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Changes
Internal links to the dispersion models.
* Changed the Python readline link for MS Windows in the installation chapter of the manual. This now points to https://pypi.python.org/pypi/pyreadline as the iPython link is broken.
* Implemented system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for [[B14 full ]] model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for [[NS CPMG 2SITE 2-site 3D full ]] model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for [[NS CPMG 2SITE STAR 2-site star full ]] model. This is to catch the wrong unpacking of R2A and R2B when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Added synthetic data generator script which created the data to test against. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Split system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster up in different tests. A setup function which is: setup_bug_22146_unpacking_r2a_r2b_cluster(self, folder=None, model_analyse=None): And then the tests: test_bug_22146_unpacking_r2a_r2b_cluster_B14 test_bug_22146_unpacking_r2a_r2b_cluster_CR72 test_bug_22146_unpacking_r2a_r2b_cluster_NS_3D test_bug_22146_unpacking_r2a_r2b_cluster_NS_STAR. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Modified profiling script to get closer to the implementation in relax. An additional test function is setup to figure out how to reshape the numpy arrays in the target function. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Updated profiling text for [[CR72 ]] model. Now it is tested for 3 fields. This is related to: [https://gna.org/task/index.php?7807 Task #7807]: Speed-up of dispersion models for Clustered analysis.
* Added searching for environment variable PYTHON_INCLUDE_DIR if Python.h is not found in standard Python library. This can be very handsome, if one has a Python virtual environment for multiple users. This relates to the wiki page: http://wiki.nmr-relax.com/Epd_canopy.
* The lib.compat.norm() replacement function for numpy.linalg.norm() now handles no axis argument. This is to allow the function to be used in all cases where numpy.linalg.norm() is used, while providing compatibility with the axis argument and all numpy versions.
* Fix for wrong path testing of Python.h. Python.h would be in PYTHON_PREFIX/include/pythonX.Y/Python.h and not in PYTHON_PREFIX/include/Python.h.
* Better handling of the control-C keyboard interrupt signal in the relax test suite. This includes two changes. The Python 2.7 and higher unittest.installHandler() function is now called, when present, to terminate all tests using the unittest module control-C handler. The second change is that the keyboard interrupt signal is caught in a try-except statement, a message printed out, and the tests terminated. This should be an improvement for all systems.
* Adding last profiling information for model [[CR72]].* Added system test for model [[LM63 3 -site]]. According to results folder in test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site. This should pass, but it doesn't.
* Created an initial Relax_disp.test_lm63_3site_synthetic system test. This should have been set up a long time ago. It uses the synthetic noise-free data in the test_suite/shared_data/dispersion/lm63_3site directory which was created for a system test but never converted into one. The test still needs modifications to allow it to pass.
* Modifications for the Relax_disp.test_lm63_3site_synthetic system test. The r2eff_values.bz2 saved state file has been updated, as it was too old to use in the test. The test has also had a typo bug fixed and the data pipe name updated. The test now also checks all of the optimised values.
== Bugfixes ==
* Fix for the wrong unpacking of R20A and R20B in model [[CR72 full]]. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model [[B14 full]]. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model [[NS CPMG 2SITE 2-site 3D full ]] model. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A and R20B in model [[NS CPMG 2SITE STAR 2-site star full ]] model. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models.
* Bug fix for the lib.io.file_root() function for multiple file extensions. The function will now strip off all file extensions.
* Fix for [https://gna.org/bugs/?22210 bug #22210], the failure of the '[[LM63 3-site' ]] dispersion model. The problem is described in the bug report - the multiplication in the tanh() function is a mistake, it must be a division.
* Fix for the Library.test_library_independence verification test on MS Windows. The tearDown() method now uses the error handling test_suite.clean_up.deletion() function to remove the copied version of the relax library.
* Fixed the packing out of parameter tex for global analysis in model IT99. [https://gna.org/bugs/index.php?22220 Bug #22220]: Unpacking of parameters for global analysis in model IT99, is performed wrong.