Relax 3.3.0 - Revision history

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2020-10-16T20:34:50Z

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2020-10-16T20:25:12Z

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2020-10-16T20:18:03Z

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2020-10-16T08:47:55Z

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2020-10-15T12:17:39Z

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Bugman: Fixes for all the broken Gna! forum links.

2020-10-08T20:56:59Z

Fixes for all the broken Gna! forum links.

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

2020-10-08T20:48:05Z

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

Bugman: /* CHANGES file */ Switch to the {{relax url}} template for the CHANGES file URL.

2017-10-27T11:55:33Z

CHANGES file: Switch to the {{relax url}} template for the CHANGES file URL.

Bugman: /* Links */ Fix for the Gna! mailing list archive link.

2017-10-27T11:28:07Z

Links: Fix for the Gna! mailing list archive link.

Bugman at 09:16, 17 November 2015

2015-11-17T09:16:35Z

@@ Line 1,282: / Line 1,282: @@
 * Added the R<sub>1</sub> parameter fitting GUI element to the dispersion GUI tab.  This is a simple Boolean toggle element that allows the R<sub>1</sub> optimisation to be turned on.  The value is passed into the auto-analysis.
 * Added the r1_fit argument to the relaxation dispersion auto-analysis.  When this is True, the [http://www.nmr-relax.com/manual/relax_disp_r1_fit.html relax_disp.r1_fit user function] will be called to turn R<sub>1</sub> parameter fitting on.
-* Added the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function] to the dispersion GUI.  This has been added to the pop up menu in the spectrum list GUI element, when the relax_disp_flag has been set.  It simply mimics the relax_disp.spin_lock_field functionality already present.  This follows from [https://gna.org/task/?7820 task #7820].
+* Added the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function] to the dispersion GUI.  This has been added to the pop up menu in the spectrum list GUI element, when the relax_disp_flag has been set.  It simply mimics the relax_disp.spin_lock_field functionality already present.  This follows from {{gna task link|7820}}.
 * Fix for the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function] in the dispersion GUI tab.  This is in the spectrum list element popup menu.
-* Added the offset column to the spectrum list GUI element for the dispersion analysis.  This is to complete [https://gna.org/task/?7820 task #7820].  The spectrum list GUI element add_offset() method has been added to insert the offset column when the relax_disp_flag is set.  This is called by the update_data() method to fill and update the GUI element.
+* Added the offset column to the spectrum list GUI element for the dispersion analysis.  This is to complete {{gna task link|7820}}.  The spectrum list GUI element add_offset() method has been added to insert the offset column when the relax_disp_flag is set.  This is called by the update_data() method to fill and update the GUI element.
 * Implemented the GUI test Relax_disp.test_bug_22501_close_all_analyse to catch [https://gna.org/bugs/?22501 bug #22501, 'Close all analyses' raises error].
 * Inserted intermediate system test, to profile R<sub>2eff</sub> calculation for R<sub>1&rho;</sub>.  System test is: Relax_disp.test_bug_9999_slow_r1rho_r2eff_error_with_mc.  This system test actually fails, if one tries to do a grid search.  This is related to the R<sub>2eff</sub> values stored as dictionary, and pipe_control.minimise.grid_setup() will fail.  The function 'isNaN(values[i])' cannot handle dictionary.

@@ Line 1,292: / Line 1,292: @@
 * Created the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb Structure.test_create_diff_tensor_pdb system test].  This is to show the failure of the [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb user function] when no structural data is present.
 * Created the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb2 Structure.test_create_diff_tensor_pdb2 system test].  This is to catch another situation leading to [https://gna.org/bugs/?22505 bug #22505, the failure of the structure.create_diff_tensor_pdb user function when no structural data is present].
-* Added an optimisation script for the test_suite/shared_data/diffusion_tensor/ellipsoid relaxation data.  This is to help catch [https://gna.org/bugs/?22502 bug #22502, the geometric prolate diffusion representation does not align with axis in PDB], as reported by [https://gna.org/users/mab Martin Ballaschk].  The PDB files of the optimised tensor demonstrate exactly the same problem as seen in the files attached to the bug report.  The oblate and spherical diffusion tensor representations match that of the ellipsoid.  But the prolate axis and tensor orientation are both different from the ellipsoid as well as themselves.
+* Added an optimisation script for the test_suite/shared_data/diffusion_tensor/ellipsoid relaxation data.  This is to help catch [https://gna.org/bugs/?22502 bug #22502, the geometric prolate diffusion representation does not align with axis in PDB], as reported by {{gna link|url=gna.org/users/mab|text=Martin Ballaschk}}.  The PDB files of the optimised tensor demonstrate exactly the same problem as seen in the files attached to the bug report.  The oblate and spherical diffusion tensor representations match that of the ellipsoid.  But the prolate axis and tensor orientation are both different from the ellipsoid as well as themselves.
 * Updated the diffusion tensor PDB representation files.  This replaces the broken prolate representation with the corrected representation.
 * Deleted the duplicated [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure-pysrc.html#Structure.test_create_diff_tensor_pdb Structure.test_create_diff_tensor_pdb system test].
@@ Line 1,588: / Line 1,588: @@
 * Fix for [https://gna.org/bugs/?22505 bug #22505, the failure of the structure.create_diff_tensor_pdb user function when no structural data is present].  The solution was simple - the CoM of the representation is set to the origin when no structural data is present, and the check for the presence of data removed.
 * Another fix for [https://gna.org/bugs/?22505 bug #22505, the failure of the structure.create_diff_tensor_pdb user function when no structural data is present].  Now the cdp.structure data structure is checked, when present, if it contains any data using its own empty() method.
-* Fix for [https://gna.org/bugs/?22502 bug #22502, the problem whereby the geometric prolate diffusion representation does not align with axis in PDB], as reported by [https://gna.org/users/mab Martin Ballaschk].  This problem was not the main prolate tensor axis, but that the geometric object needed to be rotated 90 degrees about the z-axis to bring the object and axis into the same frame.
+* Fix for [https://gna.org/bugs/?22502 bug #22502, the problem whereby the geometric prolate diffusion representation does not align with axis in PDB], as reported by {{gna link|url=gna.org/users/mab|text=Martin Ballaschk}}.  This problem was not the main prolate tensor axis, but that the geometric object needed to be rotated 90 degrees about the z-axis to bring the object and axis into the same frame.
 * Fix for time not extracted for CPMG experiments in target_function.  [https://gna.org/bugs/?22461 Bug #22461: NS R1rho 2-site_fit_r1 has extremely high &chi;<sup>2</sup> value in system test Relax_disp.test_r1rho_kjaergaard_missing_r1].
 * Fix for interpolating time points, when producing xmgrace files for CPMG experiments.  [https://gna.org/bugs/?22461 Bug #22461: NS R1rho 2-site_fit_r1 has extremely high &chi;<sup>2</sup> value in system test Relax_disp.test_r1rho_kjaergaard_missing_r1].

@@ Line 599: / Line 599: @@
 * Renamed system test test_r1rho_kjaergaard to test_r1rho_kjaergaard_auto.  This corresponds to the use of the automatic analysis method.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
 * Split system test test_r1rho_kjaergaard into test_r1rho_kjaergaard_auto and test_r1rho_kjaergaard_man.  This is to test use of the manual way to analyse.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
-* Modified all of [https://gna.org/users/tlinnet Troels'] dispersion profiling scripts to work with older relax versions.  This is in preparation for obtaining some powerful timing statistics.  The calls to the r2eff_*() functions are unnecessary and are the only failure point in the scripts between the current code in the disp_spin_speed branch and trunk or older versions of relax.  So these function calls have been eliminated.
+* Modified all of {{relax developer link|username=tlinnet|text=Troels'}} dispersion profiling scripts to work with older relax versions.  This is in preparation for obtaining some powerful timing statistics.  The calls to the r2eff_*() functions are unnecessary and are the only failure point in the scripts between the current code in the disp_spin_speed branch and trunk or older versions of relax.  So these function calls have been eliminated.
 * Implemented system test test_r1rho_kjaergaard_missing_r1, for safety check if R<sub>1</sub> data is not loaded.  The system test passes, so target function is safe.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
 * Python 3 support for the dispersion profiling scripts.  The xrange() builtin function does not exist in Python 3, so this is now aliased to range() which is the same thing.
 * Replaced double or triple hash-tags "##" with single hash-tags "#".  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
-* Copyright fixes for all the models, where [https://gna.org/users/tlinnet Troels E. Linnet] have made changes to make them functional for higher dimensional data.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
+* Copyright fixes for all the models, where {{relax developer link|username=tlinnet|text=Troels E. Linnet}} have made changes to make them functional for higher dimensional data.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
-* Copyright fix for model [[TSMFK01]].  [https://gna.org/users/semor Sebastien Morin] did not take part of implementing the [[TSMFK01]] model.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
+* Copyright fix for model [[TSMFK01]].  {{relax developer link|username=semor|text=Sebastien Morin}} did not take part of implementing the [[TSMFK01]] model.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
 * Created a super script for profiling the relaxation dispersion models.  This script will execute all of the current profiling scripts in the directory test_suite/shared_data/dispersion/profiling for both the current version of relax and any other specified version (current set to the [[relax 3.2.2|3.2.2 relax]] tag).  It will run the scripts and relax versions interleaved N=10 times and extract the func_*() target function call profile timings.  This interleaving makes the numbers much more consistent.  Averages and standard deviations are then calculated, as well as the speed up between the two relax versions.  The results are printed out in a format suitable for the relax release messages.
 * Increased the number of iterations to 1000 in all of the profiling scripts.  This is for better statistics in the disp_profile_all.py script, and makes the number consistent between the different models.
@@ Line 953: / Line 953: @@
 * Unit test fix for Mac OS X.  This is for the test_ns_mmq_2site_korzhnev_2005_15n_dq_data_complex128 test of test_suite.unit_tests._lib._dispersion.test_matrix_exponential.Test_matrix_exponential.  The tests no longer check for exact values, but use the assertAlmostEqual() calls instead.
 * Deleted the ancient optimisation_testing.py development script, as this no longer works and is of no use.
-* Implemented the pipe_control.mol_res_spin.format_info_full() function.  This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534.  This is a verbose representation of the spin information which can be used for presenting to the user.  Functions for shorter string versions will also be of great use, for example as described by [https://gna.org/users/tlinnet Troels] at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6535.
+* Implemented the pipe_control.mol_res_spin.format_info_full() function.  This follows from http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6534.  This is a verbose representation of the spin information which can be used for presenting to the user.  Functions for shorter string versions will also be of great use, for example as described by {{relax developer link|username=tlinnet|text=Troels}} at http://thread.gmane.org/gmane.science.nmr.relax.scm/22522/focus=6535.
 * Created a unit test for the pipe_control.mol_res_spin.format_info_full() function.  This comprehensive test covers all input argument combinations.
 * Changed the behaviour of the pipe_control.structure.mass.pipe_centre_of_mass() function.  This function returns the CoM and optionally the mass of the structural data loaded into the current data pipe.  However it was matching the structural data to the molecule-residue-spin data structure and skipping spins that were deselected.  This illogical deselection part has been eliminated, as spins can be deselected for various analysis purposes and this should not change the CoM.  The deletion also significantly speeds up the function.

@@ Line 353: / Line 353: @@
 * Updated the script for finding unused imports in the relax source code.  Now the file name is only printed for Python files which have unused imports.
 * Completely removed all mentions of Freecode from the release document.  The [http://freecode.com/projects/nmr-relax old relax links are still there], but [http://freecode.com/about Freecode is dead].
-* Updated the minfx version in the release checklist document to [https://gna.org/forum/forum.php?forum_id=2471 1.0.8].  This version has not been released yet, but it will include important fixes and additions for constrained parallelised grid searches.
+* Updated the minfx version in the release checklist document to {{gna link|url=gna.org/forum/forum.php?forum_id=2471|text=1.0.8}}.  This version has not been released yet, but it will include important fixes and additions for constrained parallelised grid searches.
 * Fix for a broken link in the development chapter of the relax manual.
 * Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax manual.  The [[B14]] model links to http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken as the B in [[B14]] was capitalised.
-* Sent in the verbosity argument value to the [http://home.gna.org/minfx/minfx.grid-module.html#grid_split minfx.grid.grid_split() function].  The minfx function in the next release ([https://gna.org/forum/forum.php?forum_id=2471 1.0.8]) will now be more verbose, so this will help with user feedback when running the model-free analysis on a cluster or multi-core system using MPI.
+* Sent in the verbosity argument value to the [http://home.gna.org/minfx/minfx.grid-module.html#grid_split minfx.grid.grid_split() function].  The minfx function in the next release ({{gna link|url=gna.org/forum/forum.php?forum_id=2471|text=1.0.8}}) will now be more verbose, so this will help with user feedback when running the model-free analysis on a cluster or multi-core system using MPI.
 * The [http://www.nmr-relax.com/manual/time.html time user function] now uses the chronometer [https://en.wikipedia.org/wiki/Oxygen_Project Oxygen icon] in the GUI.
 * Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings.  This is for the pipe_control.minimise module.
@@ Line 765: / Line 765: @@
 * Improved the relax version printouts for the dispersion model master profiling script.  This now reports both relax versions.
 * Removed a tonne of unused imports from the dispersion model profiling scripts.  This is to allow most of the scripts to run on the relax 3.1.x versions, as well as to clean up the scripts.  The unused imports were found using the command:  pylint test_suite/shared_data/dispersion/profiling/*.py --disable=all --enable=unused-import.
-* Added a relaxation dispersion model profiling log file for relax version [[relax 3.2.1|3.2.1]] vs. [[relax 3.2.0|3.2.0]].  This is the output from the dispersion model profiling master script.  It shows a 2.2 times increase in speed for the [[B14]] and [[B14 full]] models, with all other models remaining at the same speed.  This matches the changes for relax [[relax 3.2.1|3.2.1]] (https://gna.org/forum/forum.php?forum_id=2462), the main feature of which is a major bugfix for the [[B14]] models.
+* Added a relaxation dispersion model profiling log file for relax version [[relax 3.2.1|3.2.1]] vs. [[relax 3.2.0|3.2.0]].  This is the output from the dispersion model profiling master script.  It shows a 2.2 times increase in speed for the [[B14]] and [[B14 full]] models, with all other models remaining at the same speed.  This matches the changes for relax [[relax 3.2.1|3.2.1]], the main feature of which is a major bugfix for the [[B14]] models.
 * The 'relax -v' command is now used for the dispersion model profiling script initial printout.  This is to show the two different relax versions being compared.
 * Modifications to the dispersion model profiling master script.  The info.print_sys_info() function of the current relax version is being called at the start to show all information about the current system.  This is useful to know the speed of the machine, the OS, the Python version and numpy version.  The numpy version is important as future versions might optimise certain functions that are currently very slow, hence that could be a cause of model speed differences.  In addition, the path variables path1 and path2 have been renamed to path_new and path_old to make it clearer which is which.  And the individual profiling scripts are no longer copied to the base directory of the relax versions being compared, and are run in place.
-* Added a relaxation dispersion model profiling log file for relax version [[relax 3.2.2|3.2.2]] vs. [[relax 3.2.1|3.2.1]].  This is the output from the dispersion model profiling master script.  It shows that the relax [[relax 3.2.2|3.2.2]] release did not in fact feature "a large speed up of all analytic relaxation dispersion models" as described in the release notes at https://gna.org/forum/forum.php?forum_id=2465.  For the CPMG models there is a 1 to 2 times increase in speed.  But for the R<sub>1&rho;</sub> models, there is a 1 to 2 times decrease in speed.
+* Added a relaxation dispersion model profiling log file for relax version [[relax 3.2.2|3.2.2]] vs. [[relax 3.2.1|3.2.1]].  This is the output from the dispersion model profiling master script.  It shows that the relax [[relax 3.2.2|3.2.2]] release did not in fact feature "a large speed up of all analytic relaxation dispersion models" as described in the release notes at {{gna url|gna.org/forum/forum.php?forum_id=2465}}.  For the CPMG models there is a 1 to 2 times increase in speed.  But for the R<sub>1&rho;</sub> models, there is a 1 to 2 times decrease in speed.
 * Added a relaxation dispersion model profiling log file for relax version [[relax 3.2.0|3.2.0]] vs. [[relax 3.1.7|3.1.7]].  This is the output from the dispersion model profiling master script.  It shows that there are no speed differences.
 * Added a relaxation dispersion model profiling log file for relax version [[relax 3.1.7|3.1.7]] vs. [[relax 3.1.6|3.1.6]].  This is the output from the dispersion model profiling master script.  It shows that there are no speed differences.
@@ Line 856: / Line 856: @@
 * Removed unnecessary repetitive calculation of k<sub>ex</sub><sup>2</sup> in model [[DPL94]].  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
 * API documentation fixes, where a "\" is the last character on the line.  There should be a space " ", ending this character.  [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
-* Updated the [https://gna.org/forum/forum.php?forum_id=2472 minfx version number to 1.0.9] in the release checklist document.  This as of yet unreleased version contains an important fix for parallelised grid searches when the number of increments is set to one (i.e. a preset parameter).
+* Updated the {{gna link|url=gna.org/forum/forum.php?forum_id=2472|text=minfx version number to 1.0.9}} in the release checklist document.  This as of yet unreleased version contains an important fix for parallelised grid searches when the number of increments is set to one (i.e. a preset parameter).
 * Fix for the _prompt.test_align_tensor.Test_align_tensor.test_init_argfail_params unit test.  As the alignment tensor can now be initialised as None, the None value can be accepted and a different RelaxError is raised when the params argument is incorrectly supplied.
 * Added a new set of icons for use with the minimisation user functions.  These are of the Rosenbrock function and are much better suited for small icons than the current OpenDX 3D isosurface plots.  The matplotlib figure originates from public domain code at http://commons.wikimedia.org/wiki/File:Rosenbrock_function.svg.
@@ Line 925: / Line 925: @@
 * Created two new model-free system tests.  These are Mf.test_m0_grid_with_grid_search and Mf.test_m0_grid_vs_m1_with_grid_search.  Their aim is to better test the grid search in a model-free analysis when parameters are preset.
 * Converted the model-free analysis to the new grid bounds and scaling factor design.  The parameter object now registers the grid bounds and scaling factors for all of the model-free parameters.  This includes the functions rex_scaling() and rex_upper() in the specific_analyses.model_free.parameter_object module for calculating some of these values.  The base parameter object has also been updated as that is where the diffusion parameters are defined.  Here the da_lower() and da_upper() have been defined to handle the different Da value constraints.  The specific_analyses.model_free.parameters.assemble_scaling_matrix() function has been deleted as this is now provided by the upstream code in pipe_control.minimise.  And the API methods grid_search() and minimise() has been modified to accept the list of scaling matrices.  As the grid bounds and increments are now handled by the upstream pipe_control.minimise.grid_setup() function, the grid_search_config(), grid_search_diff_bounds() and grid_search_spin_bounds() functions in the specific_analyses.model_free.optimisation module were redundant and were deleted.  The new API function print_model_title() has been implemented to handle the grid search setup printouts.
-* Modified the pipe_control.minimise.grid_setup() function for when no parameters are present.  For the current version of minfx to function correctly ([https://gna.org/forum/forum.php?forum_id=2471 1.0.8]), the lower, upper and inc values should be set to [] rather than None.
+* Modified the pipe_control.minimise.grid_setup() function for when no parameters are present.  For the current version of minfx to function correctly ({{gna link|url=gna.org/forum/forum.php?forum_id=2471|text=1.0.8}}), the lower, upper and inc values should be set to [] rather than None.
 * Fix for the lib.arg_check.is_num_or_num_tuple().  When the can_be_none flag is set to True, the tuple of None values is now considered valid.  This enable the [http://www.nmr-relax.com/manual/diffusion_tensor_init.html diffusion_tensor.init user function] to accept the spheroid tensor values of (None, None, None, None), and the ellipsoid tensor values as a tuple of 6 None.
 * Fix for the _prompt.test_diffusion_tensor.Test_diffusion_tensor.test_init_argfail_params unit test.  As the diffusion tensor can now be initialised as None, the None value can be accepted and a different RelaxError is raised when the params argument is incorrectly supplied.
@@ Line 1,554: / Line 1,554: @@
 * Added a derivation of the R<sub>2eff</sub>/R<sub>1&rho;</sub> error estimate for the two-point measurement to the manual.  This is from http://thread.gmane.org/gmane.science.nmr.relax.devel/6929/focus=6993 and is for the rate uncertainty of a 2-parameter exponential curve when only two data points have been collected.  The derivation has been added to the dispersion chapter of the manual.
 * Equation fixes for the two-point exponential error derivation in the dispersion chapter of the manual.
-* Updated the minfx version numbers in the release checklist document.  The version is now [https://gna.org/forum/forum.php?forum_id=2475 1.0.10], which has not been released yet but will contain the implementation of the log-barrier constraint algorithm gradient and Hessian.
+* Updated the minfx version numbers in the release checklist document.  The version is now {{gna link|url=gna.org/forum/forum.php?forum_id=2475|text=1.0.10}}, which has not been released yet but will contain the implementation of the log-barrier constraint algorithm gradient and Hessian.
 * Fix for the minfx version checking logic in the dep_check module.  Now newer versions of minfx will be handled.
 * Fixes for the Relax_disp.test_estimate_r2eff_err system test.  The k<sub>ex</sub> parameter value checks have all been scaled by 1e<sup>-5</sup> to allow for a meaningful floating point number comparison.  The number of significant figures have also been scaled.  This allows the test to now pass on one 64-bit GNU/Linux system.

@@ Line 1,601: / Line 1,601: @@
 * [http://wiki.nmr-relax.com/Relax_3.3.0 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2476 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2476|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/58 Gmane mailing list archive].
 * [http://www.nmr-relax.com/mail.gna.org/public/relax-announce/2014-09/msg00000.html Local archives].

@@ Line 318: / Line 318: @@
 Version 3.3.0 <br/>
 (3 September 2014, from /trunk) <br/>
-http://svn.gna.org/svn/relax/tags/3.3.0
+{{relax url|tag=3.3.0}}
 <section end=metadata/>

← Older revision		Revision as of 09:16, 17 November 2015
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	{{:relax release announcements}}		{{:relax release announcements}}
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	== See also ==		== See also ==