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 R2, model-free chapters with screenshots in of the GUI in operationPython 2.3 to 3.* Restored 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 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/relax_data_modelnew_protocol_in_GUI.html relax data model chapter] of the user manual to explain how to set up data in relax in all UI modes (with screenshots GUI tutorial in the GUI mode).* Creation of the [http://www.nmrmodel-relax.com/manual/Preface_citing_relax.html citations free chapter] of the user relax manual to help users properly cite the parts of relax that they use.* A complete rewrite of the [http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html relaxation curve-fitting chapter] number 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 to be more multi-processor friendlyPython 3 __pycache__ directories. * The message saying that Small edit to the optimised chi2 is an improvement or not now includes installation chapter of the spin ID string if present. This is more informative for the multi-processor mpi4py printoutsuser manual.* Added Decreased the use of the program 'nice' Python version dependency from 2.5 to 2.3 in the model-free GUI tutorial in installation chapter of the user manual.* Removed More error checking for the out associate_auto() method of date and useless README file the data pipe editor window.* Added data pipe bundle error checking for the HTML version of the user manualGUI pipe editor window associate_auto() method.* Added a BMRB section to some error checking for the end of data pipe bundle in the auto model-free chapter of the user manualanalysis GUI code.* Massive expansion of the model-free chapter of the user manual including script and GUI tutorialsAdded some special RelaxErrors for data pipe bundles. * The model-free chapter now has step-by-step tutorials Added some bug catching code for both the prompt/script mode and GUI mode for the new automated model-free protocol (the dobserver objects. In some rare cases a registered method'Auvergne protocol)[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]s key was set to None. This includes is now caught and a large set of screenshots for the GUI modeRelaxError thrown to prevent later indecipherable errors.* Created the User_functionsThe setup.test_value_set GUI test demonstrating py application building script now complains if the failure of the [http://www.nmr-relax.com/manual/value.set user function]Python setuptools are not installed.* Modified Updated the relax prompt mode figure in the intro chapter of the dauvergne_protocol sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] user manual to handle tryptophan indole NE1 datathe more modern prompt.* Improvements to the API documentation compilation. The graphics.fetch_icon() function argument 'format' can now be set excluded files and directories, as well as hidden ones, are no longer included in the list of files/directories to add to None. This will return the file path without the extensiondocumentation.* Improvements to Added a file with the duplicate relax user manual title finding script.* Created a simple shell script to find duplicate titles in functions used for the relax user manualprompt screenshots. This is important for the HTML version of the manual as duplicated titles causes HTML pages to be overwritten. For example all chapters, sections and subsections titled "Introduction" will load the introductionwebsite.html file which will contain the text of the last section with that title!* * Additions to Added the scripting section of the relaxation curve-fitting chapter of public domain LaTeX nth.sty style file for the user manual.* A small edit to the intro chapter for Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing the multi-processor operation and loggingPDF manual to compile on more systems.* Added some labelling to Fixes for weird print statements with double brackets generated by the infrastructure chapter of the user manual for referencing2to3 Python conversion script.* A number Removed a debugging printout.* Python 3 fixes for one of updates and edits to the intro chapter of the user manualtest data scripts - print statement with function call replacements. * The modelPython 3 fixes for non-used Python code -free GUI screenshot has been shifted converted print statements to function calls.* Python 3 fixes for the intro chapter in preparation script for a full tutorial with screenshots in the model-free chaptergenerating plots of magnetic field lines.* Updated the data model chapter of Another print statement to function Python 3 fix for the user manual to cover the handling of protons. * This change includes The Python print statements in the modification of the PDB reading screenshot user manual are now function calls to demonstrate the reading of a specific model and the naming of the moleculebe Python 3 compatible.* All of Python 3 fix for the GUI strings and text are now formatted with a small sans serif font in the user manualgeneric_fns.structure.geometric.angles_regular() function. This is because in the GUI, a sans serif font is almost always used be defaultInteger divisions no longer produce integers.* Modified Better formatting of the User_functions.test_structure_pdb_read() GUI test to catch another bugsuite summary. * This The text relax controller log is no longer cleared when a bug recently introduced with reset occurs. This allows the fixes test suite results to the other sequence editor still be presented in GUI window problemsmode.* Created Even cleaner exiting of the User_functions.test_structure_pdb_read GUI test for checking - the interpreter thread is terminated by the sequence editor windowexit_gui() method. * This new user function GUI testing class The GUI is now cleanly exited with a call to be used for testing out the special GUI elements not invoked within the unit testingwx.App.ExitMainLoop rather than wx. The test_structure_pdb_read() test specifically shows a number of failures of the sequence editor windowExit.* Modified Python 3 fix for the operation of compat module - the sequence GUI element Queue2 object needs to have access to the sequence editor windowalways be defined. * This is to allow this GUI element to be blasted within Added support for Python 2.2 and earlier for the compilation of the test suiteC modules.* Improvements to the descriptions Removed an unused import of the [http://www.nmrQueue module from the multi-relax.com/manual/structure.read_xyz user function] argumentsprocessor.* Improvements to Python 3 fix for the descriptions ScientificPython PDB reader unit tests. The order of the [http://www.nmr-relax.com/manual/structure.read_pdb user function] argumentskeys returned by a dictionary's keys() method changes randomly in Python 3, so now they are sorted prior to comparison.* Added @HE1 to the spin ID list of Redesigned the [http://www.nmr-relax.com/manual/structurereset.load_spins html reset] user function]backend. This is now no only seen in clears out the relax data store, but it also resets the GUIif present.* Created Some of the new generic_fns.result_files for standardising reset code comes from the handling tearDown() method of results filesthe GUI tests. This fixes All windows but the bug where results files main GUI window are closed and the relax controller gauges are repetitively added set to zero and the listlog window text cleared. All of the code touching cdp.result_files now uses this module insteadThese changes should allow GUI tests after an error or failure to pass, something which is currently problematic.* Updated the scripting section of Disabled the initial relax intro chapter of printout from the GUI when running the test suite. This prevents the intro text from appearing in the user manual for non-technical usersfirst failed test.* Expanded the spin ID list Fix for the [http://wwwMf.nmr-relax.com/manual/structuretest_read_results_1_3_v2_broken() system test for Python 3.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. The compat module is now imported at the very start to allow the builtins to be set before any other imports.* Changed the RelaxError for missing relaxation times in The sorted() builtin method is now mimicked and the relaxation curve-fitting analysesos.devnull string set for Python 2.3 and earlier.* Modified Fix for the test_bug_20152_read_dc_fileMf.test_write_results() GUI system test to catch the RelaxErrorfor Python 3.1. This error The XML version in Python 3.1 is because of the old PDC formatstyle. Therefore the old results file is being used to check this Python 3.1 result.* Created Small improvements to the test_bug_20152_read_dc_file() GUI multiple Python version test suite testing script.* Reactivated support for catching [https://gnaPython 2.3.org/bugs/?20152 bug #20152] This mainly skips the missing 'subprocess' module. This includes truncated data taken from the bug report (with data for only the first 3 residues)however decreases relax's functionality a little.* Set up the Bruker Dynamics Center system tests as GUI testsCreated a special script for testing out relax with Python versions 1.0 all the way to 3.3. This is builds the C modules for each Python version in preparation for catching [https:~//gnabin and then runs the test suite, outputting everything to log files.org/bugs/?20152 bug #20152].* * Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.* A few small edits of The Results system tests are no longer dependent on the relaxation curve-fitting chapterC modules. This is allows these tests to reinforce run when the exact time of the relaxation time periodmodule cannot be imported.* Added some text to explain why Python 2.5 and lower fix for the test_write_protein_sequence() unit test only J. The byte array is wrapped in an eval(0) is discussed whereas statement to allow Python 2.5 and lower to parse the script also calculated F_R2 code without failing, and F_etathe byte array comparison is now only used for Python 3+.* All system and GUI tests reliant on the relax-fit C modules are deactivated if import fails. This was suggested by [https://gna.org/users/bugman Edward d'Auvergne] in removes a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00044.htmlpile of useless error messages from the test suite and presents a table of skipped tests at the end.* Big clean up of the Bibtex bibliography file More Python 3 fixes for the relax user manualuse of now non-existent string module functions.* Small edits of Python 3 fix for the consistency testing figure caption in the relax user manualmodel-free BMRB export - many string module methods no longer exist.* Editing and a number Mass conversion of fixes/cleanups for the consistency testing chapter of alignment tensor data structures to the same new design as the user manualdiffusion tensor.* Editing of the "Values, gradients, and Hessians" chapter This large set of changes matches all of those revisions for the user manual to make it fit betterdiffusion tensor already committed. The context of this chapter has been specified by changing the title to "Optimisation of relaxation alignment tensor data -- values, gradientsstructures are now read only, and Hessians" and can only be modified via the intro text has been updatedset() method. As this chapter This is no longer straight after the model-free chapter, this is needed.* Made a small correction to a reference such that a superscript is correctly displayedmuch simplified design which works on all Python versions.* Added Small clean ups of the bounding box and a centerline command to diffusion tensor data structure code.* Deleted the code for now unused _update_sim_set() method of the figure for consistency testingdiffusion tensor data structure. * This follows two remarks by Edward d'Auvergne at https://mail.gna.org/public/relax-devel/2012-09/msg00030.html and https://mail.gna.org/public/relax-devel/2012-09/msg00032.htmlRemoved the now unused _update_sim_append() method from the diffusion tensor data structure.* Added more text to describe Cleaned up the docstring of the consistency testing approachdiffusion tensor data object __setattr__() method. * Also includes a very basic point by point protocol for consistency testingUpdated all of the diffusion tensor unit tests to the new design. * This was proposed by [https://gnaFix for the reading of model-free results files from relax 1.org/users/bugman Edward d'Auvergne] at https://mail2 when simulation data is missing.gna.org/public/* Fix for the reading of relax-devel/2012-09/msg000281.html. This also follows a discussion started by [https://gna.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-devel/2012-09manual/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 The diffusion tensor set_fixed() method is now used.* Fix for the XML output of the diffusion tensor - only the modifiable parameters are output.agr (xmgrace), eps (gzipped), 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-develmanual/2012-09/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 bibliography entries whih were still in plain text and not as a Latex \cite call. Also renamed diffusion tensor fixed() method to set_fixed() to avoid clashing with the MorinGagne09 entry to MorinGagne09a 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'fixed' object.* Added Fix for the DOI to reference Morin11 and fixed indentation model-free specific analysis duplicate_data(10.1016/j.pnmrs.2010.12.003)method for the new design. This follows a comment by Edward d'Auvergne at https://mail.gna.org/public/relax-devel/2012-09/msg00022.htmlThe diffusion tensor __mod_attr__ object is now called _mod_attr.* Deletion of Fix for the relax version LaTeX file - this is automatically created anywaydiffusion tensor to_xml() method for the new design.* Added text to detail For some reason the usage methods of the consistency testing scriptElement class are no longer blacklisted. * This text was modified from Converted the corresponding text for jw_mappingdiffusion tensor data structure from_xml() method to the new tensor design. * This follows a discussion started by [https://gnaFix for the Diffusion_tensor.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relaxtest_copy system test -devel/2012the simulation parameters are now read-09/msg00019only.html Instead, the diffusion tensor set() method needs to be called.* Added some text and a reference to The setting of list values for the consistency testing chapterDiffTensorSimList object now works correctly. This follows a discussion started The private _set() method now works correctly by [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.htmlcalling the base class method, and the normal setting of diffusion tensor simulation values produces a RelaxError.* Editing of Fix for the nmrPipe script in diffusion tensor __deepcopy__() replacement method for the Rx curve-fitting chapter of the manualnew design.* Some editing of The model-free specific analysis _disassemble_param_vector() method now uses the NOE chapter of the relax user manualnew diffusion tensor design.* The old R1 and R2 analysis screenshots have been shifted Modified the setUp() method for the diffusion tensor system tests to use the intro chapternew design.* Editing of the relax data model chapter of the user manualRedesigned how diffusion tensor simulation structures are handled. The design is now much cleaner and works with all Python versions.* Large expansion and lots of editing of Removed all the relaxation curve-fitting chapter of the user manualunused imports from specific_fns. The GUI section has been added which includes step-by-step instructions on how to use relax,illustrated with screenshots at each stepmodel_free. There has been general editing of the whole of the chapter as wellmain.* Added a tonne A number of GUI screenshots of an R1 analysis. These will be used in private diffusion tensor objects and methods have switched to the relaxation curve-fitting chapter of the user manualsingle leading '_' format.* Added some Grace plots from an NOE analysis for use in Improvements to the user manualdiffusion tensor set() method.* Small edits of the relax data model chapter of the user manualThe parameters, errors and simulations are now properly differentiated and stored.* Editing of Converted the relaxation curve-fitting and NOE chapters of old diffusion tensor __setattr__() method into the user manualset() method. This is to synchronise the format of the two chaptersonly way in which diffusion tensor parameters, errors and includes the swapping of text between themsimulations can be set.* Added trp indole NH loading into Renamed the relaxation curve-fitting sample scriptdiffusion tensor data structure type() method to set_type().* Large edits of This is because the consistency testing chapter of type is stored as the user manual.* Activated 'type' object, clashing with the consistency testing chapter of the user manualmethod name.* Added a LaTeX label to Created the Jdiffusion tensor data structure type(w) mapping chaptermethod for setting the tensor type.* Added the other consistency testing references This is to remove the citation chapter "cdp.diff_tensor.type = 'x'" code from the core of relax, as the manualstructure is now read only.* Added The new diffusion tensor fixed() method has been created to allow the Fushman et al., 1998 referencefixed flag to be changed.* Fix for the Farrow et al.initialisation of the diffusion tensor data structure, 1995 DOI number.now that it is read-only.* Changed the order of the Rx curveThe diffusion tensor data structure has been completely converted into a read-fitting and NOE chapters in the relax manualonly structure. This 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.* Clean up of a paragraph of The __setattr__() method now will always raise a RelaxError, and the diffusion tensor simulation data model chapter of structure objects __setitem__() method will raise the user manualsame error.* Improved the consistency in Updated the relax version numbers and 'trunk' used relax user manual by using . For example the information about checking out the main development line was still talking about 1.3 rather than the new LaTeX commandstrunk. * These changes are throughout Python 3 fix for the manual setting of diffusion and affect all the text of user functions, menu items, prompt examples, GUI elements, files, directories, etcalignment tensor simulation values. The previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.* Removed some '()' text from Python 3 fix for the end of the user functions 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 function documentationXML changes from Python 2.7.3 onwards.* Added some more LaTeX functions for formatting consistencyThe relaxation curve-fitting system tests are now skipped if the module is missing or broken.* Defined This improves the printouts from the test suite and shows a new set summary of skipped tests rather than a pile of LaTeX commands for prompt/script/GUI strings traceback messages and elements for errors.* The message about skipping the user manual. These will be used GUI tests due to regularize the text throughout the manual, as this wxPython being missing is currently quite mixed upnow more specific.* More rearrangements of data model and NOE chapters This was being shown for all runs of the relax manual. The test suite when it only needs to appear if GUI spin deselection part of the NOE chapter has tests have been shifted into the data model chapter. And the GUI loading of spins from a sequence file section has been completedrun.* Added screenshots a Python 3 version of the spin viewer spin loading wizard sequencetruncated OMP model-free results file.read page This was created with trunk.* Redesign of Removed the data model chapter of the user manual. This includes the moving of all of the spin viewer window text and screenshots from the NOE chapterPython 3 byte array hack which should have been removed earlier.* Shifted the spin viewer screenshots into their own directoryThe OMP model-free results file generation script now outputs for any relax version.* Changed Python 3 fix for the Mf.test_latex_table system test. The latex_mf_table.py model-free system test script docstring contains backslashes, so the raw string format r"View->Spin view" menu item to "View->Spin viewerText"""is now used.* Created a directory Python 3 support for screenshots of the spin viewer window operation[[Modelfree4]] and [[DASHA]]. The subprocess.Popen class works with byte arrays rather than strings in Python 3+.* The NOE auto-analysis GUI test Python objects are now checks interconverted when the support for Trp indole N data as wellPython 3 encode() and decode() methods are detected.* The [http://www.nmr-relax.com/manual/spectrum.read_intensities Removed the pickle format information and arguments from the state user function] now prints out a list of the intensities read indefinitions. * This is for better user feedback Eliminated the State.test_state_pickle() system test as to what the user function has actually donepickled states are no longer supported.* Created Removed the GUI wizard _apply() method for executing ability to save and restore states using the current page's _apply() methodpickle module. This A pickled state is for the GUI tests of no use to relax anymore. It's removal is needed for Python 3 support. So now everything defaults to simulate a click on the 'Apply' buttonXML formatted output.* Removed a debugging print outPython 3 fix - removed the use of the string module from generic_fns.spectrum.* Modified Python 3 fix for the NOE system test to catch [https://gnarelax_io.org/bugs/?20120 bug #20120]open_write_file() function.* Lots of editing of This now matches the NOE chapter of the user manual.* Significant update behaviour of open_read_file() in that there are three different behaviours for opening bz2 and gz files for writing to for the NOE chapter of the user manualdifferent Python versions (one for Python 2, one for Python 3.0 to 3. The sample script used in this chapter was incredibly out of date2, and one for Python 3.3+). All byte streams have been eliminated as open_write_file() is for creating text files.* Modified Python 3 fix for the NOE Noe.test_noe_analysis() system test to test for the usage of Trp indole ¹⁵N datagrace.write precision changes. * This is to catch For consistency between Python 2 and 3, the [httpshttp://gnawww.nmr-relax.orgcom/bugsmanual/?20119 bug #20119grace_write.html grace.write user function]outputs to 15 decimal places. This increased precision will only be of use in the relax test suite.* Added some Trp peak data Python 3 fix for the Pipes.test_pipe_bundle(backbone and indole N) to the Sparky steady-state NOE peak listssystem test. This The order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in preparation for Python 3.* The C module compilation testing script now accepts the modification of the NOE system test to catch [https://gna.org/bugs/?20119 bug #20119]Python version as a first argument.* Modified the NOE sample script to include Trp indole NH dataThe relax_io.open_read_file() now supports all Python versions over 2.4.* Added a step-by-step tutorial This required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the GUI NOE auto-analysis to Bzip2Fixed and GzipFixed classes overriding the user manualincomplete and buggy bz2.BZ2File and gzip.GzipFile modules, and being wrapped around io. This includes 22 screenshots of all the stepsTextIOWrapper().* Added a section label.* Added some Sparky info the IO module to the Rx curve-fitting chapter of the user manualrelax information printout and dependency checks.* Allowed the raggedbottom LaTeX setting as this The manual C module compilation script is better for the screenshot layout in the user manualnow executable.* Added Renamed the nth package for 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the user manual LaTeX compilationscripts.* The NOE chapter now points to Finished off the recommendations in the Rx fitting chapterC module compilation testing script.* Added a new section called 'From spectra to peak intensities' to script for testing out the Rx fitting chapter of the manualC module compilation on multiple Python targets. * This adds a number of recommendations for high quality relaxation ratesThe relax_fit specific analysis module now supports both Python 2 and 3.* Added the Viles et al., 2001 referenceThe relaxation curve-fitting C module now supports compilation on both Python 2 and 3.* Small description edit for the Created the simple Sequence.test_sequence_copy() system test to catch [httphttps://wwwgna.nmr-relax.comorg/manualbugs/relax_data.temp_control user function?20213 bug #20213].* Added The Mf.test_bug_20213_asn_sidechain() system test now uses a LaTeX label to the NOE chapter of the user manualtemporary directory for output.* Added a paragraph to the model-free chapter of the user manual explaining the JMf.test_bug_20213_asn_sidechain(w) equation formssystem test to catch [https://gna.org/bugs/?20213 bug #20213].* Added a label to the The data model chapter of and script comes from the user manualfiles 'sh3-47.2.* Created an initial rough version of the RSDM chapter of the user manualzip' and 'run.* Better figure layout in py' attached to the NOE chapter of bug report https://gna.org/bugs/?20213. The PDB now only contains Asp47, the optimisation parameters have been made almost insignificant, and all models but 'tm0' have been removed from the user manualanalysis.* The relax data model chapter of the user manual now uses the higher quality graphicsPython 3 dictionary values() method no longer returns a list, so a list() call is needed.* Some more high quality graphics.* Added more high resolution graphics Python 3 bug fix for use in the relax user manualgeometric structure module - another integer division to float problem.* Expanded The Mf.test_write_results system test can now select the size of the specific analysis graphics - mainly correct file to compare against in Python 3. The algorithm for use in determining if the relax user manual'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.* Added Python 3 fix for the specific analysis graphics to the start format detection of each chapter of the relax user manualresults and save files.* Small edit of Python 3 import fixes for the 'Citations' chapter of the relax user manualgeneric_fns.structure package using relative paths.* Added EPS versions Python 3 fix - removed the use of the specific analysis graphics for use string.lower() function in the user manualOpenDX mapping code.* Added Python 3 fix for the Fushman et alframe order system tests. As float to string conversions behave differently, 1999 reference for consistency testing the %.1f formatting is used to the intro chapter of the user manualforce only a single decimal place float.* More chapter cross referencing in Python 3 fix for the relax user manualframe order system tests - float to string conversions behave differently.* Added Now the Horne 2007 paper explicit %.1f formatting is used to the 'Citations' chapter of the user manual. Whitespace has also been cleaned up, and force only a chapter label addedsingle decimal place float.* Added the Horne 2007 paper Python 3 integer division to float fix for the 'Supported NMR theories' subsection of the user manual intro.frame order analysis.* Shortened Python 3 bug fix for the Literature subsection of the intro chapter to point to the citations chapterframe order analysis - another int division problem. * This part Python 3 fixes - eliminated all usage of the user manual is now redundantdictionary has_key() calls as they are no longer present.* Small edits of Python 2 and 3 support in the relax user manualgeneric_fns.relax_data module using 2to3. One print call was fixed after running 2to3.* Edits to Python 3 bug fix for the abbreviations chapter of the relax user manualStructure.test_read_pdb_mol_2_model_scientific system tests.* Added another abbreviationThis is again an integer division problem returning a float.* Expansion of Python 3 fix for the abbreviations chapter of the relax user manualtest_write_protein_sequence() unit test. This is again a string verses byte verses unicode problem.* Added a tonne of DOI numbers to Python 3 fix for the relax user manual bibliographyfunction docstring creation in the prompt UI mode. This will simplify accessing these references for Again this is the userproblem of a division now returning a float rather than an int.* Added and fixed DOI numbers Python 3 bug fix for many bibliographic entriesthe N-state model target function setup.* The LaTeX bibliography style for PhD theses now includes num_tensors variable needs to be an integer, but the DOI hyperlink. This is for the user manualPython 3 division will create a float type.* Slight modification of the DOI hyperlink formatting bibliography style Python 3 fix for the user [http://www.nmr-relax.com/manual/results_read.html results.read user function] matching that of state.load.* Modified Python 3 bug fix for the relax LaTeX bibliography style file relaxrelax_io.bst to convert DOI numbers to hyperlinksread_spin_data() function. This The built in max() function cannot handle the value of None, therefore the filter() function is used to add links to remove all instances of None from the references within the relax user manuallist.* Created the new 'Citations' chapter of Python 3 bug fix for the [http://www.nmr-relax .com/manual/state_load.html state.load user manualfunction]. The header line of pickled states (rather than the standard XML states) is of the b'' byte format. This is now converted to clearly outline a string, and the search expression is comparing it to the user the citations required raw string r"<\?xml".* Better support for both Python 2 and 3 in the various components of relaxdata store.* Added The 2to3 script was used on all of the Fushman 1999 reference and a few formatting fixes files in other referencesthe data package.* Improvements to Python 3 preparation - the 'Supported NMR theories' section of relax data store (the user manual introduction. This includes the addition of the Morin data package) now supports both Python 2 and Gagne 2009 reference3.* Added Python 3 fix - the Morin and Gagne 2009 reference for the consistency testingrelax_errors.AllRelaxErrors object is now a proper tuple.* Added some more abbreviations Due to the relax user manualbad coding, it was previously a nested tuple. This nested tuple worked in Python 2, but is fatal for Python 3.* Created a new chapter for Python 3 fixes - the relax user manual titled character '\' is now properly escaped as 'The relax data model\\'in the stereochemistry auto-analysis.* Fix for the pipe editor window screenshot width in the relax manualtest suite summary for Python 3.* Converted some more wizard graphics to the EPS format for the user manualThe test suite now runs, but fails miserably, under Python 3.* Updates and small expansion of Fix for the intro chapter running of the relax user manualtest suite under Python 3.* The user manual zip() function used in the loadTestsFromTestCase() function is now specifies an iterator, so it needs to be passed through the repository revision if list() function to generate a non-tagged version is built. This enables easier tracking and editing of the manuallist.* Updates to Fix for the test_parse_token_multi_element_name() unit test, as parse_token() no longer sorts.* Python 3 fix for the generic_fns.mol_res_spin.id_string_doc documentation structureparse_token() function.* Updated the screenshot of the pipe editor windowMixed lists for int and string can no longer be sorted.* Created EPS versions of a number of wizard graphics for use in the user manualThis sort call is not needed anyway.* Removed some now useless whitespace from Automatically converted the top of each user function subsection of the manualgeneric_fns.mol_res_spin module to support both Python 2 and 3.* Redesigned the formatting of the user function chapter of For running relax with Python 2, the relax manual__builtin__. The fetch_docstrings.py now forces each user range() function to start in a new columnhas been replaced with xrange. This increases causes large speed ups (speed that was lost with the size of the manualearlier xrange() to range() conversions), and memory decreases. For example on one system, but makes the reading of the user function documentation much easiersystem test time decreased from 513.029s to 487.586s. * The user function class and function icons (128x128 format) are compat module now placed between has the top bar and the subsection title and are left and right justifiedpy_version variable specifying if this is Python 2 or 3. * This prettification simply allows Import fix for the OpenDX mapping package, recently broken with the user functions to be more quickly identifiedrelative import for Python 3 change.* Large expansion More usage of the relax icon setis_unicode() function in the generic_fns. All 128x128 versions of the icons used by the user functions have been added as both PNG and gzipped EPS files. A few gzipped SVG and non-sized icons have been added as wellmol_res_spin module.* Large expansion of Created the Oxygen icons within relaxcheck_types.is_unicode() function for Python 2+3 compatibility. All 128x128 versions of the icons This is used by in the user functions have been added as both PNG and gzipped EPS filesgeneric_fns. A number of gzipped SVG icons has been added as wellmol_res_spin module.* Modified the graphics.fetch_icon Another raise() function call to return different file formats. This will be used statement change for the relax manual where eps.gz files are required2to3 preparations.* Improvements Converted some raise() function calls to the final section of the relaxation curve-fitting chapter. The Xmgrace screenshot and page references raise statements in preparation for the user functions have been added2to3 conversion.* Added screenshots of Xmgrace displaying relaxation curvesConverted the ScientificPython PDB reader to support both Python 2 and 3.* The fetch_docstrings.py now adds LaTeX labels __repr__() method was manually modified due to each user function section. This has the form of 'uf: list' followed by variable clashing with the user function name, and is for referencing purposes within the main text'list'type.* Rewrote the relaxation curve-fitting chapter of the relax manual. This chapter was quite out of date Created a new module for simultaneous Python 2 and was of no use to modern 3 support in relax versionscalled 'compat'.* Redesign of how Python 3 fixes - the GPL license list() function is presented now used in combination with range() to generate the userordered list. The old prompt.gpl module with range() in Python 3 is an iterator object (just as xrange was), so now the version 2 of the license list() function has been deletedto be called. * Now the text form the docs/COPYING file is passed through pydocPython 3 preparations - mass conversion of all xrange() calls to range().pager for * Created the 'special check_types./relax --licence' and the prompt mode GPL object, and is simply printed to STDOUT is_filetype() function for checking for the GUI help systemfiles in all Python versions.* Import clean ups for the NPython 3 -state model specific moduleeliminated an unneeded xrange call.* Added Python 3 - eliminated the 'unit' argument to use of the [http://wwwmap() function, as this behaves differently in Python 3.nmr* Python 3 -relaxremoved the use of the string.com/manual/dipole_pairlower() function as it is missing in Python 3.read_dist* Python 3 fix for the relax information printout.html dipole_pair The try blocks seem to now operate slightly differently in Python 3.read_dist] and [http://www* Python 2 fixes - the Python 3 fixes for the ScientificPython module imports broke Python 2.nmr* Python 3 -relaxthe cStringIO.com/manual/dipole_pairStringIO import switches to io.set_dist.html dipole_pair.set_dist] user functionsStringIO if missing. * This is Python 3 - relative module paths are now used for the test suite runner.* Python 3 fixes for the version module for catching empty lists.* Python 3 fix - ensure an integer is actually an integer (division now converts ints to allow distances in Angstroms to be read into relax floats).* Python 3 - fixes for the renaming of the Queue package.* Python 3 - converted the last of the except error catching statements to be Python 2.4+ compatible.* Python 3 - removal of the use of the string.atoi and string.atof 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 in 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 [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 ===

= Announcements ={{:relax release announcements}}Links ==

= References =Announcements =={{:relax release announcements}}

== See also ==