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Changes
User function link improvements.
* 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.
* Redesign of the optimisation user functions [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]. In preparation for expanding the number of optimisation user functions, these three current user functions have been shifted into the new minimise user function class. The calc user function is now accessed as [http://www.nmr-relax.com/manual/minimise_calculate.html minimise.calculate]. The grid search as [http://www.nmr-relax.com/manual/minimise_grid_search.html minimise.grid_search]. And minimisation is via the [http://www.nmr-relax.com/manual/minimise_execute.html minimise.execute user function[]. The icon used for the new user function class is the Rosenbrock function or the banana optimisation problem. As this is such a radical change, a huge number of changes in the relax source code, the sample scripts, the user manual, and the test suite were required.
* Created the new [http://www.nmr-relax.com/manual/minimise_grid_zoom.html minimise.grid_zoom user function]. This allows the grid zoom level to be set. The value is stored in the current data pipe and will be used later by the [http://www.nmr-relax.com/manual/minimise_grid_search.html minimise.grid_search user function].
* The [http://www.nmr-relax.com/manual/minimise_grid_zoom.html minimise.grid_zoom user function] now uses the zoom-in Oxygen icon.
* Epydoc docstring fixes for the keyword arguments of the pipe_control.minimise module.
* Shifted the constraints Boolean argument to the end of the grid_search() function argument list.
* Major change to the grid search [http://www.nmr-relax.com/manual/grid_search.html grid_search user function]. The [http://www.nmr-relax.com/manual/minimise_grid_search.html minimise.grid_search user function] now accepts the skip_preset flag. When True, the grid search will skip any parameters with a preset value. This allows the user to set parameters via the [http://www.nmr-relax.com/manual/value_set.html value.set user function] and then have these parameters skipped in the grid search. The new skip_preset argument is passed into the pipe_control.minimise.grid_setup() function in the backend. This then sets both the grid lower and upper bounds to the preset parameter value and sets the number of increments to 1 for that parameter so that it is essentially skipped in the grid search.
* Small change to the table printed out during the minimise.grid_search setup.
* Fix for the skipping of preset parameters in the grid search. Dictionary and list type parameters are now handled correctly.
* Modified the grid search upper bounds functions for the relaxation curve-fitting. This is for both the exponential relaxation curve-fitting analysis and the same fitting in the dispersion analysis. The intensity values are doubled and then rounded to the next order. This ensures that I<sub>0</sub> and I<sub>∞</sub> will be within the grid bounds. Hence the zooming grid search can be used for these curves.
* Expanded the [documentation for the http://www.nmr-relax.com/manual/minimise_calculate.html minimise.calculate user function]. This now explains the dual operations of the user function.
* Fixes for some relaxation dispersion system tests not converted to the new optimisation user functions. Minimisation is now via the [http://www.nmr-relax.com/manual/minimise_execute.html minimise.execute user function], which used to be the [http://www.nmr-relax.com/manual/minimise.html minimise user function].
* Added a 128x128 pixel version of the zoom-in Oxygen icon. This icon size is not available in the repository located at svn://anonsvn.kde.org/home/kde/trunk/kdesupport/oxygen-icons. Therefore the scalable/actions/small/48x48/zoom-in.svgz file was copied and then exported into a 128x128 PNG, and finally converted to a Gzipped EPS file for the relax manual.
* The frame order grid search bound functions can now handle increment values of None or 1. These cases are now caught and the full lower or upper bound is now returned.