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Relax 2.2.0

14 bytes added, 18:49, 11 September 2014
Tracker links with full descriptions.
* Small syntax fix in the release checklist document.
* Added the MARC archive links to the development chapter of the relax user manual. These links are: http://marc.info/?l=relax-announce&r=1&w=2, http://marc.info/?l=relax-users&r=1&w=2, http://marc.info/?l=relax-devel&r=1&w=2, and http://marc.info/?l=relax-commits&r=1&w=2.
* The model-free overfit deselection algorithm now fails with a RelaxError when no spins are selected. This is to avoid situations such as bug #20277 ([https://gna.org/bugs/?20277)bug #20277].
* The pipe.display user function now uses relax_io.write_data() for better output formatting.
* Created the N_state_model.test_data_copying system test for the rdc.copy and pcs.copy user functions. These user functions do not exist yet, but this test will be used to implement them.
* Created the N_state_model.test_absolute_rdc_menthol system test to demonstrate a pseudo-atom failure. This is a test of the long range, absolute RDCs for menthol.
* Added a check for the second Q factor in the N_state_model.test_absolute_rdc_menthol system test.
* Modified the N_state_model.test_populations system test to catch [https://gna.org/bugs/?20335 bug #20335]. This simply adds calls to the rdc.delete and pcs.delete user functions, and then reloads the RDC and PCS data.
* Modified the temperature user function - the value can be set twice if it is the same value.
* Modified the frq.set user function - the value can be set twice if it is the same value.
* The rdc.back_calc user function now handles absolute RDCs.
* Created the Align_tensor.test_copy system test to catch bug #20338 ([https://gna.org/bugs/?20338)bug #20338].
* The spin.create_pseudo user function 'members' argument is no longer read only in the GUI. This allows the user to type in shorter spin IDs rather than selecting them from the list.
* Shifted and renamed the arg_check.check_float() function to check_types.is_float().
* The frq.set user function now warns if the frequency is lower than 100 MHz or higher than 2 GHz.
* Updated the diffusion tensor minimisation sample script as the code is very old and useless.
* Created the State.test_align_tensor_with_mc_sims system test to catch bug #20414. The report is at [http://gna.org/bugs/?20414bug #20414].
* Modified the align_tensor_mc.bz2 save file to catch a strange and rare bug. This is caught by the State.test_align_tensor_with_mc_sims system test.
* Spun out the maths_fns.rotation_matrix.random_rot_axis() function into its own module. The function is now called maths_fns.vectors.random_unit_vector().
* Fix for the relax_io.write_data() function - it can now handle no data being sent in.
* Bugfix for the use of pseudo-atoms for RDCs in the N-state model analysis. If the second atom of the pair in the intermolecular data container holding the RDC data was a pseudo-atom, then the N-state model optimisation setup would fail. Now both the first and second atoms being pseudo-atoms is supported.
* Fix for bug #20335 ([https://gna.org/bugs/?20335)bug #20335]. The global alignment ID data structure now has the RDC or PCS ID string correctly removed.* Fix for bug #20338 ([https://gna.org/bugs/?20338)bug #20338], the new tensor name is now set.
* Bugfix for the catching of errors in the GUI user functions - the sys module import was missing.
* Bugfix for the GUI combo_list input element SetValue() method. Values not belonging to the combo lists can now be set. This fixes the spin.create_pseudo user function in the test suite, a bug triggered by the N_state_model.test_absolute_rdc_menthol GUI test.
* Bugfix for the RelaxNoAlignError error class - the printout statement was broken.
* Bugfix for the rdc.copy user function - it is now functional. The code was old and untested, and still assumed that the RDC values were held in spin containers rather than the interatomic data containers.
* Partial fix for bug #20378 ([https://gna.org/bugs/?20378)bug #20378]. The gui_raise() function was operating differently under the command line run test suite and the GUI run test suite. The operation of the function is now consistent, and no RelaxError is raised (unless the raise_flag argument is set).* Full fix for bug #20378 ([https://gna.org/bugs/?20378)bug #20378]. As no RelaxError is no longer raised in this Bruker.test_bug_20152_read_dc_file GUI test (well only in the command line operation of the GUI tests), instead the current data pipe is checked to make sure no relaxation data was loaded.* Fix for bug #20414 (http[https://gna.org/bugs/?20414)bug #20414]. The variable for the number of simulations in the AlignmentTensorList object is now set prior to setting the simulation parameter values.* Fix for bug #20417 ([https://gna.org/bugs/?20417)bug #20417]. The backwards compatibility hook for the loading of old relax state and results files can now handle the presence of proton spins. The data structures are now correctly converted to the current data pipe design. This is only the case for old files containing PCS data.* Fix for bug #20420 ([https://gna.org/bugs/?20420)bug #20420]. The problem was in the generic_fns.mol_res_spin.create_spin() function. The index_molecule() and index_residue() functions where not taking alternative, non-current data pipes into account.* Fix for bug #20421 ([https://gna.org/bugs/?20421)bug #20421]. The loading of relax state files was only updating the spin ID metadata structures for the current data pipe. Now all loaded data pipes are updated.
* RDC data fix for the _back_compat_hook() method for converting old relax state and results files. The RDC data was not being shifted into the corresponding interatomic data container and remained in the spin containers.
* Fix for the bug caught by the N_state_model.test_mc_sim_failure system test. If no RDC error is present, then the returned error from the N-state model analysis specific method return_error() is None.
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