Relax 3.0.1 - Revision history

Bugman: Switch to the {{gna link}} template to remove dead Gna! links.

2020-10-16T09:06:10Z

Switch to the {{gna link}} template to remove dead Gna! links.

Bugman: /* Changes */ Switch to the {{relax developer link}} template to remove dead Gna! links.

2020-10-15T11:41:14Z

Changes: Switch to the {{relax developer link}} template to remove dead Gna! links.

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-14T11:27:47Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: /* Changes */ Minfx link fix.

2020-10-06T21:37:32Z

Changes: Minfx link fix.

Bugman: Internal link to Modelfree4.

2015-12-15T16:13:16Z

Internal link to Modelfree4.

Bugman: Added an infobox.

2015-11-03T10:34:55Z

Added an infobox.

Bugman: Increased the sectioning depth.

2015-11-03T10:34:10Z

Increased the sectioning depth.

Bugman: /* See also */ Added a link to the API documentation.

2014-11-26T10:31:43Z

See also: Added a link to the API documentation.

Bugman: Links to Troels' Gna! page.

2014-09-12T17:40:16Z

Links to Troels' Gna! page.

Bugman: Fixes for the user function links.

2014-09-11T14:43:49Z

Fixes for the user function links.

@@ Line 135: / Line 135: @@
 *  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 [https://gna.org/bugs/?21187 bug #21187].  The bug was reported by [https://gna.org/users/mab Martin Ballaschk].
+*  Created the Structure.test_bug_21187_corrupted_pdb system test to catch [https://gna.org/bugs/?21187 bug #21187].  The bug was reported by {{gna link|url=gna.org/users/mab|text=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.
@@ Line 161: / Line 161: @@
 *  Fix for latex bibtex string 'cp' instead of 'cj'.  Progress [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 [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 was reported by [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.
+*  Fix for [https://gna.org/bugs/?21187 bug #21187 - the corrupted PDB issue with protons atom numbers of zero].  The bug was reported by {{gna link|url=gna.org/users/mab|text=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 [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.
 <section end=bugfixes/>

@@ Line 96: / Line 96: @@
 *  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.
+*  Updated the nmrPipe processing script in the relax user manual.  This is in response to the post by {{relax developer link|username=tlinnet|text=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.

@@ Line 170: / Line 170: @@
 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]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2414|text=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]

@@ Line 100: / Line 100: @@
 *  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 [https://gna.org/bugs/?21001 bug #21001] in relax, which is really a fix for an upstream [https://gna.org/projects/minfx/ minfx] [https://gna.org/bugs/?21090 bug #21090].
+*  The model-free optimisation code now handles minfx returning nothing.  This is due to the fix of [https://gna.org/bugs/?21001 bug #21001] in relax, which is really a fix for an upstream [{{minfx homepage}} minfx] [https://gna.org/bugs/?21090 bug #21090].
 *  Created the Mf.test_bug_21079_local_tm_global_selection system test.  This is to catch [https://gna.org/bugs/?21079 bug #21079].
 *  Extended the Mf.bug_21079_local_tm_global_selection system test for all Monte Carlo simulation steps.

@@ Line 56: / Line 56: @@
 *  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.
+*  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.
@@ Line 151: / Line 151: @@
 <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.
+*  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 [https://gna.org/bugs/?21042 bug #21042].
 *  Fix for [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.

← Older revision		Revision as of 10:34, 3 November 2015
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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 ==		== Description ==

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+== Download ==
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+== CHANGES file ==
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-== Features ==
+=== Features ===
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-== Changes ==
+=== Changes ===
 <section begin=changes/>
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-== Bugfixes ==
+=== Bugfixes ===
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-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/3.0/ The relax 3.0 API documentation]
 {{:relax release see also}}
 [[Category:GUI]]

@@ Line 49: / Line 49: @@
 *  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.
+*  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'.
+*  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.
+*  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.
@@ Line 65: / Line 65: @@
 *  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.
+*  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 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.
+*  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 &omega;<sub>1</sub>, the indirect dimension in a 2D experiment.  The description has also been fixed.
+*  Changes for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function] dim argument.  The default is now &omega;<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 &omega;<sub>1</sub> and &omega;<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 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.
+*  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 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.
+*  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.
@@ Line 94: / Line 94: @@
 *  Created the Mf.test_bug_21079_local_tm_global_selection system test.  This is to catch [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 [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 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.
@@ Line 123: / Line 123: @@
 *  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].
+*  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.
+*  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 [https://gna.org/bugs/?21187 bug #21187].  The bug was reported by [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.