Trusted, Bureaucrats
4,228
edits
Changes
Extended the tracker links to include the description.
* Punctuation fixes throughout the CHANGES document.
* Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug #22017: ([https://gna.org/bugs/?22017) bug #22017: LinAlgError, for all numerical CPMG models]. System test was renamed from test_cpmg_synthetic_cr72 to test_cpmg_synthetic_ns3d_to_cr72, to reflect which model create the data and which model fits the data.* Modified cpmg_synthetic script to first create all time structures before doing back-calculation. Bug #22017: ([https://gna.org/bugs/?22017) Bug #22017: LinAlgError, for all numerical CPMG models]. The numerical models need all time points which are defined in setup to be present when calculating.* Renamed system test to test_cpmg_synthetic_ns3d_to_cr72_noise_cluster. The model that creates the data has been changed to numerical model. Bug #22017: ([https://gna.org/bugs/?22017) Bug #22017: LinAlgError, for all numerical CPMG models].* Implemented system test Relax_disp.test_cpmg_synthetic_ns3d_to_b14. Bug #22021: ([https://gna.org/bugs/?22021) Bug #22021: model B14 shows bad fitting to data]. This is to catch model B14 showing bad fitting behaviour.* Parameter precision increase for system test Relax_disp.test_baldwin_synthetic. The correct implementation of the trigonometric functions allow for higher precision. Bug #22021: ([https://gna.org/bugs/?22021) Bug #22021: model B14 shows bad fitting to data]. Duplicate line codes were also removed.* Code cleanup in system test Relax_disp.test_baldwin_synthetic_full. Bug #22021: ([https://gna.org/bugs/?22021) Bug #22021: model B14 shows bad fitting to data]. The precision could also be increased by 1 digit.* Code cleanup in system test Relax_disp.test_baldwin_synthetic. Bug #22021: ([https://gna.org/bugs/?22021) Bug #22021: model B14 shows bad fitting to data]. Removing many unnecessary lines of code.
* Added 7 unit tests demonstrating edge case 'no Rex' failures of the 'NS CPMG 2-site expanded' model. This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858. These tests cover all parameter value combinations which result in no exchange: dw = 0.0; pA = 1.0; kex = 0.0; dw = 0.0 and pA = 1.0; dw = 0.0 and kex = 0.0; pA = 1.0 and kex = 0.0; dw = 0.0, pA = 1.0, and kex = 0.0. Such tests should be replicated for all dispersion models.
* Created the Structure.test_bug_22069_structure_delete_helix_attribute system test. This is to catch bug #22069 ([https://gna.org/bugs/?22069)bug #22069, the failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'"].* Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test. This is to catch bug #22070 ([https://gna.org/bugs/?22070)bug #22070, the failure of the structure.superimpose user function after deleting atoms with structure.delete].
* Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test. These tests reveal the real problem - that the atoms of the second model have not been removed by the structure.delete user function.
* Added git-svn support for the relax version information module. This allows the subversion revision number and repository URL to be displayed on program startup, so that it is stored in log files. This is very useful for debugging purposes.
* Improvement for the unit test printouts when run with the --time command line option. The full unit test name is now printed out, reverting to the old behaviour. However the shortened test names are preserved for the other test suite categories.
* Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test. This is a demonstration, showing the 'NS CPMG 2-site expanded' model with no exchange when kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used for all dispersion models to make sure that they model this edge case correctly as well. This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5906.
* Attempt at fixing [https://gna.org/bugs/?22071 bug #22071, the relax unit test and system test not functioning. This is reported at https://gna.org/bugs/?22071]. The fix here is that the git commands to show the current subversion revision number only works when run from the relax base directory, or one of the subdirectories. This should now be fixed, as the pipe running the command will first 'cd' to the relax base directory.* Another attempt at fixing [https://gna.org/bugs/?22071 bug #22071, the relax unit test and system test not functioning. This is reported at https://gna.org/bugs/?22071]. This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been replaced with "cd %s; git svn info".
* Changed most default dispersion parameter values to avoid edge cases where there is no exchange. The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever used for an optimisation starting point - which it never should, apart from development, test suite, and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away from the no exchange condition of pA = 1.0. This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
* Fixes for 3 dispersion system tests for the change in default parameter values. The default values are used in the auto-analysis in the test suite to avoid the grid search. The changed values affected the optimisation of two spins from Flemming Hansen's data located at test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue 70 used as an example where data is only available at one field. The system test Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these default values.
== Bugfixes ==
* Extremely important fix for the [[B14|model B14]]. This was discovered by author Andrew Baldwin by inspecting his code in relax. Bug #22021: ([https://gna.org/bugs/?22021) [[B14|Bug #22021: model B14]] shows bad fitting to data]. The implementation was performed wrong for calculation of g3 and g4. The implementations should be performed by trigonometric functions. The [[B14|model B14]] was previously in a state of non-functioning. The [[B14|B14 model]] now shows excellent performance.* Fix for bug #22069 by only deleting helix and sheet data with structure.delete when it exists. This is bug #22069 ([https://gna.org/bugs/?22069)bug #22069, the failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'"].
* Fix for all edge case [[No Rex]] failures of the [[NS CPMG 2-site expanded]] model. This uses the no exchange checking idea, modified to function in the relax trunk, from http://article.gmane.org/gmane.science.nmr.relax.devel/5847. This is importantly on line 1 of the function. The recently introduced set of 7 unit tests comprehensively showing these failures now all pass.
* Important bug fix for the structure.delete user function when multiple models are present. This is to fix bug #22070 ([https://gna.org/bugs/?22070)bug #22070, the failure of the structure.superimpose user function after deleting atoms with structure.delete]. The problem is that structure.delete was removing the atoms from the first model but none of the others. This is because it was using the structural object atom_loop() method to find the atoms to be deleted, but this method operates on the first model. So when the second model is reached, the atoms are already gone.