Changes

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This is a major feature and bugfix release. A comprehensive tutorial has been added to the relaxation dispersion chapter of the manual which shows, step-by-step, the [http://www.nmr-relax.com/manual/relaxation_dispersion_auto_analysis_in_GUI.html dispersion analysis in the GUI] using screenshots. Other changes include improved PDB chain ID support, a new mode for running a relax script and then entering the prompt UI mode, multiple file reading by the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function], and improvements to the relaxation dispersion analysis. A number of major bugs in the dispersion analysis concerning different relaxation delay times for different experiments and for improved handling of the offset have also been fixed. A number of important GUI bugs have also been fixed. All users are recommended to upgrade to this version of relax.

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).

http://svn.gna.org/svn/relax/tags/3.1.6

* Full support for PDB chain IDs in the internal structural object.

* Improvements for the devel_scripts/python_seek.py for finding all installed Python versions and modules. Individual modules can now be specified on the command line.

* Improved colour coding of relax log messages in the relax manual.

* The relaxation dispersion auto-analysis now creates the chi2.out text file. This is for more easily comparing the chi-squared values between analyses.

* Converted the chain ID list in the internal structural object to the CHAIN_ID_LIST module variable.

* The internal structure object method _pdb_chain_id_to_mol_index() now uses the CHAIN_ID_LIST string. This allows for the full PDB chain ID range to be supported.

* Epydoc docstring fix for the pipe_control.structure.main.load_spins() function.

* Created the Mf.test_bug_21615_incomplete_setup_failure GUI tests. This is designed to catch [https://gna.org/bugs/?21615 bug #21615] as reported by Ivan Leung (ivanhoe dott leung att chem dott ox dot ac dot uk). Included are the data files Ivan attached to the bug report truncated to two residues. The GUI test follows exactly the steps outlined by Ivan.

* Shifted the pedantic flag to escalate flag. The option -p would instead be used for the option --prompt. Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].

* Added the -p --prompt option for running a relax script and inspect interactively. Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].

* Added the unit test infrastructure for testing the specific_analyses.relax_disp package. This currently includes the package __all__ list unit test.

* Updated the specific_analyses.relax_disp package __all__ list. This was identified in the previously committed unit test.

* Created two new LaTeX commands for improving the layout of Python code in the relax manual. These are \pysep and \pyus which will be used to format the Python module separator character and the Python underscore character respectively. They are used in the \module{}, \pycode{}, etc. commands to add the '.\linebreak[0]' and '\_\linebreak[0]' text to allow for improved and consistent line breaking.

* Complete reformatting of the base LaTeX files. The paragraph structure has been changed so that each sentence now starts on a new line. This is for better tracking of changes (via 'svn diff' for example), for better searchability of certain text elements using command line tools such as 'grep', and for easier easier use of the 'sed' tool. The change tracking is most important as it allows for finer granularity - a small change will now only be shown as a change in one sentence rather than the whole paragraph, allowing the change to be identified more easily. It also allows for easier commit maintenance.

* Removed functional return of reference intensity in R_1ρ, since this does not exists. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R_1ρ dataset with missing combinations of time and spin-lock field strengths].

* Removed function return_intensity(), as this is no longer in use. Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R_1ρ dataset with missing combinations of time and spin-lock field strengths]. Reference: http://www.mail-archive.com/relax-devel@gna.org/msg05020.html.

* Minor bugfix for the internal structural object add_model() method. The internal structural object was being called with self as an argument, which would default to the chain_id keyword argument. The result would be relax state files with multiple copies of the internal structural object embedded in the structural XML section.

* Fix for [https://gna.org/bugs/?21605 bug #21605, the failure of the Frame_order.test_generate_rotor2_distribution system test]. The bug is due to the fact that numpy.float16 is not defined on all systems. Older numpy versions do not have this. Therefore the float16 value is now imported from lib.check_types where it is aliased to float32 when not defined.

* Fix for [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].

* Fix for [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R_1ρ dataset with missing combinations of time and spin-lock field strengths].

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