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Relax 3.0.1

15 bytes removed, 14:04, 11 September 2014
Tracker links with full descriptions.
* LaTeX fix for the curvefit chapter of the user manual.
* The isInf() and isNan() functions of lib.float can now handle values of None. If None is encountered, the functions simply return False.
* The model-free optimisation code now handles minfx returning nothing. This is due to the fix of bug #21001 ([https://gna.org/bugs/?21001) bug #21001] in relax, which is really a fix for an upstream minfx ([https://gna.org/projects/minfx/) bug (bug #21090 at minfx] [https://gna.org/bugs/?21090)bug #21090].* Created the Mf.test_bug_21079_local_tm_global_selection system test. This is to catch bug #21079 ([https://gna.org/bugs/?21079)bug #21079].
* Extended the Mf.bug_21079_local_tm_global_selection system test for all Monte Carlo simulation steps.
* The model_free.select_model user function GUI element now uses unicode for the model parameters. The tau character is now used for the tm, te, tf, and ts parameters. And a superscript 2 is used for the order parameters.
* Added multi-processor support for Monte Carlo simulations. This simply involves accessing the multi-processor box singleton and running the processor.run_queue() method within the pipe_control.minimise.minimise() function. This currently does nothing as the processor queue is always empty. But if the code in the specific_analyses package is modified to add slave commands to the processor but not execute the run_queue() method, then the Monte Carlo simulations will be automatically parallelised.
* Updated the spectrum.error_analysis user function backend to use the lib.statistics.std() function. This simplifies the code. It affects only the peak intensity error analysis when spectra have been replicated.
* Created the Structure.test_bug_21187_corrupted_pdb system test to catch bug #21187. The bug at [https://gna.org/bugs/?21187 bug #21187]. The bug was reported by Martin Ballaschk ([https://gna.org/users/mab)Martin Ballaschk].
* Bug fix for the specific analysis API _data_init_spin() method. This is used for the API init_spin() method. This is a latent bug which does not affect any of the current analyses in relax. It was discovered in the relaxation dispersion branch.
* Addded a new is_queued() method to the Processor object of the multi package. This allows the Processor object for the uni and mpi4py multi-processor to be queried to see if any slave commands have been queued.
* Bibtex fixes required for proper latex2html compilation.
* Fix for the Palmer.test_palmer_omp for the different Modelfree4 binaries. The gcc and pdf binaries are now properly detected and the slightly different results are now correctly checked for.
* The graphics.fetch_icon() function can now return either the absolute or relative path to the icon. This is a partial solution for bug #21042 ([https://gna.org/bugs/?21042)bug #21042].* Fix for bug #21042 ([https://gna.org/bugs/?21042)bug #21042]. The docs/latex/fetch_docstrings.py now asks the graphics.fetch_icon() function for the relative path to the icon rather than the absolute path.
* The fetch_docstrings.py script now asks for the Unix '/' separator through graphics.fetch_icon(). This is a final fix for bug 21042 (https://gna.org/bugs/?21042). The graphics.fetch_icon() function now accepts the 'sep' argument. This defaults to os.sep. But the docs/latex/fetch_docstrings.py script uses the Unix '/' separator to obtain a LaTeX correct path on MS Windows.
* Modified the create_mc_data() method to partly fix bug #21079 ([https://gna.org/bugs/?21079)bug #21079]. Some spins with local tm models remain selected despite not containing any data. These are handled explicitly. Instead of a RelaxNoModelError being raised, the method returns None to indicate that something went wrong.* Final fix for bug #21079 ([https://gna.org/bugs/?21079). This is bug #21079, the failure of the dauvergne_protocol auto-analysis when the "local tm" global model is selected]. The Monte Carlo create_data() method not skips data from the base_data_loop() if the create_mc_data() method returns None.* Fix for bug #21097 ([https://gna.org/bugs/?21097)bug #21097]. This was a simple typo. It has not been encountered before because it is in a rarely encountered RelaxError.* Fix for bibtex warning 'Warning--string name "mb" is undefined'. Progress sr #3071: [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.* Fix for latex bibtex string 'cp' instead of 'cj'. Progress sr #3071: [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.* Another fix for bibtex string 'cp' instead of 'cj'. Progress sr #3071: [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.* Fix for [https://gna.org/bugs/?21187 bug #21187 - the corrupted PDB issue with protons atom numbers of zero]. The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk ([https://gna.org/users/mab)Martin Ballaschk]. The fix was to allow for spin containers in the relax data store to have the same atom number, as long as the atom names are different.* Modified the Monte Carlo simulation printout behaviour for the minimisation related user functions. This is to help in fixing bug #21190 ([https://gna.org/bugs/?21190)bug #21190]. This includes the calculate, grid_search, and minimise user functions. The new multi-processor is_queued() method is used to determine if the optimisation code of the specific analysis has queued rather than run the calculations. If queued, the 'Simulation X' text will not be printed out. This avoids printing out all the text at the start before anything has happened. The specific multi-processor optimisation code must provide it's own printouts when each calculation is complete.
<section end=bugfixes/>
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