]> wrote: >> Greetings, >> >> I now have access to the most recent builds of both relax (relax-1.3) and >> minfx. Running full_analysis.py through the updated versions continues to >> generate the same writing error (same list of commands from the Traceback >> log). Any suggestions? As always, many thanks. >> >> Regards, >> >> Chris >> >> >> -----Original Message----- >> From: Tyler Reddy [mailto:[EMAIL PROTECTED] >> Sent: Wed 11/5/2008 2:23 PM >> To: Edward d'Auvergne >> Cc: Brosey, Chris A; [email protected] >> Subject: Re: Writing/displaying output from full_analysis.py >> >> Since I've been setting up relax on other machines I also remembered that >> you >> will have problems if you don't get the latest build of minfx by going >> into the >> directory for minfx and using subversion: >> >> svn co svn://svn.gna.org/svn/minfx/trunk minfx >> >> (and then all further updates can be done with svn up, as Edward says) >> >> Also, for minfx, don't forget to actually install the new version. You have >> to >> change directory to the nested minfx folder and run >> >> python setup.py install >> >> Tyler >> >> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >> >>> Cheers! That response pretty much covers it. I'm not sure if this is >>> exactly the error I fixed for you Tyler, but I think the repository >>> version doesn't have this problem. It would be useful to get the >>> repository version anyway as then the debugged version will be >>> instantly acessable by typing: >>> >>> $ svn up >>> >>> in the directory of the checked out copy. I can't guarantee a quick >>> response time though as RSI in my wrist is slowing things down >>> significantly - writing an email only with my left hand is hard >>> enough, and debugging one handed would be a nightmare! >>> >>> Regards, >>> >>> Edward >>> >>> >>> On Wed, Nov 5, 2008 at 8:03 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >>>> For the sequence input file I think you want Spin_Name to be N if >>>> this is 15N >>>> relaxation data. I'm also thinking it's not a bad idea to update to >>>> the latest >>>> build of relax using subversion (can easily find/download this software >>>> via >>>> google). This looks vaguely similar to some of the problems Edward had >>>> debugged >>>> for me, so probably worth the time to update if you're going to use this >>>> script. >>>> >>>> The command to execute in the relax directory would be: >>>> >>>> svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 >>>> >>>> And then a newer version of relax is put in a nested folder in the relax >>>> directory. You want to make sure that the system path refers to the >>>> newer build >>>> of relax instead of the one you originally downloaded. When you type >>>> 'relax' it >>>> should say something like 'system repository checkout' instead of 'relax >>>> 1.3.2.' >>>> >>>> So the new directory would be ../relax-1.3.2/relax-1.3 >>>> >>>> Edward will probably have a more effective response, but this stuff will >>>> probably prevent other problems in any case. >>>> >>>> Tyler >>>> >>>> >>>> Quoting "Brosey, Chris A" <[EMAIL PROTECTED]>: >>>> >>>>> Greetings, >>>>> >>>>> I have encountered a problem running the script full_analysis.py >>>>> using v1.3.2 of relax (and python v2.5). I am currently executing >>>>> the script with the MI option (DIFF_MODEL = 'local_tm'). I find that >>>>> the script successfully reads in data files and carries out the grid >>>>> search and minimization specified under the multi_model function for >>>>> the very first 'tm0' model. However, it appears that there is a >>>>> problem executing the final command of the function - writing the >>>>> results to an output file (see reproduction of log file and traceback >>>>> below). The proper directory and file are created, but the 'results' >>>>> file remains empty; and the script returns the error message >>>>> 'IndexError: list index out of range'. >>>>> >>>>> I obtain the same error using various formatted versions of my own >>>>> data files, as well as the test data files found in >>>>> /test_suite/shared_data/model_free/S2_0..0.149/, modified to include >>>>> None for data values of GLY 1. Running multi_model commands manually >>>>> through the relax prompt also returns the same error for both >>>>> 'results.write' and 'results.display.' I also obtain the same result >>>>> running the analysis with sample_scripts/model-free.py. >>>>> >>>>> I am new to python and the relax interface and apologize if I am >>>>> bringing up a very basic question. I appreciate any help and >>>>> suggestions you might have. Thanks! >>>>> >>>>> Regards, >>>>> >>>>> Chris >>>>> >>>>> >>>>> Log File (edited) >>>>> >>>>> relax> pipe.create(pipe_name='tm0', pipe_type='mf') >>>>> >>>>> relax> sequence.read(file='noe.500.out', >>>>> dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None, >>>>> res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, >>>>> sep=None) >>>>> Opening the file >>>>> '/home/broseyca/relax/relax-1.3.2/sample_scripts/data/noe.500.out' >>>>> for reading. >>>>> Mol_name Res_num Res_name Spin_num Spin_name >>>>> None 1 GLY None None >>>>> None 2 ALA None None >>>>> >>>>> relax> relax_data.read(ri_label='R1', frq_label='500', >>>>> frq=500100000.0, file='r1.500.out', >>>>> dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None, >>>>> res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, >>>>> data_col=2, error_col=3, sep=None) >>>>> Opening the file >>>>> '/home/broseyca/relax/relax-1.3.2/sample_scripts/data/r1.500.out' for >>>>> reading. >>>>> >>>>> #(A total of 6 relaxation files were read in). >>>>> >>>>> relax> model_free.select_model(model='tm0', spin_id=None) >>>>> >>>>> relax> grid_search(lower=None, upper=None, inc=11, constraints=True, >>>>> verbosity=1) >>>>> >>>>> relax> minimise(*args=('newton',), func_tol=1e-25, >>>>> max_iterations=10000000, constraints=True, scaling=True, verbosity=1) >>>>> >>>>> relax> results.write(file='results', dir='local_tm/tm0', force=True, >>>>> format='xml', compress_type=1) >>>>> Opening the file 'local_tm/tm0/results.bz2' for writing. >>>>> >>>>> >>>>> Traceback Message >>>>> >>>>> 77 sweet:/home/broseyca/relax/relax-1.3.2% Traceback (most recent >>>>> call last): >>>>> File "relax", line 410, in <module> >>>>> Relax() >>>>> File "relax", line 127, in __init__ >>>>> self.interpreter.run(self.script_file) >>>>> File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>>>> 270, in run >>>>> return run_script(intro=self.__intro_string, local=self.local, >>>>> script_file=script_file, quit=self.__quit_flag, >>>>> show_script=self.__show_script, >>>>> raise_relax_error=self.__raise_relax_error) >>>>> File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>>>> 531, in run_script >>>>> return console.interact(intro, local, script_file, quit, >>>>> show_script=show_script, raise_relax_error=raise_relax_error) >>>>> File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line >>>>> 427, in interact_script >>>>> execfile(script_file, local) >>>>> File "prompt/full_analysis2.py", line 668, in <module> >>>>> Main(self.relax) >>>>> File "prompt/full_analysis2.py", line 221, in __init__ >>>>> self.multi_model(local_tm=True) >>>>> File "prompt/full_analysis2.py", line 664, in multi_model >>>>> results.write(file='results', dir=dir, force=True) >>>>> File "/home/broseyca/relax/relax-1.3.2/prompt/results.py", line 173, >>>>> in write >>>>> results.write(file=file, directory=dir, force=force, >>>>> format=format, compress_type=compress_type) >>>>> File "/home/broseyca/relax/relax-1.3.2/generic_fns/results.py", line >>>>> 164, in write >>>>> write_function(results_file) >>>>> File "/home/broseyca/relax/relax-1.3.2/data/__init__.py", line 222, >>>>> in to_xml >>>>> self[self.current_pipe].to_xml(self.xmldoc, pipe_element) >>>>> File "/home/broseyca/relax/relax-1.3.2/data/pipe_container.py", line >>>>> 234, in to_xml >>>>> self.mol.to_xml(doc, element) >>>>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>>>> 690, in to_xml >>>>> self[i].res.to_xml(doc, mol_element) >>>>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>>>> 492, in to_xml >>>>> self[i].spin.to_xml(doc, res_element) >>>>> File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line >>>>> 242, in to_xml >>>>> desc = return_data_desc(name, spin=self[i]) >>>>> File >>>>> "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", >>>>> line 2082, in return_data_desc >>>>> rex_units = self.return_units('rex', spin=spin) >>>>> File >>>>> "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", >>>>> line 2285, in return_units >>>>> return spin.frq_labels[0] + ' MHz' >>>>> IndexError: list index out of range >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-users >>>> >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >> >> >> >> >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
