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{{infobox relax release| version = 1.3.16| prev = 1.3.15| next = 2.2.0| keywords = Manual| type = Documentation| date = 11 May 2012| manual = yes}} == Description ==
<section begin=description/>
This is mainly a documentation release. The [http://www.nmr-relax.com/manual/index.html relax user manual] has been significantly updated - changes include the expansion and completion of the [http://www.nmr-relax.com/manual/Model_free_analysis.html model-free analysis chapter], addition of graphical user interface (GUI) screenshots and descriptions, a description of [https://{{gna link|url=gna.org/users/varioustoxins |text=Gary Thompson's] }} [http://www.nmr-relax.com/manual/multi_processor_framework.html multi-processor framework], and general updates and improvements throughout. For those who install relax using the scons 'install' target, the pyc and pyo files are now properly created for faster startup. The Bruker Protein Dynamics Centre user function class 'pdc' has been renamed to 'bruker' because of Bruker's absorption of the PDC into the Bruker Dynamics Centre. These user functions, as well as the BMRB user functions, have been added to the menu system in the GUI. Finally a test suite bug triggered in the Fink relax installation has been eliminated. If you would like improved documentation or would like to use any of the other changes, please update to this version.
<section end=description/>
== Download ==
<section begin=download/>
<section end=download/>
== CHANGES file ==
<section begin=metadata/>
<section end=metadata/>
=== Features ===
<section begin=features/>
* The scons 'install' target now creates both *.pyc and *.pyo files during installation - this should result in faster relax startup times.
* The test suite now passes on the Fink relax installation on Mac OS X as the ancient and very dead PyXML module is now being detected and worked around.
* Renamed the 'pdc' user function class to [http://www.nmr-relax.com/api/1.3/prompt.bruker-module.html 'bruker' ] and removed all references to 'protein' - this is due to the Bruker absorption of the Protein Dynamics Centre into the Bruker Dynamics Centre announced at https://mail.{{gna.org/public/mailing list url|relax-users/2012-04/msg00011.html }} (Message-id: <4F7AE13B.6010309@bruker.de>) by Dr. Klaus-Peter Neidig (peter dott neidig att bruker-biospin dott de).* Updates and improvements throughout the [http://www.nmr-relax.com/manual/index.html relax user manual].* Added a new section to the introduction chapter of the user manual for [https://{{gna link|url=gna.org/users/varioustoxins |text=Gary Thompson's] }} [http://www.nmr-relax.com/manual/multi_processor_framework.html multi-processor framework].
* Added screenshots and descriptions of the graphical user interface (GUI) to the introduction and all of the analysis chapters of the relax user manual.
* The GUI and logging/teeing modes are now compatible with each other.
<section end=features/>
=== Changes ===
<section begin=changes/>
* Improved debugging of the observers in the status singleton object.
* Changed the behaviour of the [http://www.nmr-relax.com/api/1.3/arg_check -module .html arg_check module] so that the functions can return answers.* The [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.bmrb.Bmrb-class.html#test_bmrb_rw Bmrb.test_bmrb_rw GUI test ] now uses the base [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.base_classes.GuiTestCase-class.html#execute_uf execute_uf() method ] for the [http://www.nmr-relax.com/manual/pipe_create.html pipe.create ] call - this is part of the simplification of the user function interfaces.* A number of the pipe GUI user function front ends now use the [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html wizard page ] element_*() methods to simplify the code base.* The [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html#element_string_list wizard page element_string_list() method ] can now create the special Combo_list objects.* Created the [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html#ResetChoices wizard page ResetChoices() method ] for resetting the list of values in a ComboBox.* Created a [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html#Clear Clear() wizard page method ] for clearing a specific GUI element.* The [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html#element_string wizard page element_string() GUI element creator read_only flag ] now defaults to False.* The [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value-class.html read_only=True flag to wizard_elements.Base_value ] now sets a TextCtrl to the background colour.* The [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value-class.html#SetValue wizard_elements.Base_value.SetValue() method ] now works properly with the ComboBox.* The [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value -class .html wizard_elements.Base_value class] now can set the element to be read only.* Created [http://www.nmr-relax.com/api/1.3/generic_fns.pipes-module.html#PIPE_DESC_LIST generic_fns.pipes.PIPE_DESC_LIST ] which is the PIPE_DESC as a list, sorted by VALID_TYPES (to be used in the GUI user functions).* Better ComboBox support in [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value -class .html wizard_elements.Base_value class] - now strings and data are separate (if the data is supplied), and the GetValue() method now returns the client data rather than the string value.* Modified the [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value-class.html wizard_elements.Base_value base GUI element class ] to handle combo boxes.* The [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.bmrb.Bmrb-class.html#test_bmrb_rw Bmrb.test_bmrb_rw GUI test ] now uses the new [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.base_classes.GuiTestCase-class.html#execute_uf execute_uf() ] method for the [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation user function].* Created the [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.base_classes.GuiTestCase-class.html#execute_uf GUI test base method execute_uf() ] for executing a user function.* The [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation] GUI user function now uses the new [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html wizard page ] element_*() methods for the GUI elements.* Created a [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Integer-class.html new wizard element for inputting integers].* Created a [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.String-class.html new wizard element for inputting strings].* Created the [http://www.nmr-relax.com/api/1.3/test_suite.gui_tests.bmrb.Bmrb-class.html#test_bmrb_rw Bmrb.test_bmrb_rw GUI test].* Completed the GUI interface for the [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation user function].* Created a [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.String_list_of_lists-class.html new wizard GUI element for lists of lists of strings].* Abstracted out most of the [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.String_list-class.html String_list wizard element ] into the [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.List-class.html List base class].* The [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation] GUI user function now uses the new wizard page string list GUI element.* Completed the [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.String_list-class.html wizard string list GUI element].
* Added the edit-rename Oxygen icons.
* Created a [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.String_list-class.html new String_list wizard GUI element class ] and associated [http://www.nmr-relax.com/api/1.3/gui.wizard.Wiz_page-class.html#element_string_list element_string_list() method].
* Created a new infrastructure in the wizards for handling more advanced GUI elements.
* The [http://www.nmr-relax.com/api/1.3/test_suite.system_tests.model_free.Mf-class.html#test_write_results Mf.test_write_results system test ] now checks for the ancient PyXML.* Added the xml module import tests to the [http://www.nmr-relax.com/api/1.3/dep_check-module.html dep_check module].
* The relax system information print out now includes information about the XML modules.
* Added an initial but far from complete [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation user function] page and menu element.
* Added the BMRB icon in various sizes to the graphics directory and icon paths.
* Updated all the [http://www.nmr-relax.com/api/1.3/prompt.bmrb-module.html BMRB user function front ends ] to the modern docstring design.
* Created a special Bruker add icon for use in the relaxation data GUI element.
* Added a button to the relaxation data GUI element for calling the [http://www.nmr-relax.com/manual/bruker.readbruker_read.html bruker.read user function].* Improved the [http://www.nmr-relax.com/manual/bruker.readbruker_read.html bruker.read user function] docstring.* Created the [http://www.nmr-relax.com/manual/bruker.readbruker_read.html bruker.read] GUI user function page and menu entry.
* Added the Bruker logo in various formats for use in the relax GUI.
* Converted the [http://www.nmr-relax.com/manual/bruker.readbruker_read.html bruker.read user function] prompt interface to the new design.
* Renamed the PDC to Bruker DC in the test suite.
* Updated the [http://www.nmr-relax.com/manual/relax_development.html development chapter of the relax user manual ] to be more current - this includes removing the text saying that the GUI is yet to be coded!
* Added mpi4py to the list of relax dependencies in the manual.
* Added GUI sections to the end of the NOE, R1R<sub>1</sub>+R2 R<sub>2</sub> and model-free chapters of the user manual.* The [http://www.nmr-relax.com/manual/List_of_Figures.html list of figures in the relax user manual ] is now on a new page.* Updated the [http://www.nmr-relax.com/manual/Open_source_infrastructure.html open source infrastructure chapter of the relax user manual].* Added a screenshot of the new [[relax 1.3.15 ]] version in script mode.* Significant updates to the [http://www.nmr-relax.com/manual/Introduction.html introduction chapter of the relax user manual]: The text has been updated to match the current relax versions. All mention of the dead SRLS theory has been eliminated. Screenshots of all the GUI windows and analyses have been added to prettify the chapter, and the text for the GUI has been rewritten for the new GUI design.* Added a number of GUI screenshots for use in the [www.nmr-relax.com/manual/index.html relax user manual ] - these were taken from http://www.nmr-relax.com/screenshots.html.* Added colons to all entries of the [http://www.nmr-relax.com/manual/Abbreviations.html abbreviation chapter in the relax user manual].* Updated and completed the [http://www.nmr-relax.com/manual/Installation_instructions.html installation chapter of the relax user manual ] - a lot of the text was 4-6 years out of date.
* Some small edits to the release checklist document.
* Removed more maths from the HTML user manual section titles.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* Improved error reporting for multiple vectors in a model-free analysis ([https://gna.org/bugs/?18807 bug #18807]).
* Updated the [http://www.nmr-relax.com/manual/deselect.readdeselect_read.html deselect.read user function] call in the noe.py sample script to match relax_fit.py ([httphttps://gna.org/bugs/?19717 bug #19717]).* The relax_fit.py sample script [http://www.nmr-relax.com/manual/deselect.readdeselect_read.html deselect.read user function] now has all columns specified ([httphttps://gna.org/bugs/?19717 bug #19717]).* Improved the error message system for the spin ID matching multiple spins ([httphttps://gna.org/bugs/?19717 bug #19717]).* Fix for the test suite GUI tests - one of the state system tests was removing the frame order analysis from the [http://www.nmr-relax.com/api/1.3/generic_fns.pipes-module.html#VALID_TYPES generic_fns.pipes.VALID_TYPES list ] with a pop() call.* Simplified the [http://www.nmr-relax.com/api/1.3/gui.wizard_elements.Base_value-class.html#ResetChoices wizard_elements.Base_value ResetChoices() method ] - this is an attempt to fix some racing conditions under wxGTK, triggered in the test suite.* Fix for the [http://www.nmr-relax.com/manual/bmrb.citationbmrb_citation.html bmrb.citation user function] documentation.* The [http://www.nmr-relax.com/api/1.3/test_suite.system_tests.model_free.Mf-class.html#test_write_results Mf.test_write_results system test ] now checks for the ancient PyXML - this ancient version from 2004 which should be eliminated, if installed, causes the toprettyxml() changes in Python 2.7.3 to be overridden.
* The alignment tensor user functions can now all handle the situation whereby no tensors exist.
* Fix for the scons 'install' target for the byte-compilation of the *.pyc files.
* Fix for the chi2 χ<sup>2</sup> references in the [http://www.nmr-relax.com/manual/Optimisation_of_relaxation_data_values_gradients_and_Hessians.html maths chapter of the relax user manual].
* Fix for the ANSI escape sequences for colouring text for when an isatty() method does not exist.
* Fix for the creation of the HTML user manual http://www.nmr-relax.com/manual/index.html file.
<section end=bugfixes/>
== Links == <section begin=links/>For reference, the following links are also part of the announcement for this release:* [http://wiki.nmr-relax.com/Relax_1.3.16 Official release notes]* {{gna link|url=gna.org/forum/forum.php?forum_id=2348|text=Gna! news item}}* [http://article.gmane.org/gmane.science.nmr.relax.announce/4 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00028.html Mail archive]* [https://mail.gna.org/public/relax-announce/2012-05/msg00001.html Local archives]* [http://marc.info/?l=relax-announce&m=135070664825020&w=2 MARC]<section end=links/> == Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
{{:relax release see also}}
[[Category:Documentation]]