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User function HTML manual links.
* Epydoc docstring improvements/fixes for the API documentation.
* Many updates using 2to3 preparing for a transition to Python 3.x.
* Renamed the [http://www.nmr-relax.com/manual/pipe_list.html pipe.list() user function ] to [http://www.nmr-relax.com/manual/pipe_display.html pipe.display()].
* Created a base class for the user function classes. More user function back end simplifications.
* Addition of many new RelaxError classes for the user function interface.
* Added a very basic, and completely empty module and class for SRLS analysis.
* Redesign of the relax state loading for adding support for a XML formatted state file.
* Shifted the [http://www.nmr-relax.com/manual/results_write.html results.write() ] force arg to the end.
* Created the relax data store is_empty() method.
* Renamed the [http://www.nmr-relax.com/manual/state_load.html state.load() ] and [http://www.nmr-relax.com/manual/state_save.html state.save() ] directory argument from dir_name to dir for consistency with the rest of relax.
* Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
* Redesigned the N-state model grid search setup around the new minfx interface.
* Redesigned the model-free grid search setup around the new minfx interface.
* Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
* Added the spin_id_col arg to the [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() user function].* Changes to the [http://www.nmr-relax.com/manual/pcs_read.html pcs.read() ] and [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() ] user function interfaces.
* Column numbering now starts at 1 rather than 0 within the user functions.
* The relax_io.read_spin_data_file() function has been created to handle all columnar text files where each row corresponds to a spin.
* Added user variable checking to the full_analysis.py script.
* Added functions for determining the element name and isotope number from an isotope name.
* Added frame order methods necessary for the [http://www.nmr-relax.com/manual/dx_map.html dx.map() user function].
* Huge clean up / redesign of the specific analysis internal API.
* Better layout of the user functions in the relax manual significantly dropping the page count.
* Modified the alignment tensor print out to be more compact.
* The PCS centre can now be forcefully overwritten.
* Added the back end to the [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc() user function ] (making it functional).
* Modified all the specific analysis overfit_deselect() methods to warn when spins are deselected.
* [http://www.nmr-relax.com/manual/align_tensor_display.html align_tensor.display() ] now prints the magnetic susceptibility tensor.
* The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
* Simplifications and clean up of the prompt and script UI code.
* Partially removed the need for downstream Fink specific modifications.
* Creation of the NOE auto-analysis module.
* Fixes for the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins() user function ] docstring for RNA/DNA work.* The [http://www.nmr-relax.com/manual/n_state_model_select_model.html n_state_model.select_model() user function ] can now change the model.
* Added a maximum global iteration arg and check into the dauvergne_protocol.py module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
<section end=changes/>
* Fix for the calls to transpose_14().
* Bug fix for the relaxation curve-fitting difference plot script.
* Fix for the [http://www.nmr-relax.com/manual/spin_number.html spin.number() user function], the number can be None to reset the values.* Fix for the [http://www.nmr-relax.com/manual/script.html script() user function], the function intro flag at the end of executing an external script was not being restored.
* Improvements to the optimisation tests ([https://gna.org/bugs/?14173 bug #14173], [https://gna.org/bugs/?14174 bug #14174], [https://gna.org/bugs/?14175 bug #14175], [https://gna.org/bugs/?14176 bug #14176], [https://gna.org/bugs/?14177 bug #14177], [https://gna.org/bugs/?14182 bug #14182]).
* Fix for the R_euler_zyz() rotation matrix function.
* Fixed the PDF manual compilation ([https://gna.org/bugs/?14464 bug #14464]).
* Fix for the retrieval of bond vectors for the N-state model.
* Fixes for the [http://www.nmr-relax.com/manual/dx_map.html dx.map() user function ] interface.
* Epydoc docstring fixes.
* Fix for when [https://gna.org/bugs/?14872 the selection string (i.e. spin_id) is unicode (bug #14872)].
