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Changes
Converted links to the wiki format.
* The [http://www.nmr-relax.com/manual/structure_delete.html structure.delete user function can now delete individual models as well as select atoms in individual models].
* Addition of the [http://www.nmr-relax.com/manual/error_analysis_covariance_matrix.html error_analysis.covariance_matrix user function for determining parameter errors via the covariance matrix]. This is currently only implemented for the relaxation curve-fitting analysis.
* Bundling of the Numdifftools 0.6.0 package with relax ([https://code.google.com/p/numdifftools/) Numdifftools 0.6.0 package] with relax for numerically testing implementations of gradients, Hessians, and Jacobians.
* Implementation of the [http://www.nmr-relax.com/api/3.3/lib.structure.internal.object.Internal-class.html#collapse_ensemble internal structural object collapse_ensemble() method] to allow for all but one model to be deleted.
* Massive speed up of the internal structural object by [http://www.nmr-relax.com/api/3.3/lib.structure.internal.object.Internal-class.html#selection pre-processing the atom ID string into a special atom selection object]. This speeds up the [http://www.nmr-relax.com/manual/interatom_define.html interatom.define], [http://www.nmr-relax.com/manual/structure_delete.html structure.delete], [http://www.nmr-relax.com/manual/structure_rotate.html structure.rotate], [http://www.nmr-relax.com/manual/structure_translate.html structure.translate] and many other user functions which loop over structural data.
* Epydoc docstring fix for the [http://www.nmr-relax.com/api/3.3/dep_check-module.html#version_comparison dep_check.version_comparison() function].
* Removed ZZ and HD exchange from the dispersion chapter of the relax manual. These would probably require completely new analysis types added to relax to analyse such data.
* Updated the 'Announcement' section of the release checklist document. This now includes details about initially composing the message using the relax wiki ([http://wiki.nmr-relax.com)relax wiki], and then how that text and the CHANGES file are used for the email announcement ([http://news.gmane.org/gmane.science.nmr.relax.announce) email announcement] and the Gna! news item ([https://gna.org/news/?group=relax)Gna! news item].
* Small changes for the Gna! news item in the release checklist document.
* Modified the announcement section of the release checklist document. Text about removing wiki markup has been added.
* Editing of the [[relax 3.3.0]] features section of the CHANGES file. This will be used for the release notes.
* Added more test data for the repeated analysis. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Updated the Baldwin 2014 reference in the relax manual. The [http://pybliographer.org/ pybliographic software ] was used to format this BibTeX entry (http://pybliographer.org/). This was updated as volume and page number information is now available.
* Updated the Morin et al, 2014 paper (the relax relaxation dispersion paper) reference in the manual. The paper now has volume and page information.
* Added some more user function ranamings to the translation table. These were identified while preparing the release notes on the wiki (http://wiki.nmr-relax.com/Category:Release_Notes, http://wiki.nmr-relax.com/Release_notes).
* For the [http://www.nmr-relax.com/api/3.3/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html class of repeated analysis], implemented method to collect peak intensity, and function to plot the correlation. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Added [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_repeat_cpmg system test Relax_disp.test_repeat_cpmg] to be skipped, if no matplotlib module exists. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Added the Gimp XCF file for the logo of the relax wiki ([http://wiki.nmr-relax.com)relax wiki].
* Added [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_fit.Relax_fit-class.html#test_curve_fitting_height_estimate_error system test Relax_fit.test_curve_fitting_height_estimate_error()] for the manual and automated analysis of exponential fit. This is to prepare for new methods in the auto analysis protocol.
* In the auto analysis of exponential fitting, changed the minimisation method from simplex to Newton, to speed-up the fitting. This is for master Monte Carlo simulations.
* Created a basic text based progress meter in the new [http://www.nmr-relax.com/api/3.3/lib.text.progress-module.html lib.text.progress module]. This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.
* Modifications to the User_functions.test_structure_add_atom GUI test. As lists of lists are now accepted by the [http://www.nmr-relax.com/manual/structure_add_atom.html structure.add_atom user function], the operation in the GUI is now significantly different. Therefore many checks have been removed from the GUI test.
* Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the [http://www.nmr-relax.com/api/3.3/dep_check-module.html dep_check module]. This [https://gna.org/forum/forum.php?forum_id=2477 newest version handles infinite target function values preventing optimisation from continuing forever (]. The [https://gna.org/forum/forum.php?forum_id=2477). The 2475 1.0.10 version is also useful as there is full support for gradients and Hessians in the log-barrier constraint algorithm (https://gna.org/forum/forum.php?forum_id=2475)].
* Shifted the [http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.variables-module.html specific_analyses.relax_disp.variables module] into [http://www.nmr-relax.com/api/3.3/lib.dispersion.variables-module.html lib.dispersion]. This is both to minimise circular dependencies, as previously the [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp-module.html specific_analyses.relax_disp modules] import from target_functions.relax_disp and vice-versa, and to allow the relax library functions to have access to these variables. This follows from a similar change to the frame order analysis in the frame_order_cleanup branch.
* Dependency fix for the [http://www.nmr-relax.com/api/3.3/auto_analyses.relax_disp_repeat_cpmg-module.html auto_analyses.relax_disp_repeat_cpmg module]. This was causing relax to fail. SciPy is an optional dependence for relax, but this module caused relax to not start if scipy was not installed. This was detected by testing relax with PyPy.