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* Epydoc fix for the name_pipe() method of the relaxation dispersion auto-analysis for repeated data.
* Fixes for the HTML user manual compilation. The index.html file was not being created as the main page has changed from 'relax_user_manual.html' to 'The_relax_user_manual.html'.
* Added a line to the release checklist document about updating the wiki release links. These are for the combined release notes pages at [http://wiki.nmr-relax.com/Relax_releases], [http://wiki.nmr-relax.com/Relax_release_descriptions], [http://wiki.nmr-relax.com/Relax_release_metadata], [http://wiki.nmr-relax.com/Relax_release_features], [http://wiki.nmr-relax.com/Relax_release_changes], [http://wiki.nmr-relax.com/Relax_release_bugfixes], [http://wiki.nmr-relax.com/Relax_release_links].
* Updates for the release announcement section of the release checklist document.
* Created a system test to catch a rare relaxation data loading problem.
* Expansion of the align_tensor.matrix_angles user function. The new basis set 'unitary 9D' has been introduced. This creates vectors as {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} and computes the inter-vector angles. These match the 'matrix' basis set whereby the Euclidean inner product divided by the Frobenius norms is used to calculate the inter-tensor angles. In addition, the user function documentation and printouts have been improved. And the backend code has been simplified.
* Updated the script and log file for demonstrating differences between alignment tensor basis sets. This now handles the changes to the basis_set arguments used in the align_tensor.matrix_angles and align_tensor.svd user functions, and includes the new basis sets.
* Added the irreducible tensor notation of {A-2, A-1, A0, A1, A2} to the alignment tensor object. This follows from the definition of Sass et al, J. Am. Chem. Soc. 1999, 121, 2047-2055, [http://dx.doi.org/10.1021/ja983887wDOI: 10.1021/ja983887w]. The equations of (2) were converted using Gaussian elimination to obtain a reduced row echelon form, so that the equations in terms of {A-2, A-1, A0, A1, A2} were derived. These have been coded into the alignment tensor object calc_Am2, calc_Am1, calc_A0, calc_A1 and calc_A2 methods respectively, and the values can be obtained by accessing the Am2, Am1, A0, A1, and A2 objects. To check that the implementation is correct, a unit test has been created to compare the calculated values with those determined using Pales.
* Expanded the unit test of the alignment tensor {A-2, A-1, A0, A1, A2} parameters to cover all values.
* Created functions in the relax library for calculating the inter-vector angle for complex vectors. This is in the lib.geometry.vectors module. The function vector_angle_complex_conjugate() has been created to calculate the angle between two complex vectors. This uses the new auxiliary function complex_inner_product() to calculate <v1|v2>.
* More improvements for the align_tensor.matrix_angles user function description.
* Epydoc docstring fixes and expansion for the lib.io.sort_filenames() function.
* Epydoc docstring fixes for the lib.spectrum.nmrpipe module. This is for the API documentation at [http://www.nmr-relax.com/api/index.htmlAPI documentation]. The show_apod_rmsd_to_file() and show_apod_rmsd_dir_to_files() function docstrings have both been modified.* Epydoc docstring fixes for the pipe_control.opendx.map() function. This is for [http://www.nmr-relax.com/api/3.3/pipe_control.opendx-module.html#mappipe_control.opendx.map() function]. The fixes include whitespace and textwrapping changes.
* Python 2.5 fix for the align_tensor.display user function. The new irreducible spherical tensor coefficient printout was failing as the float.real variable was introduced from Python 2.6 onwards.
* Shifted the structure checks into their own module. This shifts the special check_structure Check object from pipe_control.structure.main into the new checks module. It allows the check to be performed by other modules in the pipe_control.structure package.
