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This is a major bugfix release and the first requiring numpy ≥ 1.6 to allow for faster calculations for certain analyses. There have been improvements to the GUI user functions, the ^[[?1034h escape code is finally suppressed on Linux systems, and the [http://www.nmr-relax.com/manual/structure_com.html structure.com user function]] has been added. Bugfixes include the proper handling of R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> parameters in the [[:Category:relaxation dispersion|relaxation dispersion]] models, the [[IT99]] dispersion model tex t<sub>ex</sub> parameter was incorrectly handled, the [[LM63 3-site]] dispersion models had a fatal mistake in its equations, files with multiple extensions (for example *.pdb.gz) are now correctly handled, and closing the free file format window in Mac OS X systems caused the GUI to freeze. Full details can be found below.
For this release, the Mac OS X framework used to build the universal 3-way (ppc, i386, x86_64) binaries for the stand-alone relax application has been updated. The relax application now bundles Python 2.7.8, numpy 1.8.1, scipy 0.14.0, nose 1.3.3, wxPython 2.9.3.1 osx-cocoa (classic), matplotlib 1.3.1, epydoc 3.0.1, [[OpenMPI|mpi4py 1.3.1]] and py2app 0.8.1. This should result in better formatted relax state and results files and give access to more advanced packages for power users to take advantage of.
* Fix for the wxPython link in the installation chapter of the manual. This was pointing to the scipy website for some reason.
* 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 R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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 R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for [[NS CPMG 2-site 3D full]] model. This is to catch the wrong unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> is performed wrong for clustered "full" dispersion models.* Extended system test Relax_disp.test_bug_22146_unpacking_r2a_r2b_cluster for [[NS CPMG 2-site star full]] model. This is to catch the wrong unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> when performing a clustered full dispersion model analysis. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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 R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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 R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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 R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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.
* 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.
* Removed system test test_hansen_cpmg_data_to_lm63_3site. This was a temporary implementation and has been replaced with system test Relax_disp.test_lm63_3site_synthetic.
* Fixes for all of the relaxation dispersion system tests which were failing with the new minfx code. Due to the tuning of the log barrier constraint algorithm in minfx in the commit at http://article.gmane.org/gmane.science.mathematics.minfx.scm/25, many system tests needed to be slightly adjusted. Two of the Relax_disp.test_tp02_data_to_* system tests were also failing as the optimisation can no longer move out of the minimum at pA p<sub>A</sub> = 0.5 for one spin (due to the low quality grid search in the auto-analysis).
* Updated the release checklist document for the new 1.0.7 release of minfx.
* Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. The pA p<sub>A</sub> parameter is no longer tested for one spin as it moves to random values on different operating systems and 32 vs. 64-bit systems. This is because this spin experiences no exchange, both dw δω and kex k<sub>ex</sub> are zero.
* Decreased the value checking precision in the Relax_disp.test_hansen_cpmg_data_to_lm63 system test. This is to allow the test to pass on certain operating systems and 32-bit systems.
* Modified the precision of the output from the relax_disp.sherekhan_input user function. This is simply to allow the Relax_disp.test_sod1wt_t25_to_sherekhan_input system test to pass on certain 32-bit systems, as the float output to 15 decimal places is not always the same. This system test has been updated for the change.
* Modified the Relax_disp.test_sprangers_data_to_mmq_cr72 system test to pass on certain systems. This test fails on 32-bit Linux (and probably other systems as well). To fix the test, the kex k<sub>ex</sub> values are all divided by 100 before checking them to 4 decimal places of accuracy.
* Improved how the relax installation path is determined in the status object. If the path cannot be found, the current working directory is then checked if it is where relax is installed. This is needed when importing modules outside of relax.
* Hack to permanently eliminate the ^[[?1034h escape code being produced on Linux systems. This is produced by importing the readline module. The escape code will be sent to STDOUT every time relax is executed, so it will be present in all log files. The problem is the TERM environmental variable being set to 'xterm'. The hack simply sets TERM to an empty string.
== Bugfixes ==
* Fix for the wrong unpacking of R20A R<sub>2A</sub><sup>0</sup> and R20B R<sub>2B</sub><sup>0</sup> in model [[CR72 full]]. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A R<sub>2A</sub><sup>0</sup> and R20B R<sub>2B</sub><sup>0</sup> in model [[B14 full]]. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A R<sub>2A</sub><sup>0</sup> and R20B R<sub>2B</sub><sup>0</sup> in model [[NS CPMG 2-site 3D full]] model. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> is performed wrong for clustered "full" dispersion models.* Fix for the wrong unpacking of R20A R<sub>2A</sub><sup>0</sup> and R20B R<sub>2B</sub><sup>0</sup> in model [[NS CPMG 2-site star full]] model. [https://gna.org/bugs/?22146 Bug #22146] Unpacking of R2A R<sub>2A</sub><sup>0</sup> and R2B R<sub>2B</sub><sup>0</sup> 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 t<sub>ex</sub> 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.
* Fix for [https://gna.org/bugs/?22257 bug #22257], the freezing of the GUI after using the free file format window on Mac OS X. 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().
