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Changes
Formatting of all symbols/parameters.
* Added instructions and a build script for creating a useful version of latex2html. This version is essential for building the HTML version of the manual at http://www.nmr-relax.com/manual/. The build script downloads the Debian latex2html-2008 sources as well as all Debian patches for latex2html. It then applies a number of patches for fixing and improving the relax documentation. The program is then compiled and can be installed as the root user into /usr/local/.
* Extended the number of words used in the HTML webpage file names. This is to hopefully prevent files from being overwritten by multiple files having the same name.
* Added the write out of parameters and chi2 χ<sup>2</sup> values, when creating a dx_map. [https://gna.org/task/index.php?7860 Task #7860: When dx_map is issued, create a parameter file which maps parameters to chi2 χ<sup>2</sup> value].* Created system test Relax_disp.test_dx_map_clustered_create_par_file, which must show that relax is not able to find the local minimum under clustered conditions. When creating the map, the map contain chi2 χ<sup>2</sup> values, which are lower than the clustered fitted values. This should not be the case. Running a larger map with larger bounds and more increments, which should show that there exist a minimum in the minimisation space with a lower chi2 χ<sup>2</sup> value. [https://gna.org/bugs/index.php?22754 Bug #22754: The minimise.calculate() does not calculate chi2 χ<sup>2</sup> value for clustered residues]. [https://gna.org/task/index.php?7860 Task #7860: When dx_map is issued, create a parameter file which maps parameters to chi2 χ<sup>2</sup> value].* Renamed test scripts and files for producing surface chi2 χ<sup>2</sup> plots.
* Renamed sample scripts making surface maps.
* Added scripts to make surface plots of spin independents parameters dw δω and R2aR<sub>a</sub><sup>2</sup>.* Added example surface chi2 χ<sup>2</sup> values for plots. [https://gna.org/task/index.php?7826 Task #7826: Write an python class for the repeated analysis of dispersion data].
* Added example save state for more surface plotting.
* Added boolean argument to dx.map() function, to specify the creation of a parameter and associated chi2 χ<sup>2</sup> values file. For very very special situations, the creation of this file is not desired.
* Modified that structure of points in dx.map() is always a list of numpy arrays with 3 values.
* When issuing dx.map() function with points, implemented the writing out of parameter file, with associated calculated chi2 χ<sup>2</sup> values.
* Improved the feedback in the User_functions.test_structure_add_atom system test. It is now clearer what the input and output data is.
* The devel_scripts/python_multiversion_test_suite.py script now runs relax with the --time flag. This is for quicker identification of failure points. It will also force the sys.stdout buffer to be flushed more often on Python 2.5 so that it does not appear as if the tests have frozen.
* Added check to system test Relax_disp.test_cpmg_synthetic_dx_map_points() for the creation of a matplotlib surface command plot file.
* Added the write out of a matplotlib command file, to plot surfaces of a dx map. It uses the minimum chi2 χ<sup>2</sup> value in the map space, to define surface definitions. It creates a X,Y; X,Z; Y,Z map, where the values in the missing dimension has been cut at the minimum chi2 χ<sup>2</sup> value. For each map, it creates a projected 3d map of the parameters and the chi2 χ<sup>2</sup> value, and a heat map for the contours. It also scatters the minimum chi2 χ<sup>2</sup> value, the 4 smallest chi2 χ<sup>2</sup> values, and maps any points in the point file, to a scatter point. Mapping the points from file to map points, is done by finding the shortest Euclidean distance in the space from the points to any map points.
* Fix for testing the raise of expected errors in system tests. The system test will not be tested, if Python version is under version 2.7. [https://gna.org/bugs/?22801 Bug #22801: Failure of the relax test suite on Python 2.5].
* Inserted a z_axis limit for the plotting of 2D surfaces in matplotlib.
* Added better figure control of chi2 χ<sup>2</sup> values on z-axis for surface plots.
* Narrowed in dx_map in system test Relax_disp.test_dx_map_clustered_create_par_file(). This is to illustrate the failure of relax finding the global minimum. It seems there is a shallow barrier, which relax failed to climb over, in order to find the minimum value.
* Added the verbosity argument to the pipe_control.minimise.reset_min_stats() function. All of the minimisation code which calls this now send in their verbosity arguments. This allows the text "Resetting the minimisation statistics." to be suppressed.
* Small indexing fixes for the dispersion chapter of the relax manual.
* Fix for system test Relax_disp.test_cpmg_synthetic_dx_map_points. Another import line was written to the matplotlib script.
* Speedup and fix for system test Relax_disp.test_dx_map_clustered_create_par_file. The following test was taken out, since this a particular interesting case. There exist a double minimum, where relax has not found the global minimum. This is due to not grid searching for R2aR<sub>a</sub><sup>2</sup>, but using the minimum value.
* Removed debugging code from the N_state_model.test_CaM_IQ_tensor_fit system test. This was an accidentally introduced [http://www.nmr-relax.com/manual/state_save.html state.save user function] used to catch the system test state. It would results in the 'x.bz2' file being dumped in the current directory.
* Loosened the checks in the Relax_disp.test_baldwin_synthetic_full system test. This is to allow the test to pass on Python 2.5 and 3.1 on a 32-bit GNU/Linux system.