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{{infobox relax release| version = 3.0.1| prev = 3.0.0| next = 3.0.2| type = Minor feature and bugfix release| date = 17 October 2013| manual = yes}} == Description ==
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== Download ==
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== CHANGES file ==
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Version 3.0.1<br/>(17 October 2013, from /trunk)<br/>
http://svn.gna.org/svn/relax/tags/3.0.1
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=== Features ===
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=== Changes ===
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* Updated the Mac Framework setup document to help with scipy compilation problems.
* Improved the Python seeking and module version print out script for symlinks. This should now be much more capable of finding all Python versions on a system.
* Added support for the Mac OS X [[Modelfree4 ]] binary results to the Palmer.* system tests. The Mac OS X Modelfree 4.20 binary produces different results than the Linux binaries, mainly due to a compilation problem. In the Linux binaries, the results are written out to 4 decimal places. In the Mac binaries, the results are instead written out to 4 significant figures. Therefore the number of decimal places are much less than the Linux results.
* Syntax error fix for one of the unused scripts in the relax test suite shared data directories. This problem was encountered by Jack Howarth <howarth att bromo dott med dott uc dott edu> and communicated in a private message. The issue was found by fink. This script is never used and will never be used again - it is only there for reference.
* Modification of the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] front end. The heteronuc and proton arguments have been eliminated. Instead the new dim argument is used to associate the data with the spins of any dimension in the peak list.* Replaced the 'heteronuc' and 'proton' arguments of the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] backend with 'dim'.
* Created the new lib.spectrum.objects module. This will hold temporary data structures for representing peak lists and other spectral data. The module currently contains the Peak_list class which is used to hold peak list data.
* Started to shift the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] backend to use lib.spectrum.peak_list.
* The pipe_control.spectrum.read_intensities() function now works with the Peak_list object.
* The Peak_list object is now used by the lib.spectrum.peak_list.read_peak_list() function.
* The lib.software.sparky.read_list_intensity() function now operates on the Peak_list object.
* Changed the spectrum.read_intensities dim argument default to w2 ω<sub>2</sub> and improved the long description.* Fix for the assignment handling in the lib.software.sparky.read_peak_list() function. The first element is usually the indirect dimension or w2ω<sub>2</sub>.
* Fix for many of the Peak_list system tests for the user function argument changes. The heteronuc and proton arguments have been replaced by the dim argument.
* The lib.software.xeasy.read_list_intensity() function now operates on the Peak_list object.
* The Peak_list object can now store peak intensity names. This is for peak lists such as from NMRPipe seriersTab files where the peak list covers multiple spectra.
* The NMRPipe seriesTab peak lists are now supported through the Peak_list object.
* Unit test fixes for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] argument changes.* Fixes for a few system tests for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] argument changes.* Fixes for a few GUI tests for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] argument changes.* Changes for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] dim argument. The default is now w1ω<sub>1</sub>, the indirect dimension in a 2D experiment. The description has also been fixed.* Fixes for all of the peak intensity reading functions - the w1 ω<sub>1</sub> and w2 ω<sub>2</sub> dimensions were swapped.* Updates to the sample scripts for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] argument changes.* Updates to the user manual for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function ] argument changes.* Created the Chemical_shift.test_read_sparky system test for the reading of chemical shifts. This is for the reading of shifts from a Sparky peak list. It tests the currently non-existent [http://www.nmr-relax.com/manual/chemical_shift_read.html chemical_shift.read user function].* Created some incredibly basic icons for the chemical shift user functions. These are simply an &omega ; symbol and will need to be replaced by something better in the future.* Created the [http://www.nmr-relax.com/manual/chemical_shift_read.html chemical_shift.read user function]. This includes both the front and back end code.
* Shifted all the modules from lib.software to do with peak lists to lib.spectrum. This is for a more logical organisation, as these modules are solely used by the lib.spectrum.peak_list module.
* Renamed all of read_*() functions of the lib.spectrum modules for consistency. These functions will now be used to read all types of data from a peak list, from the assignments to chemical shifts to peak intensities, and everything in between.
* Assignments can now contain lowercase letters in Sparky and NMRPipe seriesTab peak lists.
* Fix for the unit test for the reading of intensities from Sparky peak lists.
* Updated the nmrPipe processing script in the relax user manual. This is in response to the post by [https://gna.org/users/tlinnet Troels Linnet ] at http://thread.gmane.org/gmane.science.nmr.relax.user/1520. The text has also been expanded to better explain spectral processing.
* Improvements for the description of the NMRPipe processing script in the R1/R2 chapter of the user manual.
* 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 [http://www.nmr-relax.com/manual/model_free_select_model.html 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 <sup>2 </sup> is used for the order parameters.* The model lists in the model-free GUI auto-analysis now use unicode for the S2 S<sup>2</sup> parameters.
* The peak intensity wizard in the GUI is now more robust. The wizard_update_ids() method can now better handle missing data. This is encountered if a user skips the first elements of the wizard.
* Created Wiz_window.setup_page() for user function wizard pages to allow for simpler GUI tests. This method can be used to setup any user function wizard page with all its arguments set. It accepts all keyword arguments and sets these for the wizard page, translating to GUI strings as needed. This should save a lot of lines in the GUI tests.
* Defined two new functions called u() in the compat module for better unicode string support. The two functions are defined differently for Python2 and Python3. The Python3 function simply returns the text unmodified, as all strings are unicode. The Python2 function converts the str type to a unicode type.
* The new compat.u() function is now being used for all unicode strings.
* All "local tm" text in the GUI now uses a subscript <sub>m </sub> unicode character as well as the &tau ; character.
* Created the pipe_control.spectrum.test_spectrum_id() function for checking if a spectrum ID exists.
* Renamed pipe_control.spectrum.test_spectrum_id() to check_spectrum_id(). A bug in the function was also removed, and the other code in the module now uses this function.
* The model list GUI element is now centred after the autosizing.
* The titles in the model list GUI window now use a smaller font size.
* Update of the description of the [http://www.nmr-relax.com/manual/interatom_define.html interatom.define user function].
* 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 [http://www.nmr-relax.com/manual/spectrum_error_analysis.html 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.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* 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 [http://www.nmr-relax.com/manual/calculate.html calculate], [http://www.nmr-relax.com/manual/grid_search.html grid_search], and [http://www.nmr-relax.com/manual/minimise.html 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.
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== Links == <section begin=links/>For reference, the following links are also part of the announcement for this release:* [http://wiki.nmr-relax.com/Relax_3.0.1 Official release notes]* [https://gna.org/forum/forum.php?forum_id=2414 Gna! news item]* [http://article.gmane.org/gmane.science.nmr.relax.announce/44 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00039.html Mail Archive]* [https://mail.gna.org/public/relax-announce/2013-10/msg00000.html Local archives]<section end=links/> == Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/3.0/ The relax 3.0 API documentation]
{{:relax release see also}}
[[Category:GUI]]
