Changes

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

Version 2.1.2 1 <br/>(17 October 21 September 2012, from /trunk) <br/>http://svn.gna.org/svn/relax/tags/2.1.21

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

* Modified the model-free optimisation final printout to be more multi-processor friendly. The scons 'clean' target message saying that the optimised chi2 is an improvement or not now removes includes the Python 3 __pycache__ directoriesspin ID string if present.* Small edit to This is more informative for the installation chapter multi-processor mpi4py printouts.* Added the use of the program 'nice' to the model-free GUI tutorial in the user manual.* Decreased Removed the Python out of date and useless README file for the HTML version dependency from 2.5 to 2.3 in the installation chapter of the user manual.* More error checking for Added a BMRB section to the end of the associate_auto() method model-free chapter of the data pipe editor windowuser manual.* Added data pipe bundle error checking for Massive expansion of the model-free chapter of the user manual including script and GUI pipe editor window associate_auto() method.* Added some error checking tutorials. The model-free chapter now has step-by-step tutorials for both the data pipe bundle in prompt/script mode and GUI mode for the auto new automated model-free analysis GUI codeprotocol (the d'Auvergne protocol)[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008].* Added some special RelaxErrors This includes a large set of screenshots for data pipe bundlesthe GUI mode.* Added some bug catching code for Created the observer objectsUser_functions.test_value_set GUI test demonstrating the failure of the value. In some rare cases a registered method's key was set to Noneuser function. * This is now caught Modified the dauvergne_protocol sample script[d'Auvergne and Gooley, 2007][d'Auvergne and a RelaxError thrown Gooley, 2008] to prevent later indecipherable errorshandle tryptophan indole NE1 data.* The setupgraphics.py application building script fetch_icon() function argument 'format' can now complains if the Python setuptools are not installedbe set to None. This will return the file path without the extension.* Updated the relax prompt mode figure in the intro chapter of Improvements to the duplicate user manual to the more modern prompttitle finding script.* Improvements Created a simple shell script to find duplicate titles in the API documentation compilationrelax user manual. The excluded files and directories, as well as hidden ones, are no longer included in This is important for the list HTML version of files/directories to add the manual as duplicated titles causes HTML pages to be overwritten. For example all chapters, sections and subsections titled "Introduction" will load the documentationintroduction.* Added a html file with which will contain the relax user functions used for text of the prompt screenshots. last section with that title!* This is for Additions to the scripting section of the relaxation curve-fitting chapter of the user manual and the website.* Added A small edit to the public domain LaTeX nth.sty style file intro chapter for the user manualmulti-processor operation and logging. * Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing Added some labelling to the infrastructure chapter of the PDF user manual to compile on more systemsfor referencing.* Fixes A number of updates and edits to the intro chapter of the user manual. The model-free GUI screenshot has been shifted to the intro chapter in preparation for weird print statements a full tutorial with double brackets generated by screenshots in the 2to3 Python conversion scriptmodel-free chapter.* Removed a debugging printoutUpdated the data model chapter of the user manual to cover the handling of protons.* Python 3 fixes for one This change includes the modification of the PDB reading screenshot to demonstrate the reading of a specific model and the naming of the test data scripts - print statement with function call replacementsmolecule.* Python 3 fixes for non-All of the GUI strings and text are now formatted with a small sans serif font in the user manual. This is because in the GUI, a sans serif font is almost always used Python code - converted print statements to function callsbe default.* Python 3 fixes for Modified the script for generating plots of magnetic field linesUser_functions.test_structure_pdb_read() GUI test to catch another bug.* Another print statement This is a bug recently introduced with the fixes to function Python 3 fix for the user manualother sequence editor GUI window problems.* The Python print statements in Created the user manual are now User_functions.test_structure_pdb_read GUI test for checking the sequence editor window. This new user function calls GUI testing class is to be Python 3 compatible.* Python 3 fix used for testing out the generic_fnsspecial GUI elements not invoked within the unit testing.structure.geometric.angles_regular The test_structure_pdb_read() function. Integer divisions no longer produce integerstest specifically shows a number of failures of the sequence editor window.* Better formatting Modified the operation of the sequence GUI element to have access to the sequence editor window. This is to allow this GUI element to be blasted within the test suite summary.* The text relax controller log is no longer cleared when a reset occursImprovements to the descriptions of the structure. This allows the test suite results to still be presented in GUI moderead_xyz user function arguments.* Even cleaner exiting Improvements to the descriptions of the GUI - the interpreter thread is terminated by the exit_gui() methodstructure.read_pdb user function arguments.* The GUI is now cleanly exited with a call Added @HE1 to wxthe spin ID list of the structure.Appload_spins user function.ExitMainLoop rather than wx.Exit This is only seen in the GUI.* Python 3 fix Created the new generic_fns.result_files for standardising the compat module - the Queue2 object needs to always be definedhandling of results files.* Added support for Python 2.2 and earlier for This fixes the compilation of bug where results files are repetitively added to the C moduleslist.* Removed an unused import All of the Queue code touching cdp.result_files now uses this module from the multi-processorinstead.* Python 3 fix for Updated the ScientificPython PDB reader unit tests. The order scripting section of the intro chapter of the keys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to comparisonuser manual for non-technical users.* Redesigned Expanded the spin ID list for the reset structure.load_spins user function backend. This now no only clears out includes the relax data storespins "@N", "@NE1", "@C", "@H", but it also resets the GUI if present. Some of the reset code comes from the tearDown() method of the GUI tests. All windows but the main GUI window are closed and the relax controller gauges are set to zero and the log window text cleared. These changes should allow GUI tests after an error or failure to pass"@O", something which is currently problematic.* Disabled the initial relax intro printout from the GUI when running the test suite. This prevents the intro text from appearing in the first failed test"@P", ":A@C2", ":A@C8", ":G@N1",":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6".* Fix Changed the RelaxError for missing relaxation times in the Mf.test_read_results_1_3_v2_broken() system test for Python 3.2. The object comparison method no longer converts dictionaries to strings for the comparison, as the string version is different in different Python versionsrelaxation curve-fitting analyses.* Fix for Modified the Mf.test_write_resultstest_bug_20152_read_dc_file() system GUI test for to catch the Python 3 versionsRelaxError. The logic for determining Python 3 versions was broken and This error is because of the incorrect files was used for Python 3.1old PDC format.* Better Python 2.3 support. The compat module is now imported at Created the very start to allow the builtins to be set before any other importstest_bug_20152_read_dc_file() GUI test for catching [https://gna.org/bugs/?20152 bug #20152]. The sortedThis includes truncated data taken from the bug report (with data for only the first 3 residues) builtin method is now mimicked and the os.devnull string set * Set up the Bruker Dynamics Center system tests as GUI tests. This is in preparation for Python 2catching [https://gna.3 and earlierorg/bugs/?20152 bug #20152].* Fix for Re-added Dominique Marion's solvent suppression to the NMRPipe script in the Mf.test_write_results() system test for Python 3.1curve-fitting chapter. * The XML version in Python 3.1 is A few small edits of the old stylerelaxation curve-fitting chapter. Therefore the old results file This is being used to check this Python 3.1 resultreinforce the exact time of the relaxation time period.* Small improvements Added some text to explain why test only J(0) is discussed whereas the multiple Python version test suite testing scriptalso calculated F_R2 and F_eta.* Reactivated support for Python 2This was suggested by [https://gna.3. This mainly skips the missing org/users/bugman Edward d'subprocess' module. This however decreases Auvergne] in a post at:https://mail.gna.org/public/relax's functionality a little-devel/2012-09/msg00044.html.* Created a special script Big clean up of the Bibtex bibliography file for testing out the relax with Python versions 1.0 all the way to 3.3user manual. * This builds Small edits of the C modules for each Python version consistency testing figure caption in ~/bin and then runs the test suite, outputting everything to log filesrelax user manual.* The Results system tests are no longer dependent on Editing and a number of fixes/cleanups for the relaxation curve-fitting C modules. This allows these tests to run when consistency testing chapter of the module cannot be importeduser manual.* Python 2.5 Editing of the "Values, gradients, and lower fix for Hessians" chapter of the test_write_protein_sequence() unit testuser manual to make it fit better. The byte array is wrapped in an eval() statement context of this chapter has been specified by changing the title to allow Python 2.5 "Optimisation of relaxation data -- values, gradients, and lower to parse the code without failing, Hessians" and the byte array comparison is now only used for Python 3+intro text has been updated.* All system and GUI tests reliant on As this chapter is no longer straight after the relaxmodel-fit C modules are deactivated if import failsfree chapter, this is needed. * This removes Made a small correction to a pile of useless error messages from the test suite and presents reference such that a table of skipped tests at the endsuperscript is correctly displayed.* More Python 3 fixes Added the bounding box and a centerline command to the code for the use of now non-existent string module functions.* Python 3 fix figure for the model-free BMRB export - many string module methods no longer existconsistency testing.* Mass conversion of the alignment tensor data structures to the same new design as the diffusion tensorThis follows two remarks by Edward d'Auvergne at https://mail.gna. This large set of changes matches all of those revisions for the diffusion tensor already committedorg/public/relax-devel/2012-09/msg00030. The alignment tensor data structures are now read only, html and can only be modified via the set() methodhttps://mail.gna.org/public/relax-devel/2012-09/msg00032. This is a much simplified design which works on all Python versionshtml.* Small clean ups of Added more text to describe the diffusion tensor data structure codeconsistency testing approach.* Deleted the now unused _update_sim_set() method of the diffusion tensor data structureAlso includes a very basic point by point protocol for consistency testing.* Removed the now unused _update_sim_append() method from the diffusion tensor data structureThis was proposed by [https://gna.* Cleaned up the docstring of the diffusion tensor data object __setattr__() methodorg/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00028.html.* Updated all of the diffusion tensor unit tests to the new designThis also follows a discussion started by [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Fix for Added some text to describe the reading of model-free results files from relax 1.2 when simulation data is missingconsistency testing example figure.* Fix for the reading of relax 1This follows a discussion started by [https://gna.2 model-free results files for the diffusion tensor structure redesignorg/users/bugman Edward d'Auvergne] at https://mail.gna.* Another fix for the fold_angles() diffusion tensor function org/public/relax-devel/2012- again an incomplete design conversion09/msg00019.html.* Fix for the setting Added a modified version of the diffusion tensor parameter errors in the modelFigure 1 from Morin and Gagne (JBNMR, 2009 (http://dx.doi.org/10.1007/s10858-009-free specific analysis code.* Fix for the setup of the model9381-free Monte Carlo simulations for the new diffusion tensor design4)).* Another fix for the diffusion_tensorFile formats are .init user function agr (xmgrace), eps (gzipped), and png. This follows a discussion started by [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax- it was not completely converteddevel/2012-09/msg00019.html.* Fix Added a directory for the fixing of parameters in the model-free analysesplacing consistency testing graphics. The diffusion tensor set_fixed() method is now usedThis follows a discussion started by [https://gna.* Fix for the XML output of the diffusion tensor - only the modifiable parameters are outputorg/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019. This was the previous behaviour and is needed for the test suite to passhtml.* Converted Corrected the palmerbibliography entries whih were still in plain text and not as a Latex \cite call.extract user function Also renamed the MorinGagne09 entry to use the new diffusion tensor designMorinGagne09a as there 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.html.* The diffusion tensor bmrb_read() function now uses the set_fixed() method instead of fixedAdded the DOI to reference Morin11 and fixed indentation (10.1016/j.pnmrs.2010.12.003). This follows a comment by Edward d'Auvergne at https://mail.gna.org/public/relax-devel/2012-09/msg00022.html.* The fix user function now uses Deletion of the diffusion tensor set_fixed() methodrelax version LaTeX file - this is automatically created anyway.* Renamed Added text to detail the diffusion tensor fixed() method to set_fixed() to avoid clashing with usage of the 'fixed' objectconsistency testing script.* Fix for This text was modified from the model-free specific analysis duplicate_data() method corresponding text for the new designjw_mapping. The diffusion tensor __mod_attr__ object is now called _mod_attrThis follows a discussion started by [https://gna.* Fix for the diffusion tensor to_xml() method for the new designorg/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019. For some reason the methods of the Element class are no longer blacklistedhtml.* Converted the diffusion tensor data structure from_xml() method Added some text and a reference to the new tensor designconsistency testing chapter.* Fix for the Diffusion_tensorThis follows a discussion started by [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.test_copy system test org/public/relax- the simulation parameters are now readdevel/2012-only09/msg00019.html. * Instead, Editing of the nmrPipe script in the Rx curve-fitting chapter of the diffusion tensor set() method needs to be calledmanual.* The setting Some editing of the NOE chapter of list values for the DiffTensorSimList object now works correctlyrelax user manual. * The private _set() method now works correctly by calling old R1 and R2 analysis screenshots have been shifted to the base class method, and the normal setting of diffusion tensor simulation values produces a RelaxErrorintro chapter.* Fix for Editing of the diffusion tensor __deepcopy__() replacement method for relax data model chapter of the new designuser manual.* The model-free specific analysis _disassemble_param_vector() method now uses Large expansion and lots of editing of the new diffusion tensor design.* Modified relaxation curve-fitting chapter of the setUp() method for the diffusion tensor system tests to use the new design.* Redesigned how diffusion tensor simulation structures are handleduser manual. The design is now much cleaner and works GUI section has been added which includes step-by-step instructions on how to use relax,illustrated with all Python versionsscreenshots at each step.* Removed all There has been general editing of the whole of the unused imports from specific_fns.model_free.mainchapter as well.* A number Added a tonne of private diffusion tensor objects and methods have switched to the single leading '_' formatGUI screenshots of an R1 analysis.* Improvements to These will be used in the relaxation curve-fitting chapter of the diffusion tensor set() method. The parameters, errors and simulations are now properly differentiated and storeduser manual.* Converted Added some Grace plots from an NOE analysis for use in the old diffusion tensor __setattr__() method into the set() methoduser manual. * This is Small edits of the relax data model chapter of the only way in which diffusion tensor parameters, errors and simulations can be setuser manual.* Renamed Editing of the diffusion tensor data structure type() method to set_type()relaxation curve-fitting and NOE chapters of the user manual. This is because to synchronise the type is stored as format of the 'type' objecttwo chapters, clashing with and includes the method nameswapping of text between them.* Created Added trp indole NH loading into the diffusion tensor data structure type() method for setting the tensor typerelaxation curve-fitting sample script. * This is to remove Large edits of the "cdp.diff_tensor.type = 'x'" code from the core consistency testing chapter of relax, as the structure is now read onlyuser manual.* The new diffusion tensor fixed() method has been created to allow Activated the consistency testing chapter of the fixed flag to be changeduser manual.* Fix for Added a LaTeX label to the initialisation of the diffusion tensor data structure, now that it is read-onlyJ(w) mapping chapter.* The diffusion tensor data structure has been completely converted into a read-only structure. The __setattr__() method now will always raise a RelaxError, and Added the other consistency testing references to the diffusion tensor simulation data structure objects __setitem__() method will raise citation chapter of the same errormanual.* Updated Added the relax version numbers and 'trunk' used relax user manual. Fushman et al., 1998 reference.* For example Fix for the information about checking out the main development line was still talking about 1Farrow et al.3 rather than the trunk, 1995 DOI number.* Python 3 fix for Changed the setting order of diffusion the Rx curve-fitting and alignment tensor simulation valuesNOE chapters in the relax manual. The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3This is because the NOE chapter references passages from the Rx curve-fitting chapter, so it's more logical to have the Rx curve-fitting chapter first.* Python 3 fix for Clean up of a paragraph of the data model-free results file reading testschapter of the user manual. * The ordering of dictionaries is different Improved the consistency in Python 3, so now these are properly converted from strings to dictionaries before comparisonthe user manual by using the new LaTeX commands. This was not happening because of These changes are throughout the XML changes from Python 2.7.3 onwardsmanual and affect all the text of user functions, menu items, prompt examples, GUI elements, files, directories, etc.* The relaxation curve-fitting system tests are now skipped if Removed some '()' text from the module is missing or broken. This improves end of the printouts from user functions in the test suite and shows a summary of skipped tests rather than a pile of traceback messages and errorsuser function documentation.* The message about skipping the GUI tests due to wxPython being missing is now Added some more specificLaTeX functions for formatting consistency. * This was being shown Defined a new set of LaTeX commands for prompt/script/GUI strings and elements for all runs of the test suite when it only needs to appear if GUI tests have been runuser manual.* Added a Python 3 version of These will be used to regularize the truncated OMP model-free results file. This was created with trunktext throughout the manual, as this is currently quite mixed up.* Removed More rearrangements of data model and NOE chapters of the Python 3 byte array hack which should have been removed earlierrelax manual.* The OMP model-free results file generation script now outputs for any relax versionGUI spin deselection part of the NOE chapter has been shifted into the data model chapter. And the GUI loading of spins from a sequence file section has been completed.* Python 3 fix for Added screenshots of the Mfspin viewer spin loading wizard sequence.test_latex_table system testread page. * The latex_mf_tableRedesign of the data model chapter of the user manual.py model-free system test script docstring contains backslashes, so This includes the moving of all of the spin viewer window text and screenshots from the raw string format r"""Text""" is now usedNOE chapter.* Python 3 support for Modelfree4 and DashaShifted the spin viewer screenshots into their own directory. * The subprocess.Popen class works with byte arrays rather than strings in Python 3+. The Python objects are now interconverted when Changed the Python 3 encode() and decode() methods are detected"View->Spin view" menu item to "View->Spin viewer".* Removed the pickle format information and arguments from Created a directory for screenshots of the state user function definitionsspin viewer window operation.* Eliminated The NOE auto-analysis GUI test now checks the State.test_state_pickle() system test support for Trp indole N data as pickled states are no longer supportedwell.* Removed the ability to save and restore states using the pickle moduleThe spectrum. A pickled state is read_intensities user function now prints out a list of no use to relax anymorethe intensities read in. It's removal This is needed for Python 3 support. So now everything defaults better user feedback as to what the XML formatted outputuser function has actually done.* Python 3 fix - removed Created the use of GUI wizard _apply() method for executing the string module from generic_fns.spectrum.* Python 3 fix for the relax_io.open_write_filecurrent page's _apply() functionmethod. This now matches is for the behaviour of open_read_file() in that there are three different behaviours for opening bz2 and gz files for writing GUI tests to for simulate a click on the different Python versions (one for Python 2, one for Python 3.0 to 3.2, and one for Python 3.3+). 'Apply' button.* All byte streams have been eliminated as open_write_file() is for creating text filesRemoved a debugging print out.* Python 3 fix for Modified the Noe.test_noe_analysis() system NOE system test for the graceto catch [https://gna.write precision changesorg/bugs/?20120 bug #20120].* For consistency between Python 2 and 3, Lots of editing of the NOE chapter of the grace.write user function outputs to 15 decimal placesmanual. * This increased precision will only be Significant update of use in the relax test suite.* Python 3 fix for NOE chapter of the Pipes.test_pipe_bundle() system testuser manual. The order sample script used in this chapter was incredibly out of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in Python 3date.* The C module compilation testing script now accepts Modified the NOE system test to test the Python version as a first argumentusage of Trp indole ¹⁵N data.* The relax_ioThis is to catch [https://gna.open_read_file() now supports all Python versions over 2.4org/bugs/?20119 bug #20119]. * This required Added some really nasty hacks for Python 3.0, 3.1 Trp peak data (backbone and 3.2 with indole N) to the Bzip2Fixed and GzipFixed classes overriding the incomplete and buggy bz2Sparky steady-state NOE peak lists.BZ2File and gzip This is in preparation for the modification of the NOE system test to catch [https://gna.GzipFile modules, and being wrapped around io.TextIOWrapper()org/bugs/?20119 bug #20119].* Added Modified the IO module NOE sample script to the relax information printout and dependency checksinclude Trp indole NH data.* The manual C module compilation script is now executable.* Renamed Added a step-by-step tutorial for the 'scripts' directory GUI NOE auto-analysis to 'devel_scripts' so that users are less likely to ask about the scriptsuser manual.* Finished off This includes 22 screenshots of all the C module compilation testing scriptsteps.* Added a script for testing out the C module compilation on multiple Python targetssection label.* The relax_fit specific analysis module now supports both Python 2 and 3.* The relaxation Added some Sparky info to the Rx curve-fitting C module now supports compilation on both Python 2 and 3chapter of the user manual.* Created Allowed the simple Sequence.test_sequence_copy() system test to catch bug #20213 (https://gna.org/bugs/?20213)raggedbottom LaTeX setting as this is better for the screenshot layout in the user manual.* The Mf.test_bug_20213_asn_sidechain() system test Added the nth package for the user manual LaTeX compilation.* The NOE chapter now uses a temporary directory for outputpoints to the recommendations in the Rx fitting chapter.* Added a new section called 'From spectra to peak intensities' to the MfRx fitting chapter of the manual.test_bug_20213_asn_sidechain() system test to catch bug #20213 This adds a number of recommendations for high quality relaxation rates. * The data and script comes from Added the files 'sh3-47Viles et al., 2001 reference.2* Small description edit for the relax_data.zip' and 'runtemp_control user function.py' attached * Added a LaTeX label to the bug report https://gna.org/bugs/?20213. The PDB now only contains Asp47, NOE chapter of the optimisation parameters have been made almost insignificant, and all models but 'tm0' have been removed from the analysisuser manual.* The Python 3 dictionary valuesAdded a paragraph to the model-free chapter of the user manual explaining the J(w) method no longer returns a list, so a list() call is neededequation forms.* Python 3 bug fix for Added a label to the data model chapter of the geometric structure module - another integer division to float problemuser manual.* The Mf.test_write_results system test can now select Created an initial rough version of the correct file to compare against in Python 3. The algorithm for determining if RSDM chapter of the '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 3user manual.* Python 3 fix for Better figure layout in the format detection NOE chapter of results and save filesthe user manual.* Python 3 import fixes for The relax data model chapter of the user manual now uses the generic_fnshigher quality graphics.structure package using relative paths* Some more high quality graphics.* Python 3 fix - removed the Added more high resolution graphics for use of in the string.lower() function in the OpenDX mapping coderelax user manual.* Python 3 fix Expanded the size of the specific analysis graphics - mainly for use in the frame order system tests. As float to string conversions behave differently, the %.1f formatting is used to force only a single decimal place floatrelax user manual.* Python 3 fix for Added the frame order system tests - float specific analysis graphics to string conversions behave differently. Now the explicit %.1f formatting is used to force only a single decimal place floatstart of each chapter of the relax user manual.* Python 3 integer division to float fix for Small edit of the 'Citations' chapter of the frame order analysisrelax user manual.* Python 3 bug fix Added EPS versions of the specific analysis graphics for use in the frame order analysis - another int division problemuser manual.* Python 3 fixes - eliminated all usage Added the Fushman et al., 1999 reference for consistency testing to the intro chapter of the dictionary has_key() calls as they are no longer presentuser manual.* Python 2 and 3 support More chapter cross referencing in the generic_fnsrelax user manual.relax_data module using 2to3* Added the Horne 2007 paper to the 'Citations' chapter of the user manual. One print call was fixed after running 2to3Whitespace has also been cleaned up, and a chapter label added.* Python 3 bug fix for Added the Structure.test_read_pdb_mol_2_model_scientific system tests. This is again an integer division problem returning a floatHorne 2007 paper to the 'Supported NMR theories' subsection of the user manual intro.* Python 3 fix for Shortened the Literature subsection of the intro chapter to point to the test_write_protein_sequence() unit testcitations chapter. This part of the user manual is again a string verses byte verses unicode problemnow redundant.* Python 3 fix for Small edits of the relax user function docstring creation in the prompt UI modemanual. * Again this is Edits to the problem abbreviations chapter of a division now returning a float rather than an intthe relax user manual.* Python 3 bug fix for the N-state model target function setup. The num_tensors variable needs to be an integer, but the Python 3 division will create a float typeAdded another abbreviation.* Python 3 fix for Expansion of the abbreviations chapter of the results.read relax user function matching that of state.loadmanual.* Python 3 bug fix Added a tonne of DOI numbers to the relax user manual bibliography. This will simplify accessing these references for the relax_io.read_spin_data() functionuser. * The built in max() function cannot handle the value of None, therefore the filter() function is used to remove all instances of None from the listAdded and fixed DOI numbers for many bibliographic entries.* Python 3 bug fix The LaTeX bibliography style for PhD theses now includes the state.load user functionDOI hyperlink. The header line of pickled states (rather than This is for the standard XML states) is of the b'' byte formatuser manual. * This is now converted to a string, and Slight modification of the search expression is comparing it to DOI hyperlink formatting bibliography style for the raw string r"<\?xml"user manual.* Better support for both Python 2 and 3 in the Modified the relax LaTeX bibliography style file relax data store.bst to convert DOI numbers to hyperlinks. The 2to3 script was used on all of This is to add links to the files in references within the data packagerelax user manual.* Python 3 preparation - Created the relax data store (new 'Citations' chapter of the relax user manual. This is to clearly outline to the user the citations required for the data package) now supports both Python 2 and 3various components of relax.* Python 3 fix - Added the relax_errors.AllRelaxErrors object is now Fushman 1999 reference and a proper tuplefew formatting fixes in other references. * Due Improvements to bad coding, it was previously a nested tuplethe 'Supported NMR theories' section of the user manual introduction. This nested tuple worked in Python 2, but is fatal includes the addition of the Morin and Gagne 2009 reference.* Added the Morin and Gagne 2009 reference for Python 3the consistency testing.* Python 3 fixes - Added some more abbreviations to the character '\' is now properly escaped as '\\' in the stereochemistry auto-analysisrelax user manual.* Fix Created a new chapter for the test suite summary for Python 3. relax user manual titled 'The test suite now runs, but fails miserably, under Python 3relax data model'.* Fix for the running of the test suite under Python 3. The zip() function used pipe editor window screenshot width in the loadTestsFromTestCase() function is now an iterator, so it needs to be passed through the list() function to generate a listrelax manual.* Fix for Converted some more wizard graphics to the test_parse_token_multi_element_name() unit test, as parse_token() no longer sortsEPS format for the user manual.* Python 3 fix for Updates and small expansion of the intro chapter of the generic_fns.mol_res_spin.parse_token() functionrelax user manual. * Mixed lists for int and string can no longer be sortedThe user manual now specifies the repository revision if a non-tagged version is built. This sort call is not needed anywayenables easier tracking and editing of the manual.* Automatically converted Updates to the generic_fns.mol_res_spin module to support both Python 2 and 3.id_string_doc documentation structure.* For running relax with Python 2, Updated the screenshot of the __builtin__.range() function has been replaced with xrangepipe editor window. * This causes large speed ups (speed that was lost with Created EPS versions of a number of wizard graphics for use in the earlier xrange() to range() conversions), and memory decreasesuser manual. * For example on one system, Removed some now useless whitespace from the top of each user function subsection of the system test time decreased from 513.029s to 487.586smanual.* The compat module now has Redesigned the formatting of the user function chapter of the py_version variable specifying if this is Python 2 or 3relax manual. The fetch_docstrings.py now forces each user function to start in a new column.* Import fix for This increases the size of the OpenDX mapping packagemanual, recently broken with but makes the relative import for Python 3 change.* More usage reading of the is_unicode() user function in the generic_fns.mol_res_spin moduledocumentation much easier.* Created the check_types.is_unicodeThe user function class and function icons (128x128 format) function for Python 2+3 compatibilityare now placed between the top bar and the subsection title and are left and right justified. This is used in prettification simply allows the generic_fns.mol_res_spin moduleuser functions to be more quickly identified.* Another raise() function call to statement change for 2to3 preparationsLarge expansion of the relax icon set.* Converted some raise() function calls to raise statements in preparation for All 128x128 versions of the 2to3 conversion.* Converted icons used by the ScientificPython PDB reader to support user functions have been added as both Python 2 PNG and 3gzipped EPS files. The __repr__() method was manually modified due to the 'list' variable clashing with the 'list'typeA few gzipped SVG and non-sized icons have been added as well.* Created a new module for simultaneous Python 2 and 3 support in Large expansion of the Oxygen icons within relax called 'compat'.* Python 3 fixes - All 128x128 versions of the list() function is now icons used in combination with range() to generate by the ordered listuser functions have been added as both PNG and gzipped EPS files. range() in Python 3 is an iterator object (just A number of gzipped SVG icons has been added as xrange was), so now well.* Modified the list() graphics.fetch_icon function has to return different file formats. This will be calledused for the relax manual where eps.gz files are required.* Python 3 preparations - mass conversion of all xrange() calls Improvements to range().* Created the special check_typesfinal section of the relaxation curve-fitting chapter.is_filetype() function The Xmgrace screenshot and page references for checking for files in all Python versionsthe user functions have been added.* Python 3 - eliminated an unneeded xrange callAdded screenshots of Xmgrace displaying relaxation curves.* Python 3 - eliminated the use of the map() The fetch_docstrings.py now adds LaTeX labels to each user function, as this behaves differently in Python 3section.* Python 3 - removed This has the use form of 'uf: ' followed by the string.lower() user function as it name, and is missing in Python 3for referencing purposes within the main text.* Python 3 fix for Rewrote the relaxation curve-fitting chapter of the relax information printoutmanual. The try blocks seem This chapter was quite out of date and was of no use to now operate slightly differently in Python 3modern relax versions.* Python 2 fixes - Redesign of how the Python 3 fixes for GPL license is presented to the ScientificPython module imports broke Python 2user.* Python 3 - The old prompt.gpl module with the version 2 of the cStringIO.StringIO import switches to iolicense has been deleted.StringIO if missing.* Python 3 - relative module paths are now used for Now the text form the test suite runnerdocs/COPYING file is passed through pydoc.* Python 3 fixes pager for the version module for catching empty lists'.* Python 3 fix /relax -- ensure an integer licence' and the prompt mode GPL object, and is actually an integer (division now converts ints simply printed to floats)STDOUT for the GUI help system.* Python 3 - fixes Import clean ups for the renaming of the Queue package.N-state model specific module.* Python 3 - converted Added the last of the except error catching statements 'unit' argument to be Python 2.4+ compatible.* Python 3 - removal of the use of the stringdipole_pair.atoi read_dist and stringdipole_pair.atof set_dist user functions. These have been depreciated since Python 2.0! They have been replace by the int and float functions.* Python 3 - a number of fixes for running the ScientificPython modules This is to allow distances in Angstroms to be read into relax on Python 2 and 3. This includes relative imports, converting raise statements to function calls, removal of the use of many string module functions which do not exist in Python 3, etc.* Python 3 - modified some except statements to be Python 2.4+ compatible in a ScientificPython module.* Python 3 - converted some print statements to function calls in the ScientificPython modules.* Python 3 - fix for an os.chmod() call by using the stat module rather than the number 0775. The number 0755 is no longer valid in Python 3.* Python 3 - a pile of relative path fixes for many relax modules.* Python 3 - removed the use of the types module from generic_fns.sequence. The relax arg_check module is now being used instead.* Python 3 preparations - removed all of the string module functions which no longer exist in Python 3. These functions are part of the strings themselves now.* Improvements for the relax test suite synopsis for when the wxPython module is missing or broken. This is simply a printout improvement.* Python 3 preparations - removal of some unneeded xrange() calls.* Python 3 preparations - the data package now really does use the absolute path for its module imports.* Python 3 preparations - the data package now uses absolute imports for all its modules.* Python 3 preparations - eliminated the use of the types.ListType object.* 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 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 relax_data.read user function.* Fix for the Relax_data.test_read unit tests for the relax_data.read user function changes.* Fix to the Dasha system test needed for the changes to the 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 bug #20197 (https://gna.org/bugs/?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 bug #20197 (https://gna.org/bugs/?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 bug #20197 (https://gna.org/bugs/?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 converted to passmeters.