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Changes
Wiki formatting for the external links.
<section begin=changes/>
* Small updates for the wiki section of the release checklist document.
* Fixes for the links at the bottom of all HTML manual pages. This is for the automatically generated documentation at [http://www.nmr-relax.com/manual/index.htmlautomatically generated documentation], created using latex2html. The links all require double quotes, and some a trailing '/'. The links fixed are [http://www.nmr-relax.com], [http://www.nmr-relax.com/manual/ ] and [http://download.gna.org/relax/manual/relax.pdf].* Removed the repository backup file text from the relax manual. This is for [http://www.nmr-relax.com/manual/Latest_sources_the_relax_repositories.htmlrepository backup file text from the relax manual]. The gzipped repository dump file has not been created by Gna! for many, many years. The problem was identified by the W3C link checker ([http://validator.w3.org/checklink)W3C link checker].* Updated all of the [http://www.nmr-relax.com/manual/ ] links in the lib.dispersion package. This is for all of the individual model pages in the HTML manual.
* Improved the description for the [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function].
* A small code rearrangement to create the new target_functions.relax_fit_wrapper module. This follows from the idea at [https://gna.org/task/?7415#comment6]. The *func_wrapper() functions of the specific_analyses.relax_fit.optimisation module have been shifted out and converted to class methods to create the target_functions.relax_fit_wrapper module. This will be used to abstract away all of the C code, and will form the infrastructure to allow new exponential curves to be quickly supported. The modules of the specific_analyses.relax_fit and specific_analyses.relax_disp packages now import the target_functions.relax_fit_wrapper.Relax_fit_opt target function class and use that instead.
* Shifted the C code Jacobian functions into the new target_functions.relax_fit_wrapper module. This shifts all of the relaxation curve-fitting C code access into the target_functions.relax_fit_wrapper module so that the rest of relax does not need to handle the C code. This will allow for new models to be very easily supported, as they would all be set up in this target function module.
* Updated the formula in the description of the [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function].
* Modified the printouts from the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] if models are present. Instead of printing out 'MODEL', 'ATOM, HETATM, TER' and 'ENDMDL' for each model, the header 'MODEL records' is printed followed by a single '.' character for each model. For structures with many models, this results in a huge speed up of the user function which is strongly limited by how fast the terminal can display text.
* Added the synthetic saturation-recovery data in the form of Sparky peak lists to the repository. These files were created by Andras Boeszoermenyi. They are attached to the task at [http://gna.org/task/?7415 task #7415] as the Relax_sym.tar.gz file at [http://gna.org/task/download.php?file_id=22989Relax_sym.tar.gz file]. They were created for the formula I<sub>0</sub>(1 - e<sup>−R<sub>1</sub>.t</sup>) where I<sub>0</sub> = 1000000000000000.00 and R<sub>1</sub> = 0.5. These files and the associated relax_sim.py script (which needs to be updated for the latest relax version) could form the basis of a basic system test. This system test could then be used to implement the saturation-recovery experiment equations in relax.
* Updated the target_functions package __all__ list to include the relax_fit* modules.
* Modified the package __all__ list checking unit test to accept *.so C modules.
* Removal of an unused import in the relax_fit_zooming_grid.py system test script.
* Added a system test script for testing the saturation-recovery R<sub>1</sub> experiment. This was created by Andras Boeszoermenyi. The file was taken from the saturation_recovery.tar.gaz file (https://gna.org/task/download.php?file_id=22997) are attached to the task at [http://gna.org/task/?7415task #7415]. The only difference with the original script is that the [http://www.nmr-relax.com/manual/grace_view.html grace.view user function] calls have been removed, as these cannot be used in a system test.* Modified the relax_fit_saturation_recovery.py script to work as a system test. This is the script from Andras Boeszoermenyi. The change follows from the discussion of [http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369]. The status.install_path variable is now used to point to the location of the files. The relax data store ds.tmpdir variable is used for outputting all files. And commented out user functions have been deleted.* Added a copyright notice for Andras Boeszoermenyi for the newly added saturation-recovery R<sub>1</sub> script. This change follows the discussion in the message [http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369].* Created the Relax_fit.test_saturation_recovery system test. This follows from the discussion of [http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369].
* Added the saturation recovery experiment to the [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function]. This simply adds a new option and sets up a different parameter set [R<sub>x</sub>, I<sub>∞</sub>].
* Modified the Relax_fit.test_saturation_recovery system test script. The [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function] call now selects the 'sat' model.
* Removed the [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function] call from the relax_fit auto-analysis. This is to allow the user in a script, or in the GUI, to choose the model themselves.
* Added a button to the R<sub>1</sub> and R<sub>2</sub> GUI analyses for executing the [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function]. This is just after the peak list GUI element and before the optimisation settings. It allows different curve types to be selected for the analysis.
* Created the new specific_analyses.relax_fit.checks module. This creates the check_model_setup Check object, following the check_*() function design at [http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions]. This will be used to make sure that the exponential curve model is set prior to executing certain user functions.
* Improved the checking in the relaxation curve-fitting analysis. The new specific_analyses.relax_fit.checks.check_model_setup() function is now called prior to minimisation and in the get_param_names() API method to prevent Python errors from occurring due to missing data structures. In addition, the pipe_control.mol_res_spin module function exists_mol_res_spin_data() has been replaced with check_mol_res_spin_data().
* Fix for the recently broken Relax_fit.test_curve_fitting_height_estimate_error system test. The [http://www.nmr-relax.com/manual/relax_fit_select_model.html relax_fit.select_model user function] is now called as this is no longer performed in the auto-analysis.
* Prepared the "exp_3param" test for inclusion of artificial data.
* Added missing delays in the list. The duplicates had been omitted...
* Manually fix the script based on changes made during branch updating. This is as discussed by Edward d'Auvergne in a post at [https://mail.gna.org/public/relax-devel/2012-01/msg00001.html].
* Updated Séb's relax_fit_exp_3param_inv_neg.py system test script to work with the current relax design.
* Added a script for calculating the expected peak intensities for an inversion recovery curve. This is based on the values used by Sébastien Morin in his inversion-recovery branch, as the check_curve_fitting_exp_3param_inv_neg() function of the test_suite/system_tests/relax_fit.py file.
* Python 3 fix for the relax_fit_exp_3param_inv_neg.py system test script. The xrange() function does not exist in Python 3, so was replaced by range().
* Updated the memory_leak_test_relax_fit.py development script for the C module changes. This is only the docstring description which changed.
* Epydoc docstring fixes for the lib.io module - keyword arguments were not correctly identified. These were identified by Troels in the post at [http://thread.gmane.org/gmane.science.nmr.relax.scm/24565/focus=7384].
* Created the State.test_bug_23017_ieee_754_multidim_numpy_arrays system test. This is to catch [https://gna.org/bugs/?23017 bug #23017, the multidimensional numpy arrays are not being stored as IEEE 754 arrays in the XML state and results files]. This test checks a rank-2 float64 numpy array stored in the current data pipe against what the IEEE 754 int list should be for it.
* Grammar fix for a warning from the [http://www.nmr-relax.com/manual/pymol_display.html pymol.display user function].