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 number of the [http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html relaxation curve-fitting chapter] of the relax manualbugfixes.* General Small improvements and expansions throughout the user manual (the manual is now 15 Mb compared to 4.3 Mb for relax 2.1.0)overall.

=== Changes ===

* Modified The scons 'clean' target now removes the model-free optimisation final printout 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, 2008]s key was set to None. This includes is now caught and a large set of screenshots for RelaxError thrown to prevent later indecipherable errors.* The setup.py application building script now complains if the GUI modePython setuptools are not installed.* Created Updated the User_functions.test_value_set GUI test demonstrating relax prompt mode figure in the failure intro chapter of the value.set user functionmanual to the more modern prompt.* Modified Improvements to the dauvergne_protocol sample script[d'Auvergne API documentation compilation. The excluded files and Gooleydirectories, 2007][d'Auvergne and Gooleyas well as hidden ones, 2008] are no longer included in the list of files/directories to add to handle tryptophan indole NE1 datathe documentation.* The graphics.fetch_icon() function argument 'format' can now be set to NoneAdded a file with the relax user functions used for the prompt screenshots. This will return is for the file path without manual and the extensionwebsite.* Improvements to Added the public domain LaTeX nth.sty style file for the duplicate user manual title finding script.* Created a simple shell script to find duplicate titles in Some LaTeX distributions do not have this style file and, as it is public domain, it can be legally distributed with relax allowing the relax user PDF manualto compile on more systems. * This is important Fixes for weird print statements with double brackets generated by the HTML version of the manual as duplicated titles causes HTML pages to be overwritten. 2to3 Python conversion script.* For example all chapters, sections and subsections titled "Introduction" will load the introductionRemoved a debugging printout.html file which will contain the text of the last section with that title!* Additions to the scripting section Python 3 fixes for one of the relaxation curvetest data scripts -fitting chapter of the user manualprint statement with function call replacements.* A small edit to the intro chapter Python 3 fixes for the multinon-used Python code -processor operation and loggingconverted print statements to function calls.* Added some labelling to Python 3 fixes for the infrastructure chapter script for generating plots of the user manual for referencingmagnetic field lines.* A number of updates and edits Another print statement to the intro chapter of function Python 3 fix for the user manual. * The model-free GUI screenshot has been shifted to the intro chapter in preparation for a full tutorial with screenshots Python print statements in the model-free chapteruser manual are now function calls to be Python 3 compatible.* Updated Python 3 fix for the data model chapter generic_fns.structure.geometric.angles_regular() function. Integer divisions no longer produce integers.* Better formatting of the user manual to cover the handling of protonstest suite summary. * This change includes The text relax controller log is no longer cleared when a reset occurs. This allows the modification of the PDB reading screenshot test suite results to demonstrate the reading of a specific model and the naming of the moleculestill be presented in GUI mode.* All Even cleaner exiting of the GUI strings and text are - the interpreter thread is terminated by the exit_gui() method.* The GUI is now formatted cleanly exited with a small sans serif font in the user manualcall to wx.App.ExitMainLoop rather than wx.Exit. * This is because in Python 3 fix for the compat module - the GUI, a sans serif font is almost Queue2 object needs to always used be defaultdefined.* Modified the User_functionsAdded support for Python 2.test_structure_pdb_read() GUI test to catch another bug. This is a bug recently introduced with 2 and earlier for the fixes to compilation of the other sequence editor GUI window problemsC modules.* Created Removed an unused import of the Queue module from the User_functions.test_structure_pdb_read GUI test for checking the sequence editor windowmulti-processor. * This new user function GUI testing class is to be used Python 3 fix for testing out the special GUI elements not invoked within the ScientificPython PDB reader unit testingtests. The test_structure_pdb_readorder of the keys returned by a dictionary's keys() test specifically shows a number of failures of the sequence editor windowmethod changes randomly in Python 3, so now they are sorted prior to comparison.* Modified Redesigned the operation of the sequence GUI element to have access to the sequence editor window[http://www.nmr-relax.com/manual/reset. This is to allow this GUI element to be blasted within the test suitehtml reset] user function backend.* Improvements to This now no only clears out the descriptions of relax data store, but it also resets the structure.read_xyz user function argumentsGUI if present.* Improvements to the descriptions Some of the structure.read_pdb user function arguments.* Added @HE1 to reset code comes from the spin ID list tearDown() method of the structure.load_spins user functionGUI tests. This is only seen in All windows but the main GUI.* Created window are closed and the new generic_fns.result_files for standardising relax controller gauges are set to zero and the handling of results fileslog window text cleared. This fixes the bug where results files are repetitively added These changes should allow GUI tests after an error or failure to the listpass, something which is currently problematic. * All of Disabled the code touching cdpinitial relax intro printout from the GUI when running the test suite.result_files now uses this module instead.* Updated the scripting section of This prevents the intro chapter of text from appearing in the user manual for non-technical usersfirst failed test.* Expanded the spin ID list Fix for the structureMf.test_read_results_1_3_v2_broken() system test for Python 3.load_spins user function2. 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/publicmanual/relax-devel/2012-09/msg00019diffusion_tensor_init.htmldiffusion_tensor.* Added a modified version init user function] - it was not completely converted.* Fix for the fixing of Figure 1 from Morin and Gagne (JBNMR, 2009 (http://dx.doi.org/10.1007/s10858parameters in the model-009-9381-4))free analyses. File formats are .agr The diffusion tensor set_fixed(xmgrace), eps (gzipped), method is now used.* Fix for the XML output of the diffusion tensor - only the modifiable parameters are output. This was the previous behaviour and pngis needed for the test suite to pass. * This follows a discussion started by Converted the [httpshttp://gnawww.org/users/bugman Edward d'Auvergne] at https://mail.gnanmr-relax.orgcom/publicmanual/relax-devel/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.org/users/bugman Edward d'Auvergne] at https://mailnmr-relax.gna.orgcom/public/relax-develmanual/2012-09/msg00019fix.htmlfix user function] now uses the diffusion tensor set_fixed() method.* Corrected Renamed the diffusion tensor fixed() method to set_fixed() to avoid clashing with the bibliography entries whih were still in plain text and not as a Latex \cite call'fixed' object. * Also renamed Fix for the MorinGagne09 entry to MorinGagne09a as there is now also MorinGagne09bmodel-free specific analysis duplicate_data() method for the new design. This was proposed by Edward d'Auvergne in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00025.htmlThe diffusion tensor __mod_attr__ object is now called _mod_attr.* Added Fix for the DOI to reference Morin11 and fixed indentation (10diffusion tensor to_xml() method for the new design.1016/j For some reason the methods of the Element class are no longer blacklisted.pnmrs.2010.12.003* Converted the diffusion tensor data structure from_xml()method to the new tensor design. * This follows a comment by Edward d'Auvergne at https://mailFix for the Diffusion_tensor.gna.org/public/relaxtest_copy system test -devel/2012the simulation parameters are now read-09/msg00022only.html Instead, the diffusion tensor set() method needs to be called.* Deletion The setting of list values for the relax version LaTeX file - this is automatically created anywayDiffTensorSimList object now works correctly. The private _set() method now works correctly by calling the base class method, and the normal setting of diffusion tensor simulation values produces a RelaxError.* Added text to detail Fix for the usage of diffusion tensor __deepcopy__() replacement method for the consistency testing scriptnew design. * The model-free specific analysis _disassemble_param_vector() method now uses the new diffusion tensor design.* This text was modified from Modified the corresponding text setUp() method for jw_mappingthe diffusion tensor system tests to use the new design. * This follows a discussion started by [https://gnaRedesigned how diffusion tensor simulation structures are handled.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html The design is now much cleaner and works with all Python versions.* Added some text Removed all the unused imports from specific_fns.model_free.main.* A number of private diffusion tensor objects and a reference methods have switched to the consistency testing chaptersingle leading '_' format. * This follows a discussion started by [https://gnaImprovements to the diffusion tensor set() method.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html The parameters, errors and simulations are now properly differentiated and stored.* Editing of Converted the nmrPipe script in old diffusion tensor __setattr__() method into the Rx curve-fitting chapter of the manualset() method.* Some editing of This is the NOE chapter of the relax user manual.* The old R1 only way in which diffusion tensor parameters, errors and R2 analysis screenshots have been shifted to the intro chaptersimulations can be set.* Editing of Renamed the relax diffusion tensor data model chapter of structure type() method to set_type(). This is because the type is stored as the 'type' object, clashing with the user manualmethod name.* Large expansion and lots of editing of Created the relaxation curve-fitting chapter of diffusion tensor data structure type() method for setting the user manualtensor type. The GUI section has been added which includes step-by-step instructions on how This is to use relax,illustrated with screenshots at each stepremove the "cdp.diff_tensor. There has been general editing of type = 'x'" code from the whole core of relax, as the chapter as wellstructure is now read only.* Added a tonne of GUI screenshots of an R1 analysisThe new diffusion tensor fixed() method has been created to allow the fixed flag to be changed. * These will be used in Fix for the initialisation of the relaxation curvediffusion tensor data structure, now that it is read-fitting chapter of the user manualonly.* Added some Grace plots from an NOE analysis for use in the user manualThe diffusion tensor data structure has been completely converted into a read-only structure.* Small edits of The __setattr__() method now will always raise a RelaxError, and the relax diffusion tensor simulation data model chapter of structure objects __setitem__() method will raise the user manualsame error.* Editing of Updated the relaxation curve-fitting relax version numbers and NOE chapters of the 'trunk' used relax user manual. This is to synchronise For example the format of information about checking out the two chapters, and includes the swapping of text between themmain development line was still talking about 1.* Added trp indole NH loading into 3 rather than the relaxation curve-fitting sample scripttrunk.* Large edits of Python 3 fix for the consistency testing chapter setting of the user manualdiffusion and alignment tensor simulation values.* Activated the consistency testing chapter of the user manualThe previous code somehow worked in Python 2 but was not formally correct and broke in Python 3.* Added a LaTeX label to Python 3 fix for the J(w) mapping chaptermodel-free results file reading tests.* Added the other consistency testing references The ordering of dictionaries is different in Python 3, so now these are properly converted from strings to the citation chapter of the manualdictionaries before comparison.* Added This was not happening because of the Fushman et alXML changes from Python 2., 1998 reference7.* Fix for the Farrow et al., 1995 DOI number3 onwards.* Changed the order of the Rx curveThe relaxation curve-fitting and NOE chapters in system tests are now skipped if the relax manualmodule is missing or broken. This is because improves the NOE chapter references passages printouts from the Rx curve-fitting chapter, so it's more logical to have the Rx curve-fitting chapter first.test suite and shows a summary of skipped tests rather than a pile of traceback messages and errors.* Clean up of a paragraph of The message about skipping the data model chapter GUI tests due to wxPython being missing is now more specific. This was being shown for all runs of the user manualtest suite when it only needs to appear if GUI tests have been run.* Improved Added a Python 3 version of the consistency in the user manual by using the new LaTeX commandstruncated OMP model-free results file. This was created with trunk. * These changes are throughout Removed the manual and affect all the text of user functions, menu items, prompt examples, GUI elements, files, directories, etcPython 3 byte array hack which should have been removed earlier.* The OMP model-free results file generation script now outputs for any relax version.* Removed some '()' text from Python 3 fix for the end of Mf.test_latex_table system test. The latex_mf_table.py model-free system test script docstring contains backslashes, so the user functions in the user function documentationraw string format r"""Text""" is now used.* Added some more LaTeX functions Python 3 support for formatting consistency.* [[Modelfree4]] and [[DASHA]]. Defined a new set of LaTeX commands for prompt/script/GUI The subprocess.Popen class works with byte arrays rather than strings and elements for the user manualin Python 3+. These will be used to regularize The Python objects are now interconverted when the text throughout the manual, as this is currently quite mixed upPython 3 encode() and decode() methods are detected.* More rearrangements of data model Removed the pickle format information and NOE chapters of arguments from the relax manualstate user function definitions. * The GUI spin deselection part of Eliminated the NOE chapter has been shifted into the data model chapter. And the GUI loading of spins from a sequence file section has been completedState.test_state_pickle() system test as pickled states are no longer supported.* Added screenshots of Removed the ability to save and restore states using the spin viewer spin loading wizard sequence.read pagepickle module.* Redesign A pickled state is of the data model chapter of the user manualno use to relax anymore. It's removal is needed for Python 3 support. This includes So now everything defaults to the moving of all of the spin viewer window text and screenshots from the NOE chapterXML formatted output.* Shifted Python 3 fix - removed the spin viewer screenshots into their own directoryuse of the string module from generic_fns.* Changed the "View->Spin view" menu item to "View->Spin viewer"spectrum.* Created a directory Python 3 fix for screenshots of the spin viewer window operationrelax_io.open_write_file() function.* The NOE auto-analysis GUI test This now checks matches the support for Trp indole N data as well.* The spectrum.read_intensities user function now prints out a list behaviour of the intensities read open_read_file() in. This is that there are three different behaviours for opening bz2 and gz files for better user feedback as writing to what for the user function has actually donedifferent Python versions (one for Python 2, one for Python 3.0 to 3.2, and one for Python 3.3+). All byte streams have been eliminated as open_write_file() is for creating text files.* Created Python 3 fix for the GUI wizard _applyNoe.test_noe_analysis() method system test for executing the current page's _apply() method. This is for the GUI tests to simulate a click on the 'Apply' buttongrace.write precision changes.* Removed a debugging print out.* Modified For consistency between Python 2 and 3, the NOE system test to catch [httpshttp://gnawww.nmr-relax.orgcom/bugsmanual/?20120 bug #20120grace_write.html grace.write user function]outputs to 15 decimal places.* Lots of editing This increased precision will only be of use in the NOE chapter of the user manualrelax test suite.* Significant update of Python 3 fix for the NOE chapter of the user manualPipes.test_pipe_bundle() system test. The sample script used order of bundle names returned by generic_fns.pipes.bundle_names() is not guaranteed in this chapter was incredibly out of datePython 3.* Modified The C module compilation testing script now accepts the NOE system test to test the usage of Trp indole ¹⁵N data. This is to catch [https://gna.org/bugs/?20119 bug #20119].Python version as a first argument.* Added some Trp peak data The relax_io.open_read_file(backbone and indole N) to the Sparky steady-state NOE peak listsnow supports all Python versions over 2.4. This is in preparation required some really nasty hacks for Python 3.0, 3.1 and 3.2 with the modification of Bzip2Fixed and GzipFixed classes overriding the NOE system test to catch [https://gnaincomplete and buggy bz2.BZ2File and gzip.org/bugs/?20119 bug #20119]GzipFile modules, and being wrapped around io.* Modified the NOE sample script to include Trp indole NH dataTextIOWrapper().* Added a step-by-step tutorial for the GUI NOE auto-analysis IO module to the user manual. This includes 22 screenshots of all the stepsrelax information printout and dependency checks.* Added a section labelThe manual C module compilation script is now executable.* Added some Sparky info Renamed the 'scripts' directory to 'devel_scripts' so that users are less likely to ask about the Rx curve-fitting chapter of the user manualscripts.* Allowed Finished off the raggedbottom LaTeX setting as this is better for the screenshot layout in the user manual.C module compilation testing script.* Added the nth package a script for testing out the user manual LaTeX C module compilationon multiple Python targets.* The NOE chapter relax_fit specific analysis module now points to the recommendations in the Rx fitting chaptersupports both Python 2 and 3.* Added a new section called 'From spectra to peak intensities' to the Rx fitting chapter of the manual. This adds a number of recommendations for high quality relaxation ratesThe relaxation curve-fitting C module now supports compilation on both Python 2 and 3.* Added Created the Viles et alsimple Sequence., 2001 reference.* Small description edit for the relax_datatest_sequence_copy() system test to catch [https://gna.temp_control user functionorg/bugs/?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.zip' and 'run.* Created an initial rough version of py' attached to the RSDM chapter of the user manualbug report https://gna.org/bugs/?20213.* Better figure layout in The PDB now only contains Asp47, the NOE chapter of 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 graphicsPython 3 bug fix for the geometric structure module - another integer division to float problem.* Added more high resolution graphics for use The Mf.test_write_results system test can now select the correct file to compare against in the relax user manualPython 3.* Expanded The algorithm for determining if the size of the specific analysis graphics - mainly '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.* Python 3 fix for use in the relax user manualformat detection of results and save files.* Added Python 3 import fixes for the specific analysis graphics to the start of each chapter of the relax user manualgeneric_fns.structure package using relative paths.* Small edit Python 3 fix - removed the use of the 'Citations' chapter of string.lower() function in the relax user manualOpenDX mapping code.* Added EPS versions of Python 3 fix for the specific analysis graphics for use in the user manualframe order system tests.* Added As float to string conversions behave differently, the Fushman et al%., 1999 reference for consistency testing 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 introframe order analysis.* Shortened the Literature subsection of Python 3 bug fix for the intro chapter to point to the citations chapter. This part of the user manual is now redundantframe order analysis - another int division problem.* Small edits Python 3 fixes - eliminated all usage of the relax user manualdictionary has_key() calls as they are no longer present.* Edits to the abbreviations chapter of Python 2 and 3 support in the relax user manualgeneric_fns.relax_data module using 2to3.* Added another abbreviationOne print call was fixed after running 2to3.* Expansion of Python 3 bug fix for the abbreviations chapter of the relax user manualStructure.test_read_pdb_mol_2_model_scientific system tests. This is again an integer division problem returning a float.* Added a tonne of DOI numbers to Python 3 fix for the relax user manual bibliographytest_write_protein_sequence() unit test. This will simplify accessing these references is again a string verses byte verses unicode problem.* Python 3 fix for the userfunction docstring creation in the prompt UI mode.* Added and fixed DOI numbers for many bibliographic entriesAgain this is the problem of a division now returning a float rather than an int.* The LaTeX bibliography style Python 3 bug fix for PhD theses now includes the DOI hyperlinkN-state model target function setup. This is for The num_tensors variable needs to be an integer, but 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 is to add links to The built in max() function cannot handle the references within the relax user manualvalue of None, therefore the filter() function is used to remove all instances of None from the list.* Created the new 'Citations' chapter of Python 3 bug fix for the [http://www.nmr-relax user .com/manual/state_load. This is to clearly outline to the html state.load user the citations required for the various components of relaxfunction].* Added The header line of pickled states (rather than the Fushman 1999 reference and a few formatting fixes in other references.* Improvements to standard XML states) is of the b'Supported NMR theories' section of the user manual introductionbyte format. This includes is now converted to a string, and the addition of search expression is comparing it to the Morin and Gagne 2009 referenceraw string r"<\?xml".* Added the Morin Better support for both Python 2 and Gagne 2009 reference for 3 in the consistency testingrelax data store.* Added some more abbreviations to The 2to3 script was used on all of the relax user manualfiles in the data package.* Created a new chapter for Python 3 preparation - the relax user manual titled 'The relax data model'store (the data package) now supports both Python 2 and 3.* Fix for Python 3 fix - the pipe editor window screenshot width in the relax manualrelax_errors.AllRelaxErrors object is now a proper tuple.* Converted some more wizard graphics Due to the EPS format bad coding, it was previously a nested tuple. This nested tuple worked in Python 2, but is fatal for the user manualPython 3.* Updates and small expansion of Python 3 fixes - the intro chapter of character '\' is now properly escaped as '\\' in the relax user manualstereochemistry auto-analysis.* Fix for the test suite summary for Python 3. The user manual test suite now specifies the repository revision if a non-tagged version is builtruns, but fails miserably, under Python 3. * This enables easier tracking and editing Fix for the running of the manualtest suite under Python 3.* Updates The zip() function used in the loadTestsFromTestCase() function is now an iterator, so it needs to be passed through the generic_fns.mol_res_spin.id_string_doc documentation structurelist() function to generate a list.* Updated Fix for the screenshot of the pipe editor windowtest_parse_token_multi_element_name() unit test, as parse_token() no longer sorts.* Created EPS versions of a number of wizard graphics Python 3 fix for use in the user manualgeneric_fns.mol_res_spin.parse_token() function.* Removed some now useless whitespace from the top of each user function subsection of the manualMixed lists for int and string can no longer be sorted. This sort call is not needed anyway.* Redesigned Automatically converted the formatting of the user function chapter of the relax manualgeneric_fns. The fetch_docstrings.py now forces each user function to start in a new columnmol_res_spin module to support both Python 2 and 3. * This increases the size of the manualFor running relax with Python 2, but makes the reading of the user __builtin__.range() function documentation much easierhas been replaced with xrange. The user function class and function icons This causes large speed ups (speed that was lost with the earlier xrange() to range(128x128 format) are now placed between the top bar conversions), and the subsection title and are left and right justifiedmemory decreases. This prettification simply allows For example on one system, the user functions system test time decreased from 513.029s to be more quickly identified487.586s.* Large expansion of The compat module now has the relax icon setpy_version variable specifying if this is Python 2 or 3. * All 128x128 versions of Import fix for the icons used by OpenDX mapping package, recently broken with the user functions have been added as both PNG and gzipped EPS filesrelative import for Python 3 change. * A few gzipped SVG and non-sized icons have been added as wellMore usage of the is_unicode() function in the generic_fns.mol_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 files. A number of gzipped SVG icons has been added as wellgeneric_fns.mol_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 raise statements in preparation for the final section of 2to3 conversion.* Converted the relaxation curve-fitting chapterScientificPython PDB reader to support both Python 2 and 3. The Xmgrace screenshot and page references for __repr__() method was manually modified due to the 'list' variable clashing with the user functions have been added'list'type.* Added screenshots of Xmgrace displaying relaxation curvesCreated a new module for simultaneous Python 2 and 3 support in relax called 'compat'.* The fetch_docstrings.py Python 3 fixes - the list() function is now adds LaTeX labels used in combination with range() to each user function sectiongenerate the ordered list. This has range() in Python 3 is an iterator object (just as xrange was), so now the form of 'uf: ' followed by the user list() function name, and is for referencing purposes within the main texthas to be called.* Rewrote the relaxation curvePython 3 preparations -fitting chapter mass conversion of the relax manual. This chapter was quite out of date and was of no use all xrange() calls to modern relax versionsrange().* Redesign of how Created the GPL license is presented to the userspecial check_types. The old promptis_filetype() function for checking for files in all Python versions.* Python 3 - eliminated an unneeded xrange call.gpl module with * Python 3 - eliminated the version 2 use of the license has been deletedmap() function, as this behaves differently in Python 3. * Now Python 3 - removed the text form use of the docs/COPYING file string.lower() function as it is passed through pydocmissing in Python 3.pager * Python 3 fix for the 'relax information printout./relax --licence' and the prompt mode GPL object, and is simply printed The try blocks seem to STDOUT for the GUI help systemnow operate slightly differently in Python 3.* Import clean ups Python 2 fixes - the Python 3 fixes for the N-state model specific ScientificPython moduleimports broke Python 2.* Added Python 3 - the 'unit' argument cStringIO.StringIO import switches to the dipole_pairio.read_dist and dipole_pairStringIO if missing.set_dist user functions* Python 3 - relative module paths are now used for the test suite runner. * This 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 ==