Changes

{{infobox relax release| version = 2.1.2| prev = 2.1.1| next = 2.2.0| type = Python super-compatibility| date = 17 October 2012| manual = yes}} == Description ==

This is the Python super-compatibility release includes a major overhaul of the [http://www.nmr-relaxwill now run on Python 2.com/manual/ relax user manual] with 3 all the addition of new chapters and tutorials for all analyses and major expansions and improvements overallway to Python 3. It also includes 3, a major set span of bug fixes to re-enable the NOE, R₁ and R₂ analyses over 9 years of multiple spin types (ePython development.g Some exceptions are Python 3. 0 as numpy and scipy are not compatible with that release, the Trp sidechain indole NH)execution of external programs in Python 2.3 not being supported, window ordering fixes for and the GUI, and numerous other small currently not available on Python 3 due to the wxPython project not being compatible with this new Python design yet. A number of important bug fixesare also included. More For more details are given please see below. All users are recommended to upgrade to this newest version.

== Download ==

== CHANGES file ==

Version 2.1.1 2 <br/>(21 September 17 October 2012, from /trunk) <br/>http://svn.gna.org/svn/relax/tags/2.1.12

=== Features ===

* Creation of extensive tutorials for both the script and GUI modes for the NOE, R₁ and R_{Python 2}, model-free chapters with screenshots in of the GUI in operation.* Restored 3 to 3.3 support for multiple spin types in , including large changes throughout the NOE, R₁ and R₂ analyses allowing, for example, tryptophan sidechain indole NE1 data code to be analysed.* The activation and expansion of the [http://www.nmr-relax.com/manual/Consistency_testing.html consistency testing chapter] able to the user manual.* The completion of the [http://www.nmr-relax.com/manual/Reduced_spectral_density_mapping.html reduced spectral density mapping chapter] of the user manualrun on Python 3.* Improvements to the [http://www.nmr-relax.com/manual/Alphabetical_listing_user_functionsnew_protocol_in_GUI.html user function section of the user manual] with better visual separation and the inclusion of the icons used GUI tutorial in the GUI.* Creation of the [http://www.nmrmodel-relax.com/manual/relax_data_model.html relax data model free chapter] of the user manual to explain how to set up data in relax in all UI modes (with screenshots in the GUI mode).* Creation of the [http://www.nmr-relax.com/manual/Preface_citing_relax.html citations chapter] of the user manual to help users properly cite the parts of relax that they use.* A complete rewrite number of the [http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html relaxation curve-fitting chapter] of the relax manualbugfixes.* General Small improvements and expansions throughout the user manual (the manual is now 15 Mb compared to 4.3 Mb for [[relax 2.1.0]])overall.

=== Changes ===

* Modified The scons 'clean' target now removes the model-free optimisation final printout Python 3 __pycache__ directories.* Small edit to be more multi-processor friendlythe installation chapter of the user manual. * The message saying that Decreased the optimised &chi;^{Python version dependency from 2.5 to 2} is an improvement or not now includes .3 in the installation chapter of the spin ID string if presentuser manual. * This is more informative More error checking for the multi-processor mpi4py printoutsassociate_auto() method of the data pipe editor window.* Added data pipe bundle error checking for the GUI pipe editor window associate_auto() method.* Added some error checking for the data pipe bundle in the use of the program 'nice' to the auto model-free analysis GUI tutorial in the user manualcode.* Removed the out of date and useless README file for the HTML version of the user manualAdded some special RelaxErrors for data pipe bundles.* Added some bug catching code for the observer objects. In some rare cases a BMRB section registered method's key was set to the end of the model-free chapter of the user manualNone.* Massive expansion of the model-free chapter of the user manual including script This is now caught and GUI tutorialsa RelaxError thrown to prevent later indecipherable errors. * The model-free chapter setup.py application building script now has step-by-step tutorials for both complains if the Python setuptools are not installed.* Updated the relax prompt/script mode and GUI mode for figure in the new automated model-free protocol (intro chapter of the d'Auvergne protocol)[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008]. This includes a large set of screenshots for user manual to the GUI modemore modern prompt.* Created Improvements to the User_functionsAPI documentation compilation.test_value_set GUI test demonstrating The excluded files and directories, as well as hidden ones, are no longer included in the failure list of files/directories to add to the [http://wwwdocumentation.nmr-relax.com/manual/value.set * Added a file with the relax user function]functions used for the prompt screenshots.* Modified This is for the dauvergne_protocol sample script[d'Auvergne manual and Gooley, 2007][d'Auvergne and Gooley, 2008] to handle tryptophan indole NE1 datathe website.* The graphicsAdded the public domain LaTeX nth.fetch_icon() function argument 'format' can now be set to None. This will return the sty style file path without the extension.* Improvements to for the duplicate user manual title finding script.* Created a simple shell script to find duplicate titles in Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing the relax user PDF manualto compile on more systems. * This is important Fixes for weird print statements with double brackets generated by the HTML version of the manual as duplicated titles causes HTML pages to be overwritten2to3 Python conversion script. * For example all chapters, sections and subsections titled "Introduction" will load the introductionRemoved a debugging printout.html file which will contain the text * Python 3 fixes for one of the last section test data scripts - print statement with that title!function call replacements.* Additions to the scripting section of the relaxation curve-fitting chapter of the user manualPython 3 fixes for non-used Python code - converted print statements to function calls.* A small edit to Python 3 fixes for the intro chapter script for the multi-processor operation and logginggenerating plots of magnetic field lines.* Added some labelling Another print statement to the infrastructure chapter of function Python 3 fix for the user manual for referencing.* A number of updates and edits to the intro chapter of The Python print statements in the user manual. The model-free GUI screenshot has been shifted are now function calls to the intro chapter in preparation for a full tutorial with screenshots in the model-free chapterbe Python 3 compatible.* Updated Python 3 fix for the data model chapter of the user manual to cover the handling of protonsgeneric_fns.structure.geometric.angles_regular() function. This change includes the modification of the PDB reading screenshot to demonstrate the reading of a specific model and the naming of the moleculeInteger divisions no longer produce integers.* All Better formatting of the GUI strings and test suite summary.* The text are now formatted with relax controller log is no longer cleared when a small sans serif font in the user manualreset occurs. This is because allows the test suite results to still be presented in the GUI, a sans serif font is almost always used be defaultmode.* Modified Even cleaner exiting of the User_functions.test_structure_pdb_readGUI - the interpreter thread is terminated by the exit_gui() GUI test to catch another bugmethod. * This The GUI is now cleanly exited with a bug recently introduced with the fixes call to the other sequence editor GUI window problemswx.App.ExitMainLoop rather than wx.Exit.* Created the User_functions.test_structure_pdb_read GUI test Python 3 fix for checking the sequence editor windowcompat module - the Queue2 object needs to always be defined. * This new user function GUI testing class is to be used Added support for Python 2.2 and earlier for testing out the special GUI elements not invoked within compilation of the unit testingC modules. * The test_structure_pdb_read() test specifically shows a number of failures Removed an unused import of the sequence editor windowQueue module from the multi-processor.* Modified Python 3 fix for the operation ScientificPython PDB reader unit tests. The order of the sequence GUI element keys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to have access to the sequence editor window. This is to allow this GUI element to be blasted within the test suite.comparison.* Improvements to the descriptions of Redesigned the [http://www.nmr-relax.com/manual/structurereset.read_xyz html reset] user function] argumentsbackend.* Improvements to This now no only clears out the descriptions of the [http://www.nmr-relax.com/manual/structurerelax data store, but it also resets the GUI if present.read_pdb user function] arguments.* Added @HE1 to the spin ID list Some of the [http://www.nmr-relax.com/manual/structure.load_spins user function]. This is only seen in reset code comes from the tearDown() method of the GUItests.* Created All windows but the new generic_fns.result_files for standardising main GUI window are closed and the handling of results filesrelax controller gauges are set to zero and the log window text cleared. This fixes the bug where results files are repetitively added These changes should allow GUI tests after an error or failure to the listpass, something which is currently problematic. * All of Disabled the code touching cdp.result_files now uses this module insteadinitial relax intro printout from the GUI when running the test suite.* Updated the scripting section of This prevents the intro chapter of text from appearing in the user manual for non-technical usersfirst failed test.* Expanded the spin ID list Fix for the [http://wwwMf.test_read_results_1_3_v2_broken() system test for Python 3.nmr-relax.com/manual/structure.load_spins user function]2. This now includes The object comparison method no longer converts dictionaries to strings for the spins "@N"comparison, "@NE1", "@C", "@H", "@O", "@P", ":A@C2", ":A@C8", ":G@N1",":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6"as the string version is different in different Python versions.* Fix for the Mf.test_write_results() system test for the Python 3 versions. The logic for determining Python 3 versions was broken and the incorrect files was used for Python 3.1.* Better Python 2.3 support.* Changed The compat module is now imported at the RelaxError for missing relaxation times in very start to allow the relaxation curve-fitting analysesbuiltins to be set before any other imports.* Modified the test_bug_20152_read_dc_fileThe sorted() GUI test to catch builtin method is now mimicked and the RelaxErroros.devnull string set for Python 2. This error is because of the old PDC format3 and earlier.* Created Fix for the test_bug_20152_read_dc_fileMf.test_write_results() GUI system test for catching [https://gnaPython 3.org/bugs/?20152 bug #20152]1. This includes truncated data taken from the bug report (with data for only the first The XML version in Python 3 residues).* Set up 1 is the Bruker Dynamics Center system tests as GUI testsold style. This Therefore the old results file is in preparation for catching [https://gnabeing used to check this Python 3.org/bugs/?20152 bug #20152]1 result.* Re-added Dominique Marion's solvent suppression Small improvements to the NMRPipe multiple Python version test suite testing script in the curve-fitting chapter.* * Reactivated support for Python 2.3. A few small edits of This mainly skips the relaxation curve-fitting chaptermissing 'subprocess' module. This is to reinforce the exact time of the relaxation time periodhowever decreases relax's functionality a little.* Added some text to explain why test only J(Created a special script for testing out relax with Python versions 1.0) is discussed whereas all the script also calculated F_R₂ and F_&eta;way to 3.3. This was suggested by [https://gna.org/users/bugman Edward d'Auvergne] builds the C modules for each Python version in a post at:https:~//mail.gna.org/public/relax-devel/2012-09/msg00044.htmlbin and then runs the test suite, outputting everything to log files.* Big clean up of The Results system tests are no longer dependent on the Bibtex bibliography file for the relax user manualrelaxation curve-fitting C modules.* Small edits of This allows these tests to run when the consistency testing figure caption in the relax user manualmodule cannot be imported.* Editing Python 2.5 and a number of fixes/cleanups lower fix for the consistency testing chapter of the user manualtest_write_protein_sequence() unit test.* Editing of The byte array is wrapped in an eval() statement to allow Python 2.5 and lower to parse the "Values, gradientscode without failing, and Hessians" chapter of the user manual to make it fit betterbyte array comparison is now only used for Python 3+. * The context of this chapter has been specified by changing All system and GUI tests reliant on the title to "Optimisation of relaxation data relax-- values, gradients, and Hessians" and the intro text has been updatedfit C modules are deactivated if import fails. As this chapter is no longer straight after This removes a pile of useless error messages from the test suite and presents a table of skipped tests at the model-free chapter, this is neededend.* Made a small correction to a reference such that a superscript is correctly displayedMore Python 3 fixes for the use of now non-existent string module functions.* Added Python 3 fix for the bounding box and a centerline command model-free BMRB export - many string module methods no longer exist.* Mass conversion of the alignment tensor data structures to the code for same new design as the figure for consistency testingdiffusion tensor. This follows two remarks by Edward d'Auvergne at https://maillarge set of changes matches all of those revisions for the diffusion tensor already committed.gna.org/public/relax-devel/2012-09/msg00030.html The alignment tensor data structures are now read only, and https://mailcan only be modified via the set() method.gna This is a much simplified design which works on all Python versions.org/public/relax-devel/2012-09/msg00032.html* Small clean ups of the diffusion tensor data structure code.* Added more text to describe Deleted the now unused _update_sim_set() method of the consistency testing approachdiffusion tensor data structure. * Also includes a very basic point by point protocol for consistency testingRemoved the now unused _update_sim_append() method from the diffusion tensor data structure. * This was proposed by [https://gnaCleaned up the docstring of the diffusion tensor data object __setattr__() method.org/users/bugman Edward d'Auvergne] at https://mail* Updated all of the diffusion tensor unit tests to the new design.gna.org/public/* Fix for the reading of model-free results files from relax-devel/2012-09/msg000281.html2 when simulation data is missing. * This also follows a discussion started by [https://gnaFix for the reading of relax 1.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax2 model-devel/2012-09/msg00019.htmlfree results files for the diffusion tensor structure redesign.* Added some text to describe Another fix for the consistency testing example figurefold_angles() diffusion tensor function - again an incomplete design conversion. * This follows a discussion started by [https://gnaFix for the setting of the diffusion tensor parameter errors in the model-free specific analysis code.org/users/bugman Edward d'Auvergne] at https* Fix for the setup of the model-free Monte Carlo simulations for the new diffusion tensor design.* Another fix for the [http://mailwww.gnanmr-relax.orgcom/public/relax-develmanual/2012-09/msg00019diffusion_tensor_init.htmldiffusion_tensor.* init user function] - it was not completely converted.* Added a modified version Fix for the fixing of Figure 1 from Morin and Gagne (JBNMR, 2009 (http://dx.doi.org/10.1007/s10858parameters in the model-009-9381-4))free analyses. File formats are .agr The diffusion tensor set_fixed(xmgrace), eps (gzipped), method is now used.* Fix for the XML output of the diffusion tensor - only the modifiable parameters are output. This was the previous behaviour and pngis needed for the test suite to pass. * This follows a discussion started by Converted the [httpshttp://gnawww.org/users/bugman Edward d'Auvergne] at https://mailnmr-relax.gna.orgcom/public/relax-devel/2012-09manual/msg00019palmer_extract.htmlpalmer.extract user function] to use the new diffusion tensor design.* Added a directory for placing consistency testing graphicsThe diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixed(). * This follows a discussion started by The [httpshttp://gnawww.nmr-relax.orgcom/usersmanual/bugman Edward d'Auvergnefix.html fix user function] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.htmlnow uses the diffusion tensor set_fixed() method.* Corrected Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the bibliography entries whih were still in plain text and not as a Latex \cite call'fixed' object. * Also renamed Fix for the MorinGagne09 entry to MorinGagne09a as there model-free specific analysis duplicate_data() method for the new design. The diffusion tensor __mod_attr__ object is now also MorinGagne09b. This was proposed by Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00025.htmlcalled _mod_attr.* Added Fix for the DOI to reference Morin11 and fixed indentation diffusion tensor to_xml(10) method for the new design.1016/j For some reason the methods of the Element class are no longer blacklisted.pnmrs.2010.12.003* Converted the diffusion tensor data structure from_xml()method to the new tensor design. * This follows a comment by Edward d'Auvergne at https://mailFix for the Diffusion_tensor.gna.org/public/relaxtest_copy system test -devel/2012the simulation parameters are now read-09/msg00022only.html Instead, the diffusion tensor set() method needs to be called.* Deletion The setting of list values for the relax version LaTeX file - this is automatically created anywayDiffTensorSimList object now works correctly.* Added text to detail The private _set() method now works correctly by calling the base class method, and the usage normal setting of the consistency testing scriptdiffusion tensor simulation values produces a RelaxError. * This text was modified from Fix for the corresponding text diffusion tensor __deepcopy__() replacement method for jw_mapping. This follows a discussion started by [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.htmlthe new design.* Added some text and a reference The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.* Modified the setUp() method for the diffusion tensor system tests to use the consistency testing chapternew design. * This follows a discussion started by [https://gnaRedesigned how diffusion tensor simulation structures are handled.org/users/bugman Edward d'Auvergne] at https://mail The design is now much cleaner and works with all Python versions.gna* Removed all the unused imports from specific_fns.org/public/relax-devel/2012-09/msg00019model_free.htmlmain.* Editing A number of private diffusion tensor objects and methods have switched to the nmrPipe script in the R_x curve-fitting chapter of the manualsingle leading '_' format.* Some editing of Improvements to the NOE chapter of the relax user manualdiffusion tensor set() method. The parameters, errors and simulations are now properly differentiated and stored.* The Converted the old R₁ diffusion tensor __setattr__() method into the set() method. This is the only way in which diffusion tensor parameters, errors and R₂ analysis screenshots have been shifted to the intro chaptersimulations can be set.* Editing of Renamed the relax diffusion tensor data model chapter of structure type() method to set_type(). This is because the type is stored as the 'type' object, clashing with the user manualmethod name.* Large expansion and lots of editing of Created the relaxation curve-fitting chapter of diffusion tensor data structure type() method for setting the user manualtensor type. The GUI section has been added which includes step-by-step instructions on how This is to use relax,illustrated with screenshots at each stepremove the "cdp.diff_tensor. There has been general editing of type = 'x'" code from the whole core of relax, as the chapter as wellstructure is now read only.* Added a tonne of GUI screenshots of an R₁ analysisThe new diffusion tensor fixed() method has been created to allow the fixed flag to be changed. * These will be used in Fix for the initialisation of the relaxation curvediffusion tensor data structure, now that it is read-fitting chapter of the user manualonly.* Added some Grace plots from an NOE analysis for use in the user manualThe diffusion tensor data structure has been completely converted into a read-only structure.* Small edits of The __setattr__() method now will always raise a RelaxError, and the relax diffusion tensor simulation data model chapter of structure objects __setitem__() method will raise the user manualsame error.* Editing of Updated the relaxation curve-fitting relax version numbers and NOE chapters of the 'trunk' used relax user manual. This is to synchronise For example the format of information about checking out the two chapters, and includes main development line was still talking about 1.3 rather than the swapping of text between themtrunk.* Added trp indole NH loading into Python 3 fix for the relaxation curve-fitting sample scriptsetting of diffusion and alignment tensor simulation values. The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.* Large edits of Python 3 fix for the consistency testing chapter model-free results file reading tests. The ordering of dictionaries is different in Python 3, so now these are properly converted from strings to dictionaries before comparison. This was not happening because of the user manualXML changes from Python 2.7.3 onwards.* Activated the consistency testing chapter of The relaxation curve-fitting system tests are now skipped if the user manualmodule is missing or broken.* Added This improves the printouts from the test suite and shows a summary of skipped tests rather than a LaTeX label to the J(&omega;) mapping chapterpile of traceback messages and errors.* Added The message about skipping the other consistency testing references GUI tests due to the citation chapter wxPython being missing is now more specific. This was being shown for all runs of the manualtest suite when it only needs to appear if GUI tests have been run.* Added a Python 3 version of the Fushman et altruncated OMP model-free results file., 1998 reference.* Fix for This was created with trunk.* Removed the Farrow et al., 1995 DOI numberPython 3 byte array hack which should have been removed earlier.* Changed the order of the R_x curveThe OMP model-fitting and NOE chapters in the free results file generation script now outputs for any relax manualversion. * This is because Python 3 fix for the NOE chapter references passages from the R_x curveMf.test_latex_table system test. The latex_mf_table.py model-fitting chapterfree system test script docstring contains backslashes, so it's more logical to have the R_x curve-fitting chapter firstraw string format r"""Text""" is now used.* Clean up of a paragraph of the data model chapter of the user manualPython 3 support for [[Modelfree4]] and [[DASHA]].* Improved the consistency The subprocess.Popen class works with byte arrays rather than strings in the user manual by using the new LaTeX commandsPython 3+. These changes The Python objects are throughout now interconverted when the manual Python 3 encode() and affect all the text of user functions, menu items, prompt examples, GUI elements, files, directories, etcdecode() methods are detected.* Removed some '()' text from the end of the user functions in pickle format information and arguments from the state user function documentationdefinitions.* Added some more LaTeX functions for formatting consistencyEliminated the State.test_state_pickle() system test as pickled states are no longer supported.* Defined a new set of LaTeX commands for prompt/script/GUI strings Removed the ability to save and elements restore states using the pickle module. A pickled state is of no use to relax anymore. It's removal is needed for the user manualPython 3 support. These will be used So now everything defaults to regularize the text throughout the manual, as this is currently quite mixed upXML formatted output.* More rearrangements of data model and NOE chapters Python 3 fix - removed the use of the relax manualstring module from generic_fns.spectrum. * The GUI spin deselection part of Python 3 fix for the NOE chapter has been shifted into the data model chapterrelax_io.open_write_file() function. And This now matches the GUI loading of spins from a sequence file section has been completed.* Added screenshots behaviour of open_read_file() in that there are three different behaviours for opening bz2 and gz files for writing to for the spin viewer spin loading wizard sequencedifferent Python versions (one for Python 2, one for Python 3.read page0 to 3.* Redesign of the data model chapter of the user manual2, and one for Python 3.3+). This includes the moving of all of the spin viewer window All byte streams have been eliminated as open_write_file() is for creating text and screenshots from the NOE chapterfiles.* Shifted Python 3 fix for the spin viewer screenshots into their own directoryNoe.test_noe_analysis() system test for the grace.write precision changes.* Changed For consistency between Python 2 and 3, the "View[http://www.nmr->Spin view" menu item relax.com/manual/grace_write.html grace.write user function] outputs to "View->Spin viewer"15 decimal places.* Created a directory for screenshots This increased precision will only be of use in the spin viewer window operationrelax test suite.* The NOE auto-analysis GUI Python 3 fix for the Pipes.test_pipe_bundle() system test now checks the support for Trp indole N data as well.* The [http://wwworder of bundle names returned by generic_fns.nmr-relaxpipes.com/manual/spectrum.read_intensities user function] now prints out a list of the intensities read bundle_names() is not guaranteed in. This is for better user feedback as to what the user function has actually donePython 3.* Created The C module compilation testing script now accepts the GUI wizard _applyPython version as a first argument.* The relax_io.open_read_file() method for executing the current page's _apply() methodnow supports all Python versions over 2.4. This is required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the Bzip2Fixed and GzipFixed classes overriding the GUI tests to simulate a click on the 'Apply' buttonincomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped around io.TextIOWrapper().* Removed a debugging print outAdded the IO module to the relax information printout and dependency checks.* Modified the NOE system test to catch [https://gna.org/bugs/?20120 bug #20120]The manual C module compilation script is now executable.* Lots of editing of Renamed the NOE chapter of 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the user manualscripts.* Significant update of Finished off the NOE chapter of the user manualC module compilation testing script. * The sample Added a script used in this chapter was incredibly for testing out of datethe C module compilation on multiple Python targets.* Modified the NOE system test to test the usage of Trp indole ¹⁵N dataThe relax_fit specific analysis module now supports both Python 2 and 3.* The relaxation curve-fitting C module now supports compilation on both Python 2 and 3. * This is Created the simple Sequence.test_sequence_copy() system test to catch [https://gna.org/bugs/?20119 20213 bug #2011920213].* Added some Trp peak data The Mf.test_bug_20213_asn_sidechain(backbone and indole N) to the Sparky steady-state NOE peak lists) system test now uses a temporary directory for output. * This is in preparation for Added the modification of the NOE Mf.test_bug_20213_asn_sidechain() system test to catch [https://gna.org/bugs/?20119 20213 bug #2011920213].* Modified The data and script comes from the NOE sample script to include Trp indole NH datafiles 'sh3-47.* Added a step-by-step tutorial for the GUI NOE auto-analysis 2.zip' and 'run.py' attached to the user manualbug report https://gna.org/bugs/?20213. This includes 22 screenshots of The PDB now only contains Asp47, the optimisation parameters have been made almost insignificant, and all models but 'tm0' have been removed from the stepsanalysis.* Added The Python 3 dictionary values() method no longer returns a list, so a section labellist() call is needed.* Added some Sparky info to Python 3 bug fix for the R_x curvegeometric structure module -fitting chapter of the user manualanother integer division to float problem.* Allowed The Mf.test_write_results system test can now select the raggedbottom LaTeX setting as this is better for the screenshot layout correct file to compare against in the user manualPython 3.* Added the nth package The algorithm for determining if the user manual LaTeX compilation'final_results_trunc_1.3_v2' or 'final_results_trunc_1.3_pre_py2.7.3_v2' file should be used could not handle Python 3.* The NOE chapter now points to Python 3 fix for the recommendations in the R_x fitting chapterformat detection of results and save files.* Added a new section called 'From spectra to peak intensities' to the R_x fitting chapter of the manualPython 3 import fixes for the generic_fns. This adds a number of recommendations for high quality relaxation ratesstructure package using relative paths.* Added Python 3 fix - removed the use of the Viles et alstring., 2001 referencelower() function in the OpenDX mapping code.* Small description edit Python 3 fix for the [http://www.nmr-relax.com/manual/relax_data.temp_control user function]frame order system tests.* Added a LaTeX label As float to string conversions behave differently, the NOE chapter of the user manual%.1f formatting is used to force only a single decimal place float.* Added a paragraph to Python 3 fix for the modelframe order system tests -free chapter of float to string conversions behave differently. Now the user manual explaining the J(&omega;) equation formsexplicit %.1f formatting is used to force only a single decimal place float.* Added a label Python 3 integer division to float fix for the data model chapter of the user manualframe order analysis.* Created an initial rough version of Python 3 bug fix for the RSDM chapter of the user manualframe order analysis - another int division problem.* Better figure layout in the NOE chapter Python 3 fixes - eliminated all usage of the user manualdictionary has_key() calls as they are no longer present.* The relax data model chapter of Python 2 and 3 support in the user manual now uses the higher quality graphicsgeneric_fns.relax_data module using 2to3.* Some more high quality graphicsOne print call was fixed after running 2to3.* Added more high resolution graphics Python 3 bug fix for use in the relax user manualStructure.test_read_pdb_mol_2_model_scientific system tests. This is again an integer division problem returning a float.* Expanded Python 3 fix for the size of the specific analysis graphics - mainly for use in the relax user manualtest_write_protein_sequence() unit test. This is again a string verses byte verses unicode problem.* Added Python 3 fix for the specific analysis graphics to user function docstring creation in the start of each chapter of the relax user manualprompt UI mode.* Small edit Again this is the problem of the 'Citations' chapter of the relax user manuala division now returning a float rather than an int.* Added EPS versions of the specific analysis graphics Python 3 bug fix for use in the user manualN-state model target function setup.* Added The num_tensors variable needs to be an integer, but the Fushman et alPython 3 division will create a float type., 1999 reference * Python 3 fix for consistency testing to the intro chapter [http://www.nmr-relax.com/manual/results_read.html results.read user function] matching that of the user manualstate.load.* More chapter cross referencing in Python 3 bug fix for the relax user manualrelax_io.read_spin_data() function.* Added The built in max() function cannot handle the value of None, therefore the Horne 2007 paper filter() function is used to the 'Citations' chapter remove all instances of None from the user manuallist. * Whitespace has also been cleaned up, and a chapter label addedPython 3 bug fix for the [http://www.nmr-relax.com/manual/state_load.html state.load user function].* Added The header line of pickled states (rather than the Horne 2007 paper to standard XML states) is of the b'Supported NMR theories' subsection of the user manual intro.* byte format. Shortened This is now converted to a string, and the Literature subsection of the intro chapter to point search expression is comparing it to the citations chapter. This part of the user manual is now redundantraw string r"<\?xml".* Small edits of Better support for both Python 2 and 3 in the relax user manualdata store.* Edits to The 2to3 script was used on all of the abbreviations chapter of files in the relax user manualdata package.* Added another abbreviation.* Expansion of Python 3 preparation - the abbreviations chapter of relax data store (the relax user manualdata package) now supports both Python 2 and 3.* Added Python 3 fix - the relax_errors.AllRelaxErrors object is now a tonne of DOI numbers proper tuple. Due to the relax user manual bibliographybad coding, it was previously a nested tuple. This will simplify accessing these references nested tuple worked in Python 2, but is fatal for the userPython 3.* Added and fixed DOI numbers for many bibliographic entriesPython 3 fixes - the character '\' is now properly escaped as '\\' in the stereochemistry auto-analysis.* The LaTeX bibliography style Fix for PhD theses now includes the DOI hyperlinktest suite summary for Python 3. This is for the user manualThe test suite now runs, but fails miserably, under Python 3.* Slight modification Fix for the running of the DOI hyperlink formatting bibliography style for test suite under Python 3. The zip() function used in the loadTestsFromTestCase() function is now an iterator, so it needs to be passed through the user manuallist() function to generate a list.* Modified Fix for the relax LaTeX bibliography style file relax.bst to convert DOI numbers to hyperlinks. This is to add links to the references within the relax user manualtest_parse_token_multi_element_name() unit test, as parse_token() no longer sorts.* Created Python 3 fix for the new 'Citations' chapter of the relax user manualgeneric_fns.mol_res_spin.parse_token() function. Mixed lists for int and string can no longer be sorted. This sort call is to clearly outline to the user the citations required for the various components of relaxnot needed anyway.* Added Automatically converted the Fushman 1999 reference and a few formatting fixes in other referencesgeneric_fns.mol_res_spin module to support both Python 2 and 3.* Improvements to For running relax with Python 2, the 'Supported NMR theories' section of the user manual introduction__builtin__.range() function has been replaced with xrange. This includes causes large speed ups (speed that was lost with the addition of the Morin earlier xrange() to range() conversions), and Gagne 2009 referencememory decreases.* Added For example on one system, the Morin and Gagne 2009 reference for the consistency testingsystem test time decreased from 513.029s to 487.586s.* Added some more abbreviations to The compat module now has the relax user manualpy_version variable specifying if this is Python 2 or 3.* Created a new chapter Import fix for the relax user manual titled 'The relax data model'OpenDX mapping package, recently broken with the relative import for Python 3 change.* Fix for More usage of the pipe editor window screenshot width is_unicode() function in the relax manualgeneric_fns.mol_res_spin module.* Converted some more wizard graphics to Created the EPS format check_types.is_unicode() function for the user manualPython 2+3 compatibility. This is used in the generic_fns.mol_res_spin module.* Another raise() function call to statement change for 2to3 preparations.* Updates and small expansion of Converted some raise() function calls to raise statements in preparation for the intro chapter of the relax user manual2to3 conversion.* The user manual now specifies Converted the repository revision if a non-tagged version is builtScientificPython PDB reader to support both Python 2 and 3. This enables easier tracking and editing of The __repr__() method was manually modified due to the 'list' variable clashing with the manual'list'type.* Updates to the generic_fns.mol_res_spin.id_string_doc documentation structureCreated a new module for simultaneous Python 2 and 3 support in relax called 'compat'.* Updated Python 3 fixes - the screenshot of list() function is now used in combination with range() to generate the pipe editor windowordered list.* Created EPS versions of a number of wizard graphics for use range() in the user manual.* Removed some Python 3 is an iterator object (just as xrange was), so now useless whitespace from the top of each user list() function subsection of the manualhas to be called.* Redesigned the formatting Python 3 preparations - mass conversion of the user function chapter of the relax manualall xrange() calls to range(). * The fetch_docstringsCreated the special check_types.py now forces each user is_filetype() function to start for checking for files in a new columnall Python versions. * This increases the size Python 3 - eliminated an unneeded xrange call.* Python 3 - eliminated the use of the manualmap() function, but makes as this behaves differently in Python 3.* Python 3 - removed the reading use of the user function documentation much easierstring. The user function class and function icons lower(128x128 format) are now placed between function as it is missing in Python 3.* Python 3 fix for the top bar and the subsection title and are left and right justifiedrelax information printout. This prettification simply allows the user functions The try blocks seem to be more quickly identifiednow operate slightly differently in Python 3.* Large expansion of Python 2 fixes - the Python 3 fixes for the relax icon setScientificPython module imports broke Python 2. * All 128x128 versions of Python 3 - the icons used by the user functions have been added as both PNG and gzipped EPS filescStringIO.StringIO import switches to io. A few gzipped SVG and non-sized icons have been added as wellStringIO if missing.* Large expansion of Python 3 - relative module paths are now used for the Oxygen icons within relaxtest suite runner. * All 128x128 versions of Python 3 fixes for the icons used by the user functions have been added as both PNG and gzipped EPS filesversion module for catching empty lists. * A number of gzipped SVG icons has been added as wellPython 3 fix - ensure an integer is actually an integer (division now converts ints to floats).* Modified Python 3 - fixes for the graphicsrenaming of the Queue package.fetch_icon function * Python 3 - converted the last of the except error catching statements to return different file formats. This will be used for the relax manual where epsPython 2.gz files are required4+ compatible.* Improvements to Python 3 - removal of the final section use of the relaxation curve-fitting chapterstring.atoi and string.atof functions. These have been depreciated since Python 2. 0! The Xmgrace screenshot They have been replace by the int and page references for the user float functions have been added.* Added screenshots Python 3 - a number of Xmgrace displaying relaxation curvesfixes for running the ScientificPython modules in relax on Python 2 and 3.* The fetch_docstrings.py now adds LaTeX labels This includes relative imports, converting raise statements to each user function section. This has calls, removal of the form use of 'uf: ' followed by the user function namemany string module functions which do not exist in Python 3, and is for referencing purposes within the main textetc.* Rewrote the relaxation curve-fitting chapter of the relax manualPython 3 - modified some except statements to be Python 2.4+ compatible in a ScientificPython module. * This chapter was quite out of date and was of no use Python 3 - converted some print statements to modern relax versionsfunction calls in the ScientificPython modules.* Redesign of how Python 3 - fix for an os.chmod() call by using the GPL license is presented to stat module rather than the usernumber 0775. The old promptnumber 0755 is no longer valid in Python 3.gpl module with the version 2 * Python 3 - a pile of the license has been deletedrelative path fixes for many relax modules. * Now Python 3 - removed the text form use of the docs/COPYING file is passed through pydoctypes module from generic_fns.pager for the 'sequence./ The relax --licence' and the prompt mode GPL object, and arg_check module is simply printed to STDOUT for the GUI help systemnow being used instead.* Import clean ups for Python 3 preparations - removed all of the N-state model specific string modulefunctions which no longer exist in Python 3. These functions are part of the strings themselves now.* Added Improvements for the 'unit' argument to relax test suite synopsis for when the [http://wwwwxPython module is missing or broken.nmr-relax This is simply a printout improvement.com/manual/dipole_pair.read_dist.html dipole_pair.read_dist] and [http://www.nmr* Python 3 preparations -relaxremoval of some unneeded xrange() calls.com/manual/dipole_pair* Python 3 preparations - the data package now really does use the absolute path for its module imports.set_dist* Python 3 preparations - the data package now uses absolute imports for all its modules.html dipole_pair* Python 3 preparations - eliminated the use of the types.set_dist] user functionsListType object. * This is to allow distances in Angstroms to be read into relax Python 3 preparations - absolute module path fixes.* Python 3 preparations - support for both Python 2 __builtin__ and Python 3 builtins modules.* Python 3 preparations - absolute module path fix.* Python 3 preparations - more exception handling updates for all Python 2.4+ versions.* Python 3 preparation - all raising of RelaxErrors is now Python 2.4+ compatible.* Python 3 preparations - error handling is now Python 2 and 3 compatible in the relax_io module.* Python 3 preparations - converted the relax prompt/script interpreter to be Python 2 and 3 compatible.* Python 3 preparations - removed the use of the types.ClassType object.* Python 3 preparations - compatibility for both the Python 2 cPickle and Python 3 pickle modules.* Python 3 preparations - all usage of string.split() and string.strip() has been eliminated.* Removed the completely unused gui.components.conversion module.* Removed an unused import (which was breaking relax in Python 3).* Python 3 preparations - all os.popen3() instances in relax have been replaced by the subprocess module.* Python 3 preparations - eliminated the use of the os.popen3 function from the info module.* More exception handling changes to be Python 2.4+ compatible.* Python 3 preparations - exception handling fix to be Python 2.4+ compatible.* Python 3 conversions using 2to3.* Updated the Python 2 to 3 checklist document for the shifting of the 'relax' file to 'relax.py'.* Python 3 preparations - removed all usage of the xrange() in the generic_fns package as none are needed.* Python 3 preparation - eliminated the unneeded use of xrange().* Python 3 preparation - the use of an absolute module path for import.* Python 3 preparations - the auto_analyses package is now fully Python 2 and 3 compatible.* Python 3 preparation - the auto_analyses package now uses absolute paths for the module imports.* Python 3 preparations - the use of the queue module in the status module is now compatible with 2 and 3.* Python 3 preparations - the GUI tests are now fully Python 2 and 3 compatible.* Python 3 preparations - the queue modules for both Python versions are now supported in the GUI tests.* Python 3 preparations - the test_suite.gui_tests package now uses absolute module path imports.* Python 3 preparations - the unit tests are now fully Python 2 and 3 compatible.* Python 3 preparation - all of the _generic_fns unit tests now use absolute module imports.* Python 3 preparations - all the _prompt unit tests now use absolute module imports.* Python 3 preparation - removed all xrange() calls from the unit tests, these are not needed.* Last Python 3 compatibility update for the system tests - they are now both Python 2 and 3 compatible.* Python 3 preparation - the test_suite.system_tests package now uses the absolute module path for imports.* Python 3 preparation - changed the import of SystemTestCase to use the absolute module path.* Removed all of the xrange() calls from the system tests as these are not necessary. This is in preparation for Python 3.* Some changes in preparation for Python 3.* Removed the 'force flag' text from the RelaxWarning messages output by the [http://www.nmr-relax.com/manual/bruker_read.html bruker.read user function]. The force flag arguments of the generic_fns.mol_res_spin.name_spin() and generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to None to suppress the text.* Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the recent test suite data changes.* The CSA setting in the model-free auto GUI analysis now defaults to the '@N*' spin ID. Previously no spin ID was being used so that the protons where also having their CSA values set to that of the nitrogens. Now the execution checking code skips the proton CSA check.* Added star versions of the standard spin IDs to the spin ID GUI element (e.g. '@N*', '@H*').* Fix for the comment on the 'Export' button in the BMRB export window.* Lots of editing of the model-free GUI section of the user manual.* Fix for the Relax_data.test_delete system test for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].* Fix for the Relax_data.test_read unit tests for the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function] changes.* Fix to the [[DASHA]] system test needed for the changes to the [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read user function].* Fix for the N_state_model.test_monte_carlo_sims due to the changed sphere.pdb test suite file.* Relaxation data is no longer loaded by relax_data.read if the values and errors are both None.* Modified the Mf.test_dauvergne_protocol system test to catch [https://gna.org/bugs/?20197 bug #20197]. The sphere test data NE1 and HE1 data is now being used in this system test, triggering the bug.* Small change to the sphere model model-free test suite data. The trptophan indole data is now merged into the last residue (a glycine) to catch [https://gna.org/bugs/?20197 bug #20197].* The overfit_deselect() printouts for all specific analyses are now regularised and match the model-free printouts.* All overfit_deselect() methods now accept and use the verbose argument.* Printouts for the over-fitting deselection of spins are suppressed for the back-calculation of relaxation data. This affects the model-free Monte Carlo simulations, improving the output.* More improvements to the model-free over-fitting deselection printouts.* Improved the model-free overfitting deselection printouts prior to optimisation. Only a single message per spin is now given when the spin is deselected, minimising the amount of output.* Added a tryptophan NE1 data set to the sphere model-free model test data. This is in preparation to catch [https://gna.org/bugs/?20197 bug #20197]. The scripts have also been updated for the newer relax designs.* Added the data_check Boolean argument to all of the specific analysis overfit_deselect() methods. This allows the unit tests to meterspass.

=== Bugfixes ===

* Fix for [https://gnathe State.org/bugs/?20189 bug #20189, test_load_state_no_gui() GUI test - the Sequence GUI element can not handle values of None]data pipe bundle is now given.* The citations chapter is now included Another attempt at fixing a nasty circular import in the HTML version of the user manual. For some reason, a file named 'cite.tex' cannot be handled by latex2htmlrelax GUI.* The latex2html compilation of Fix for the relax user manual now ignores the \bibitem{} commandscompilation. This is needed The full path for an icon in the HTML version of the user manualgraphics directory was being used.* Fixed API documentation fix - a circular import has been broken. This was only a section titled 'Introduction' clashing with circular import when the intro chapter of the user manualgui package is imported from an external program like Epydoc.* Fixes PDB format fix for the user function icons in the HTML version atom numbers of zero - the user manual. These icons are now placed on the correct HTML pageatom number should be consecutive and unique.* Removed Big fixes for the text '.eps.gz' from all running of the LaTeX included graphics in the user manualGUI tests. This allows latex2html to select The GUI initialisation and use the PNG images insteadtermination, when not running in GUI mode, producing much better graphics for is now preformed outside of the online manual (http://www.nmr-relaxPython unittest framework.com/manual/index.html).* Fix for The GUI was previously initialised in the graphics.fetch_iconsetUp() function method for when no file format is specified.* Elimination of all duplicated chapterGUI tests, section and subsection titles in but for some reason this caused abrupt terminations of the user manualGUI_test_runner.run() method. This fixes [https://gna.org/bugs/?20185 bug #20185].* The HTML files for run method, when finished, would not return to the user manual now have longer names - this is needed for removing Test_suite_runner but would cause the duplicatesPython interpreter to silently die.* Fix for The result was that the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed uptest suite summary would appear not to be printed out.* Fix for [https://gnaPython 2.org/bugs/?20177 bug #20177]. This was simply a lower precision OS/Python/numpy combination causing a test suite failure - there are no practical effects 3 and only the precision of earlier fix for the system/GUI unit test has been lowered.* Another bug fix module for the sequence GUI editor windowfloat module. This bug The 'tests' class variable was being triggered by renamed so that the User_functions.test_structure_pdb_read() GUI test which now passessuite does not think that it is a unit test.* Small Bug fix for the User_functions.test_structure_pdb_read() GUI unit test.* Fix for [https://gna.org/bugs/?20184 bug #20184]runner - this restores functionality broken all the way back at r12100. The behaviour of TEST_SUITE_ROOT constant no longer exists, so the gui.string_conv.gui_to_int() and related functions has changed in the last few months and the Sequence_window() GUI element has not changed to matchcheck for it is now skipped. This has been fixed and allows tests to be run directly by the User_functions.test_structure_pdb_read() GUI test now passesscript.* Fixes Python 2.4 and earlier fixes for the User_functions.test_structure_pdb_read() GUI testQueuing module.* Fix for [httpsThe TaskQueue class from http://gnacode.activestate.orgcom/recipes/bugs475160/?20183 bug #20183 - which was added to Python 2.5+ has been added to the failure of the sequence editor window]compat module. The problem was that fields which could be either single values or lists (or tuples) This module is now used for all imports of values were not properly handledthe Queue class for all Python versions.* Fix for [https://gna.org/bugs/?20182 Test suite bug #20182 fix - the sequence element window ordering issue]. The sequence element window GUI tests now has cleanly terminate the parent wx.Window element setinterpreter thread. This prevents allows the main relax window from being set as test suite to terminate normally. With different Python versions on different operating systems, this could sometimes cause the parent and hence coming test suite to freeze at the front after end, the sequence element window is launched from a user function windowfinal printout to be missing, or other strange behaviour.* Fix for [https://gnaPython 2.org/bugs/?20181 bug #20181 3- fixes - the GUI sequence editor window TypeError problem[[Modelfree4]] and [[DASHA]]system tests are now skipped if the subprocess module is missing.* Window ordering bug Python 2.3 and earlier fix for the user function windows launched from the spin viewer windowTest_relax_re.test_search() unit test. The spin viewer window no longer hides behind the main relax window after the launch of the user functionunittest assertTrue() and assertFalse() methods do not exist, so assertEqual() is used instead.* Bug Python 2.3 and earlier fix for - the repetition of Monte Carlo simulations in the relaxation curve-fitting analysessubprocess module is only imported when present. This is in for the specific stereochem_analysis auto-analysis API, so will allow but the import kills all analysis types to repeat Monte Carlo simulations for error analysisof the auto-analyses.* MS Windows Python 2.3 fix - eliminated the NOE system and GUI tests are now less strict superfluous operator.itemgetter() call in checking the errorsdiffusion tensor code.* Proper bug Python 2.4 and earlier fix for storing the execution status of wizard and user function pagesGUI. This allows the test suite Try-except-finally statement blocks are not supported, so these have to pass againnested in two try statements. * The execution status is now properly returned from Python 2.4 fix - the unit test runner no longer uses the wizard pages run synchronously builtin set(and always set to True for asynchronous calls)method.* Fix Python 2.4 and lower fix for [https://gnathe pipe_loop() generator method. In these Python versions, a 'try' block with a 'finally' statement cannot contain 'yield' statements.org/bugs/?20173 bug #20173] This work around should be compatible with all Python versions. * The [http://wwwPython 2.nmr4 fixes -relaxthe ctypes module does not exist in Python versions 2.com/manual/palmer.create user function] should have been checking that the diffusion tensor had been initialised4 and lower. This is only used for some non-essential functionality on MS Windows, so now being performedit is deactivated if not present.* Bug fix Fix for the execution of wizard pages - the execution status is now observed. This fixes [https://gna.org/bugs/?20152 20213 bug #2015220213]. The problem was that the execution status was being lost in the protected_execgeneric_fns.sequence.generate() functionwas searching for a spin based on its spin ID generated from the spin name and not spin number. However Hence two spins with the same name but different numbers were treated as relax errors are caught in the GUI interpreter anyway same spin, and only data from one was being generated via the status is returned normally, the protected_execcopy() wrapper was removedfunction.* Bug fix for wxPython 2.9.4.0 - the creation unsetting of the user function GUI pages - the (a)synchronous arg is alpha mask for all bitmap images should now observedwork. This argument was being ignoredThe wx.Bitmap.SetMaskColour(None) call does not work, which in some wizards was causing user function calls to be asynchronousso instead a wx. This can result Colour() instance is passed in racing related crashesinstead.* The [http://www.nmr-relax.com/manual/bruker.read user function] now throws a RelaxError when old PDC files are detected. This is a partial fix Fix for [https://gna.org/bugs/?20152 20210 bug #2015220210].* Fixed the newlines in the sample script in the consistency testing chapter.* Fixed the bounding box for the consistency testing figure and also fixed some Latex unfriendly code. Problems were spotted by Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.* Fixed a bibliography entry label problem. This was spotted by Edward d'Auvergne in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00040.htmlnow runs again without having wxPython installed.* Bug fix for the creation of 2D graphs via grace.write BMRB system test initialisation for when many data sets existthe bmrblib module is missing. The algorithm for setting the Grace symbol number base __init__() method needs to be between 1 and 10 was broken!initialised first.* Fix for [https://gna.org/bugs/?20133 20201 bug #2013320201] - this was simply a missing import.* Fix for the The [http://www.nmr-relax.com/manual/spinbruker_read.html bruker.create read user function documentation] - can now handle the prompt examples were wrong.* Bug fix for situation where multiple spins per residue are already loaded prior to the generic_fns.grace.get_data() user functioncall. This was just recently introduced The isotope value from the DC file is now translated to the element name and was triggered by this is used as part of the Relax_fit.test_bug_12670_12679 system testspin ID string.* Fix for [https://gna.org/bugs/?20120 20197 bug #20120, 20197 - the bad Grace plots with multiple spin typesPyMOL and Molmol macro failure]. The grace data assembly function was not setting the correct index for when a spin type changes to a preexisting type.* Bug fix for macro creation now only operates on spins called 'N' and assumes these are the reading of Sparky peak listsbackbone nitrogens. Spin names with numbers at the end were not being correctly identified. This fix allows Trp The sidechain tryptophan indole NE1-HE1 NH data will need to be loaded.* Bug fix for the loading of peak intensities via spectrum.read_intensities. The user function could not be applied twice, preventing the loading of data from different spin systems such as Trp indole NH data.* Another fix for the relax_data.temp_control descriptiondetected and added later.* Fix for the incomplete [httphttps://wwwgna.nmr-relax.comorg/manualbugs/relax_data.temp_control user function description].* Spell fix for ?20198 bug #20198 - the [http://www.nmrrelaxation data back-relax.com/manual/relax_data.temp_calibration user function descriptioncalculation error].* Fixes for The problem was that the referencing in the J(&omega;) mapping chapter of the user manual.* Fixed some citations in call to the newly introduced model-free Joverfit_deselect(&omega;) paragraph.* Fixed a bunch of links in the development chapter of the user manual.* Small fix for the sample script in the method was deselecting any spins lacking relaxation curve-fitting chapter of the relax manualdata.* Small fix for the sample script in the NOE chapter of the relax manual.* Bug fix for the RDC Q factor calculations for when the dipolar constants are This should not all the same. Now instead of a RelaxErrorhappen, a warning is given and the Q factor normalised by 2D_a<sup>2<sup>(4 + 3R)/5 is skipped. This allows long range and mixed nuclear pairs as no spins need to be supported.* Import additions to fix the epydoc import of the 'sconstruct' script have relaxation data for the API documentation.* Epydoc docstring fixes for the API documentation.* Import fix for the epydoc building of the API documentationthis calculation.

== Links ==

* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2369 |text=Gna! news item]}}

== Announcements ==

= References = <section start=references/>* [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. ''Mol. BioSyst.'', '''3'''(7), 483–494. (DOI: [http://dx.doi.org/10.1039/b702202f 10.1039/b702202f).* [*d'Auvergne and Gooley, 2008] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. ''J. Biomol. NMR'', '''40'''(2), 121-133. (DOI: [http://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).<section end=references/><HarvardReferences /> = See also ==