Trusted, Bureaucrats, Administrators
233
edits
Changes
Jump to navigation
Jump to search
m
→Changes: More links.
* 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 old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead (http://freecode.com/about).
* 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.
* 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 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.
* The [http://www.nmr-relax.com/manual/time.html time user function] now uses the chronometer 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.
* Removed unnecessary repetitive calculation of kex**2 in model DPL94. Task #7807 (https://gna.org/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. Task #7807 (https://gna.org/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).
* 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.
* 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.
* 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 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.
* Added a derivation of the R2eff/R1rho 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.
* 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 kex parameter value checks have all been scaled by 1e-5 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.
