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* Implemented the PDB HELIX record writing function generic_fns.structure.pdb_write.helix().
* Improved PDB writing capabilities. The functions of the generic_fns.structure.pdb_write module now all use the _handle_none() function to avoid the text "None" from appearing in the PDB file and _record_validate() to be sure the record has not been corrupted with bad input causing it to be either less or greater than 80 characters.
* The Mf.test_bug_20531_molmol_macro_write_relaxfault system test now catches [https://gna.org/bugs/?20531 bug #20531]. This now uses the results file attached to the bug report https://gna.org/bugs/?20531.
* Implemented the PDB SHEET record writing function generic_fns.structure.pdb_write.sheet().
* Created a unit test for the generic_fns.structure.pdb_write.het() function.
* Many improvements to the lib.text.table module. The format_table() function now accepts arguments for text to prefix and postfix to each line,the text padding to the left and right inside the table, and the text used to separate the columns. The _blank() and _rule() private functions have been added to create distinct table elements.
* Created the lib.text.table.MULTI_COL constant for defining cells spanning multiple columns. This is not used yet.
* Modified the Mf.test_mf_auto_analysis GUI test to catch bug #20603 ([https://gna.org/bugs/?20603)bug #20603].
* Created a unit test for the lib.text.table.format_table() function to test multiple column support. Support for content spanning multiple cells is yet to be implemented.
* Implemented multi-column support in lib.text.table.format_table().
* The generic_fns.mol_res_spin.generate_spin_id_unique() function now handles missing spin containers. Previously if this function was used to generate a spin ID string of a spin not in the data store,it would fail. Now it generates an ID by defaulting to generate_spin_id().
* Converted many calls to generic_fns.mol_res_spin.generate_spin_id() to generate_spin_id_unique(). This will allow many future bugs to be avoided, as the spin ID string is most often used to retrieve spin containers. By using the generate_spin_id_unique() function, the returning of spin containers will always be correct.
* Created the Mf.test_bug_20563_missing_ri_error system test to catch bug #20563. The bug report is at [https://gna.org/bugs/?20563bug #20563]. The data added to the test suite is a highly truncated data set of a analysis completed using the data attached to the bug report.
* Modified the dauvergne_protocol model-free auto-analysis to aid in debugging. The write_results_dir argument has been added to allow the test suite to read from one directory in test suite shared data directories and redirect output to a temporary directory.
* The files from the Mf.test_bug_20563_missing_ri_error system test are now placed in a temporary directory. This is essential for the test suite to prevent files from going everywhere.
* Formatting fixes for the generic_fns.structure.pdb_write module.
* Fix for the classic_style() method of the model-free specific Macro class. This was identified by the new Mf.test_bug_20531_molmol_macro_write_relaxfault system test, but would probably never be encountered by relax users. It is not related to the bug this test is trying to catch. The problem is if spins have model-free parameters set up but there is no model-free model initialised - then the Molmol and PyMOL macro creation would fail.
* Fix for bug #20531 ([https://gna.org/bugs/?20531). This is the bug of #20531, the RelaxFault during the final stages of the auto_analysis.dauvergne_protocol model-free analysis when the Molmol and PyMOL macros are being created]. The problem was caused by model m9 (just the Rex parameter) when trying to determine what the order parameter for fast (< 200ps) motions is. The code was assuming that the model-free model would always contain an order parameter.
* Fix for the generic_fns.structure.pdb_write.het() function - the record now has trailing whitespace. The PDB records require trailing whitespace to the 80th character position.
* Fixes for many of the generic_fns.structure.pdb_write functions. The PDB records are now all filled with whitespace up to the 80th character.
* Fix for the internal PDB reading - the MASTER record was being marked as a molecule. Now this record is checked for and the molecule loop terminated.
* Bug fix for the XYZ 3D structure file reader. The atom name is now correctly set up for each atom in the file. The element type setting has also been simplified.
* Fix for bug 20603 ([https://gna.org/bugs/?20603)bug #20603, the relaxation data right click menu failure]. The problem was that there was that the last menu item specified had no contents. This item has been removed.* Fix for bug #20563 ([https://gna.org/bugs/?20563)bug #20563, the end failure of the model-free auto-analysis]. This was reported by Stanislava Panova ([https://gna.org/users/stacy)Stanislava Panova]. The problem was related to the Monte Carlo simulations. The generic_fns.monte_carlo.create_data() function is now asking for the errors associated with a certain data point, even if that data point does not exist. The solution was to check if the relaxation data ID string is present in spin.ri_data_err before accessing the key-value pair (in the specific API _return_error_relax_data() common method).
* Bug fix for the maintenance of the spin ID lookup table metadata. This is important for small molecules. Non-unique IDs were being placed into the lookup table,resulting in incorrect spin containers being sometimes used. Now the molecule container has the _res_name_count and _res_num_count metadata and the residue container the _spin_name_count and _spin_num_count structures. These are updated via metadata_update() and are used by the spin_id_variants() function to create a list of purely unique spin IDs.
* The spin_id argument to the residue.delete user function is no longer read-only. This allows spin ranges or other complicated IDs to be specified. This is needed for the Bmrb GUI tests to pass.