Author: bugman Date: Wed Sep 3 15:24:56 2014 New Revision: 25578 URL: http://svn.gna.org/viewcvs/relax?rev=25578&view=rev Log: Removed all of the index.php text from the tracker URLs in the CHANGES document. Modified: trunk/docs/CHANGES Modified: trunk/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=25578&r1=25577&r2=25578&view=diff ============================================================================== --- trunk/docs/CHANGES (original) +++ trunk/docs/CHANGES Wed Sep 3 15:24:56 2014 @@ -25,7 +25,7 @@ * Added synthetic data generator script which created the data to test against. Bug #22146: (https://gna.org/bugs/?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. Bug #22146: (https://gna.org/bugs/?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. Bug #22146: (https://gna.org/bugs/?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: Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models for Clustered analysis. + * Updated profiling text for CR72 model. Now it is tested for 3 fields. This is related to: Task #7807 (https://gna.org/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 the scons target for compiling the relax manual when using a repository checkout copy. The method for compiling the relax manual was calling the version.revision() function, however this has been replaced a while ago by the version.repo_revision variable. @@ -70,7 +70,7 @@ * Bug fix for the lib.io.file_root() function for multiple file extensions. The function will now strip off all file extensions. * Fix for bug #22210 (https://gna.org/bugs/?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. Bug #22220 (https://gna.org/bugs/index.php?22220): Unpacking of parameters for global analysis in model IT99, is performed wrong. + * Fixed the packing out of parameter tex for global analysis in model IT99. Bug #22220 (https://gna.org/bugs/?22220): Unpacking of parameters for global analysis in model IT99, is performed wrong. * Fix for bug #22257, the freezing of the GUI after using the free file format window on Mac OS X. This is reported at https://gna.org/bugs/?22257. This is a recurring problem in Mac OS X as it cannot be tested in the relax test suite. The problem is with wxPython. The modal dialogs, such as the free file format window, cannot be destroyed on Mac OS X using wx.Dialog.Destroy() - this kills wxPython and hence kills relax. The problem does not exist on any other operating system. To fix this, all wx.Dialog.Destroy() calls have been replaced with wx.Dialog.Close(). @@ -282,16 +282,16 @@ Changes: * 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/index.php?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/index.php?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/index.php?22017) LinAlgError, for all numerical CPMG models. + * Modified system test Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug #22017: (https://gna.org/bugs/?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) 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) LinAlgError, for all numerical CPMG models. * Implemented system test Relax_disp.test_cpmg_synthetic_ns3d_to_b14. Bug #22021: (https://gna.org/bugs/?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) 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) 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) 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/index.php?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/index.php?22070), the failure of the structure.superimpose user function after deleting atoms with structure.delete. + * Created the Structure.test_bug_22069_structure_delete_helix_attribute system test. This is to catch bug #22069 (https://gna.org/bugs/?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), 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. * Improvements for the git-svn support in the relax version module. Python 3 is now correctly handled and the URL is properly extracted from the git repository. @@ -308,9 +308,9 @@ Bugfixes: * Extremely important fix for the model B14. This was discovered by author Andrew Baldwin by inspecting his code in relax. Bug #22021: (https://gna.org/bugs/?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 model B14 was previously in a state of non-functioning. The 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/index.php?22069), the failure of the structure.delete user function with "AttributeError: Internal instance has no attribute 'helices'". + * 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), 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/index.php?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. + * 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), 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.