Relax 4.0.1 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-08T20:27:17Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Added relax 4.0.2 to the infobox.

2016-05-13T15:38:01Z

Added relax 4.0.2 to the infobox.

Bugman: /* Links */ Added the Mail Archive release message link.

2015-12-16T13:01:13Z

Links: Added the Mail Archive release message link.

Bugman: /* Links */ Fixes for the links.

2015-12-16T13:00:03Z

Links: Fixes for the links.

Bugman: Added Gromacs links.

2015-12-15T13:24:39Z

Added Gromacs links.

Bugman: Added `tags throughout.`


2015-12-15T11:48:40Z
Added <code> tags throughout.
Show changes



Bugman: The bug report summary is now included in the link.
2015-12-15T11:30:31Z
The bug report summary is now included in the link.

				
				
				
				
				
				← Older revision
				Revision as of 11:30, 15 December 2015
				
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  * Updated all of relax to protect against future changes occurring in the numpy Python package.  From numpy version 1.9, the FutureWarning "__main__:1: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future." is seen in a large percentage of all relax's user functions.  This is caught and turned into a RelaxWarning with the same message.  The issue is that the behaviour of the comparison operators '==' and '!=' will change with future numpy versions.  These have been replaced with 'is' and 'is not' throughout the relax code base.  Changes have also been made to the [[minfx]] and [[bmrblib]] packages to match.   * Updated all of relax to protect against future changes occurring in the numpy Python package.  From numpy version 1.9, the FutureWarning "__main__:1: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future." is seen in a large percentage of all relax's user functions.  This is caught and turned into a RelaxWarning with the same message.  The issue is that the behaviour of the comparison operators '==' and '!=' will change with future numpy versions.  These have been replaced with 'is' and 'is not' throughout the relax code base.  Changes have also been made to the [[minfx]] and [[bmrblib]] packages to match.
  * More future protection against numpy changes.  The FutureWarning is "`rank` is deprecated; use the `ndim` attribute or function instead.  To find the rank of a matrix see `numpy.linalg.matrix_rank`."  Therefore the [http://www.nmr-relax.com/api/4.0/target_functions.n_state_model.N_state_opt-class.html#paramag_info N-state model target function method paramag_info()] has been updated to use the .ndim attribute and longer use numpy.rank() function.   * More future protection against numpy changes.  The FutureWarning is "`rank` is deprecated; use the `ndim` attribute or function instead.  To find the rank of a matrix see `numpy.linalg.matrix_rank`."  Therefore the [http://www.nmr-relax.com/api/4.0/target_functions.n_state_model.N_state_opt-class.html#paramag_info N-state model target function method paramag_info()] has been updated to use the .ndim attribute and longer use numpy.rank() function.
− * Created the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_23933_relax_data_read_ids Mf.test_bug_23933_relax_data_read_ids system test].  This is designed to catch [https://gna.org/bugs/?23933 bug #23933], the "NameError: global name 'ids' is not defined" problem when loading relaxation data.  A truncated version of the PDB file and relaxation data, the full versions of which are attached to the bug report, consisting solely of residues 329, 330, and 331 have been added to the test suite shared data directories, and the system test written to catch the NameError. + * Created the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_23933_relax_data_read_ids Mf.test_bug_23933_relax_data_read_ids system test].  This is designed to catch [https://gna.org/bugs/?23933 bug #23933, the "NameError: global name 'ids' is not defined" problem when loading relaxation data].  A truncated version of the PDB file and relaxation data, the full versions of which are attached to the bug report, consisting solely of residues 329, 330, and 331 have been added to the test suite shared data directories, and the system test written to catch the NameError.
  * Updated the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_23933_relax_data_read_ids Mf.test_bug_23933_relax_data_read_ids system test] to catch the RelaxMultiSpinIDError.  This allows the system test to pass, as a RelaxMultiSpinIDError is expected.   * Updated the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_23933_relax_data_read_ids Mf.test_bug_23933_relax_data_read_ids system test] to catch the RelaxMultiSpinIDError.  This allows the system test to pass, as a RelaxMultiSpinIDError is expected.
  * Updated the [[minfx]] and [[bmrblib]] versions in the release checklist document to 1.0.12 and 1.0.4.  This is to remove the numpy FutureWarning messages about the '== None' and '=! None' comparisons to numpy data structures, which in the future will change in behaviour.   * Updated the [[minfx]] and [[bmrblib]] versions in the release checklist document to 1.0.12 and 1.0.4.  This is to remove the numpy FutureWarning messages about the '== None' and '=! None' comparisons to numpy data structures, which in the future will change in behaviour.
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  * Adding 2 tutorial scripts.   * Adding 2 tutorial scripts.
  * Fix for small spin ID error in tutorial script.   * Fix for small spin ID error in tutorial script.
− * Created a system test for catching [https://gna.org/bugs/?24131 bug #24131].  This is the BMRB export failure when the SpinContainer object has no {{:S2}} attribute, as reported by Martin Ballaschk. + * Created a system test for catching [https://gna.org/bugs/?24131 bug #24131, the BMRB export failure when the SpinContainer object has no {{:S2}} attribute], as reported by Martin Ballaschk.
  * Modified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_bmrb_deposition Mf.test_bug_24131_bmrb_deposition system test] to check for the RelaxError.  The test results in a RelaxError, as the results file contains no selected spins.   * Modified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_bmrb_deposition Mf.test_bug_24131_bmrb_deposition system test] to check for the RelaxError.  The test results in a RelaxError, as the results file contains no selected spins.
− * Added the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_missing_interaction Mf.test_bug_24131_missing_interaction system test] to catch another problem.  This is part of [https://gna.org/bugs/?24131 bug #24131], the BMRB export failure with the SpinContainer object having no {{:S2}} value.  However the previous fix of skipping deselected spins introduced a new problem of relax still searching for the interatomic interactions for that deselected spin. + * Added the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_missing_interaction Mf.test_bug_24131_missing_interaction system test] to catch another problem.  This is part of [https://gna.org/bugs/?24131 bug #24131, the BMRB export failure with the SpinContainer object having no {{:S2}} value].  However the previous fix of skipping deselected spins introduced a new problem of relax still searching for the interatomic interactions for that deselected spin.
  <section end=changes/>   <section end=changes/>
    
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  <section begin=bugfixes/>   <section begin=bugfixes/>
  * Replicated titles in the [http://www.nmr-relax.com/manual/index.html HTML version of the relax manual], and hence replicated HTML file names overwriting earlier sections, have been eliminated.   * Replicated titles in the [http://www.nmr-relax.com/manual/index.html HTML version of the relax manual], and hence replicated HTML file names overwriting earlier sections, have been eliminated.
− * Fix for [https://gna.org/bugs/?23933 bug #23933].  This is the "NameError: global name 'ids' is not defined" problem when loading relaxation data.  The bug was introduced back in November 2014, and is due to some incomplete error handling code.  The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not been specified.  Now the correct RelaxMultiSpinIDError is raised.  The 'ids' variable did not exist - it was code that was planned to be added, but never was and was forgotten. + * Fix for [https://gna.org/bugs/?23933 bug #23933, the "NameError: global name 'ids' is not defined" problem when loading relaxation data].  The bug was introduced back in November 2014, and is due to some incomplete error handling code.  The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not been specified.  Now the correct RelaxMultiSpinIDError is raised.  The 'ids' variable did not exist - it was code that was planned to be added, but never was and was forgotten.
  * Fix for the CSA constant equation in the model-free chapter of the manual.  This was spotted by [https://mail-archive.com/relax-users%40gna.org/msg01776.html  Christina Möller and reported on the relax-users mailing list].   * Fix for the CSA constant equation in the model-free chapter of the manual.  This was spotted by [https://mail-archive.com/relax-users%40gna.org/msg01776.html  Christina Möller and reported on the relax-users mailing list].
  * Bug fix for the storage of the XML structural object in the state and results files.  Previously any objects added to cdp.structure (or any structure object) would not be saved by the [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#to_xml structural object to_xml() method] unless the function is explicitly modified to store that object.  Now all objects present will be converted to XML.   * Bug fix for the storage of the XML structural object in the state and results files.  Previously any objects added to cdp.structure (or any structure object) would not be saved by the [http://www.nmr-relax.com/api/4.0/lib.structure.internal.object.Internal-class.html#to_xml structural object to_xml() method] unless the function is explicitly modified to store that object.  Now all objects present will be converted to XML.
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  * Fix for running relax at a server with no graphical display and using matplotlib.  The error was found with the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_repeat_cpmg Relax_disp.test_repeat_cpmg system test].  And the error generated was: "QXcbConnection: Could not connect to display. Aborted (core dumped)".  The backend of matplotlib has to be changed.  This is for example described in: http://stackoverflow.com/questions/2766149/possible-to-use-pyplot-without-display and http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib.   * Fix for running relax at a server with no graphical display and using matplotlib.  The error was found with the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_repeat_cpmg Relax_disp.test_repeat_cpmg system test].  And the error generated was: "QXcbConnection: Could not connect to display. Aborted (core dumped)".  The backend of matplotlib has to be changed.  This is for example described in: http://stackoverflow.com/questions/2766149/possible-to-use-pyplot-without-display and http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib.
  * Modified the behaviour of the [http://www.nmr-relax.com/manual/bmrb_write.html bmrb.write user function] backend for a model-free analysis (fix for [https://gna.org/bugs/?24131 bug #24131]).  This is in the [http://www.nmr-relax.com/api/4.0/specific_analyses.model_free.api.Model_free-class.html#bmrb_write bmrb_write() method of the model-free analysis API].  Deselected spins are now skipped and a check has been added to be sure that spin data has been assembled.   * Modified the behaviour of the [http://www.nmr-relax.com/manual/bmrb_write.html bmrb.write user function] backend for a model-free analysis (fix for [https://gna.org/bugs/?24131 bug #24131]).  This is in the [http://www.nmr-relax.com/api/4.0/specific_analyses.model_free.api.Model_free-class.html#bmrb_write bmrb_write() method of the model-free analysis API].  Deselected spins are now skipped and a check has been added to be sure that spin data has been assembled.
− * Another fix for [https://gna.org/bugs/?24131 bug #24131].  This is the BMRB export failure when the SpinContainer object has no {{:S2}} attribute.  Now no data is stored in the BMRB file if a model-free model has not been set up for the spin.  This allows the test suite to pass. + * Another fix for [https://gna.org/bugs/?24131 bug #24131, the BMRB export failure when the SpinContainer object has no {{:S2}} attribute].  Now no data is stored in the BMRB file if a model-free model has not been set up for the spin.  This allows the test suite to pass.
− * Bug fix to allow the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_missing_interaction Mf.test_bug_24131_missing_interaction system test] to pass.  This is part of [https://gna.org/bugs/?24131 bug #24131], the BMRB export failure with the SpinContainer object having no {{:S2}} value.  The problem was when assembling the diffusion tensor data.  The [http://www.nmr-relax.com/api/4.0/pipe_control.mol_res_spin-module.html#spin_loop spin_loop() function] was being called, as the diffusion tensor is reported for all residues.  Therefore the skip_desel=True has been added to match the model-free part. + * Bug fix to allow the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.model_free.Mf-class.html#test_bug_24131_missing_interaction Mf.test_bug_24131_missing_interaction system test] to pass.  This is part of [https://gna.org/bugs/?24131 bug #24131, the BMRB export failure with the SpinContainer object having no {{:S2}} value].  The problem was when assembling the diffusion tensor data.  The [http://www.nmr-relax.com/api/4.0/pipe_control.mol_res_spin-module.html#spin_loop spin_loop() function] was being called, as the diffusion tensor is reported for all residues.  Therefore the skip_desel=True has been added to match the model-free part.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: Links to the API documentation.
2015-12-15T11:28:46Z
Links to the API documentation.
Show changes


Bugman: HTML formatting fix by converting -> to →.
2015-12-15T09:38:08Z
HTML formatting fix by converting -> to →.

				
				
				
				
				
				← Older revision
				Revision as of 09:38, 15 December 2015
				
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  * Removal of the definition of a fixed-width table column from the LaTeX manual preamble.  This is required as the definition breaks latex2html compatibility, causing a corruption in the figure numbering resulting in the images in the HTML to be essentially randomised.   * Removal of the definition of a fixed-width table column from the LaTeX manual preamble.  This is required as the definition breaks latex2html compatibility, causing a corruption in the figure numbering resulting in the images in the HTML to be essentially randomised.
  * Removal of the accents package to allow the HTML manual to be compiled.  The 'accents' LaTeX package is not compatible with latex2html, so the easiest fix is to eliminate the package.   * Removal of the accents package to allow the HTML manual to be compiled.  The 'accents' LaTeX package is not compatible with latex2html, so the easiest fix is to eliminate the package.
− * Manually rotated the frame order matrix element EPS manual figures, for latex2html compatibility.  The '90 rotate' command has been deleted and the bounding box permuted as 'a b c d' -> 'b -c d -a'.  This allows the angle argument in the \includegraphics{} command to be dropped, as latex2html does not recognise this.  It allows the figures to be visible in the [http://www.nmr-relax.com/manual/index.html HTML version of the manual]. + * Manually rotated the frame order matrix element EPS manual figures, for latex2html compatibility.  The '90 rotate' command has been deleted and the bounding box permuted as 'a b c d' → 'b -c d -a'.  This allows the angle argument in the \includegraphics{} command to be dropped, as latex2html does not recognise this.  It allows the figures to be visible in the [http://www.nmr-relax.com/manual/index.html HTML version of the manual].
  * Redesign of the frame order parameter nesting table in the manual for latex2html compatibility.  The table uses the tikz package, which is fatal for latex2html, even if not used.  Therefore the table in the docs/latex/frame_order/parameter_nesting.tex file has been converted into a standalone LaTeX document to create a cropped postscript version of the tikz formatted table.  A compilation script has been added as well.  The resultant *.ps file is now included into the PCS numerical integration section, rather than this section creating the tikz table.  All tikz preamble text has been removed to allow latex2html to run.   * Redesign of the frame order parameter nesting table in the manual for latex2html compatibility.  The table uses the tikz package, which is fatal for latex2html, even if not used.  Therefore the table in the docs/latex/frame_order/parameter_nesting.tex file has been converted into a standalone LaTeX document to create a cropped postscript version of the tikz formatted table.  A compilation script has been added as well.  The resultant *.ps file is now included into the PCS numerical integration section, rather than this section creating the tikz table.  All tikz preamble text has been removed to allow latex2html to run.
  * Workaround for latex2html not being able to handle the allrunes package or associated font.  In the preamble 'htmlonly' environment, the frame order symbols are redefined using the text 'Daeg' instead of the runic character ᛞ.   * Workaround for latex2html not being able to handle the allrunes package or associated font.  In the preamble 'htmlonly' environment, the frame order symbols are redefined using the text 'Daeg' instead of the runic character ᛞ.



Bugman: Link formatting.
2015-12-15T09:02:06Z
Link formatting.

				
				
				
				
				
				← Older revision
				Revision as of 09:02, 15 December 2015
				
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  <section begin=features/>   <section begin=features/>
− * Many improvements for the compilation of the HTML version of the relax manual (http://www.nmr-relax.com/manual/index.html). + * Many improvements for the compilation of the [http://www.nmr-relax.com/manual/index.html HTML version of the relax manual].
  * Updated relax to eliminate all FutureWarnings from numpy &ge; 1.9, to future-proof relax against upcoming numpy behaviour changes.   * Updated relax to eliminate all FutureWarnings from numpy &ge; 1.9, to future-proof relax against upcoming numpy behaviour changes.
  * Ability to handle replicated {{:R2eff}} data points by the [http://www.nmr-relax.com/manual/relax_disp_r2eff_read.html relax_disp.r2eff_read user function], but adding 0.001 to the frequency value for the replicated point.   * Ability to handle replicated {{:R2eff}} data points by the [http://www.nmr-relax.com/manual/relax_disp_r2eff_read.html relax_disp.r2eff_read user function], but adding 0.001 to the frequency value for the replicated point.
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  <section begin=changes/>   <section begin=changes/>
  * Fix for the rigid frame order model 2<sup>nd</sup> degree frame order matrix in the manual.  The wrong symbol was being used.   * Fix for the rigid frame order model 2<sup>nd</sup> degree frame order matrix in the manual.  The wrong symbol was being used.
− * Removed the newparagraph and newsubparagraph definitions from the LaTeX manual.  These were causing conflicts with latex2html, preventing the HTML version of the manual at http://www.nmr-relax.com/manual/index.html from being compiled.  These definitions are unnecessary for the current set up of the sectioning in the manual. + * Removed the newparagraph and newsubparagraph definitions from the LaTeX manual.  These were causing conflicts with latex2html, preventing the [http://www.nmr-relax.com/manual/index.html HTML version of the manual] from being compiled.  These definitions are unnecessary for the current set up of the sectioning in the manual.
− * Modified the short captions in the new frame models chapter of the manual.  The runic ᛞ character has been replaced simply by 'Daeg'.  This is due to incompatibilities with latex2html which prevents the HTML manual at http://www.nmr-relax.com/manual/index.html from being compiled. + * Modified the short captions in the new frame models chapter of the manual.  The runic ᛞ character has been replaced simply by 'Daeg'.  This is due to incompatibilities with latex2html which prevents the [http://www.nmr-relax.com/manual/index.html HTML manual] from being compiled.
  * Removal of the definition of a fixed-width table column from the LaTeX manual preamble.  This is required as the definition breaks latex2html compatibility, causing a corruption in the figure numbering resulting in the images in the HTML to be essentially randomised.   * Removal of the definition of a fixed-width table column from the LaTeX manual preamble.  This is required as the definition breaks latex2html compatibility, causing a corruption in the figure numbering resulting in the images in the HTML to be essentially randomised.
  * Removal of the accents package to allow the HTML manual to be compiled.  The 'accents' LaTeX package is not compatible with latex2html, so the easiest fix is to eliminate the package.   * Removal of the accents package to allow the HTML manual to be compiled.  The 'accents' LaTeX package is not compatible with latex2html, so the easiest fix is to eliminate the package.
− * Manually rotated the frame order matrix element EPS manual figures, for latex2html compatibility.  The '90 rotate' command has been deleted and the bounding box permuted as 'a b c d' -> 'b -c d -a'.  This allows the angle argument in the \includegraphics{} command to be dropped, as latex2html does not recognise this.  It allows the figures to be visible in the HTML version of the manual at http://www.nmr-relax.com/manual/index.html . + * Manually rotated the frame order matrix element EPS manual figures, for latex2html compatibility.  The '90 rotate' command has been deleted and the bounding box permuted as 'a b c d' -> 'b -c d -a'.  This allows the angle argument in the \includegraphics{} command to be dropped, as latex2html does not recognise this.  It allows the figures to be visible in the [http://www.nmr-relax.com/manual/index.html HTML version of the manual].
  * Redesign of the frame order parameter nesting table in the manual for latex2html compatibility.  The table uses the tikz package, which is fatal for latex2html, even if not used.  Therefore the table in the docs/latex/frame_order/parameter_nesting.tex file has been converted into a standalone LaTeX document to create a cropped postscript version of the tikz formatted table.  A compilation script has been added as well.  The resultant *.ps file is now included into the PCS numerical integration section, rather than this section creating the tikz table.  All tikz preamble text has been removed to allow latex2html to run.   * Redesign of the frame order parameter nesting table in the manual for latex2html compatibility.  The table uses the tikz package, which is fatal for latex2html, even if not used.  Therefore the table in the docs/latex/frame_order/parameter_nesting.tex file has been converted into a standalone LaTeX document to create a cropped postscript version of the tikz formatted table.  A compilation script has been added as well.  The resultant *.ps file is now included into the PCS numerical integration section, rather than this section creating the tikz table.  All tikz preamble text has been removed to allow latex2html to run.
  * Workaround for latex2html not being able to handle the allrunes package or associated font.  In the preamble 'htmlonly' environment, the frame order symbols are redefined using the text 'Daeg' instead of the runic character ᛞ.   * Workaround for latex2html not being able to handle the allrunes package or associated font.  In the preamble 'htmlonly' environment, the frame order symbols are redefined using the text 'Daeg' instead of the runic character ᛞ.
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  * Renamed the replicate title finding script.   * Renamed the replicate title finding script.
  * Removed the duplicate LaTeX title finding shell script.  This is now handled by the far more advanced Python script.   * Removed the duplicate LaTeX title finding shell script.  This is now handled by the far more advanced Python script.
− * The Scons compilation of the PDF and HTML manuals now checks for replicated titles.  A new replicate_title_check target has been added to the scons scripts.  This calls the find() method of the replicate LaTeX title finding script to determine if any titles are replicated, and if so the scons target returns with a sys.exit(1) call.  This target is set at the start of the user_manual_pdf, user_manual_pdf_nofetch, user_manual_html, user_manual_html_nofetch scons targets.  The result is that the manual cannot be compiled if replicate titles exist, forcing the titles to be changed.  The result will be that the HTML pages at http://www.nmr-relax.com/manual/ will all be unique, as replicated titles results in only one HTML page being created for all the sections. + * The Scons compilation of the PDF and HTML manuals now checks for replicated titles.  A new replicate_title_check target has been added to the scons scripts.  This calls the find() method of the replicate LaTeX title finding script to determine if any titles are replicated, and if so the scons target returns with a sys.exit(1) call.  This target is set at the start of the user_manual_pdf, user_manual_pdf_nofetch, user_manual_html, user_manual_html_nofetch scons targets.  The result is that the manual cannot be compiled if replicate titles exist, forcing the titles to be changed.  The result will be that the [http://www.nmr-relax.com/manual/ HTML pages] will all be unique, as replicated titles results in only one HTML page being created for all the sections.
  * Elimination of replicated titles in the LaTeX sources that the new frame order chapters introduced.   * Elimination of replicated titles in the LaTeX sources that the new frame order chapters introduced.
  * Removal of an old replicated title in the LaTeX sources for the manual.  This is the title 'Model-free analysis' which is used for the entire specific analysis chapter as well as for the model-free analysis section of the values, gradients, and Hessians for optimisation chapter.   * Removal of an old replicated title in the LaTeX sources for the manual.  This is the title 'Model-free analysis' which is used for the entire specific analysis chapter as well as for the model-free analysis section of the values, gradients, and Hessians for optimisation chapter.
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  * Updated the minfx and bmrblib versions in the release checklist document to 1.0.12 and 1.0.4.  This is to remove the numpy FutureWarning messages about the '== None' and '=! None' comparisons to numpy data structures, which in the future will change in behaviour.   * Updated the minfx and bmrblib versions in the release checklist document to 1.0.12 and 1.0.4.  This is to remove the numpy FutureWarning messages about the '== None' and '=! None' comparisons to numpy data structures, which in the future will change in behaviour.
  * Increased the Gna! news item sectioning depth in the release checklist document.   * Increased the Gna! news item sectioning depth in the release checklist document.
− * Expanded the description of the [http://www.nmr-relax.com/manual/sequence_attach_protons.html sequence.attach_protons user function].  This follows from http://thread.gmane.org/gmane.science.nmr.relax.user/1849/focus=1855 . + * Expanded the description of the [http://www.nmr-relax.com/manual/sequence_attach_protons.html sequence.attach_protons user function].  This follows from http://thread.gmane.org/gmane.science.nmr.relax.user/1849/focus=1855.
  * Added initial data for testing data from Paul Schanda.  This will demonstrate that there are several possibilities to enhance the {{:R2eff}} point method.   * Added initial data for testing data from Paul Schanda.  This will demonstrate that there are several possibilities to enhance the {{:R2eff}} point method.
  * Added the Relax_disp.test_paul_schanda_nov_2015 system test.  This will catch the loaning of "nan" values.   * Added the Relax_disp.test_paul_schanda_nov_2015 system test.  This will catch the loaning of "nan" values.
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  * Replicated titles in the HTML version of the relax manual (http://www.nmr-relax.com/manual/index.html), and hence replicated HTML file names overwriting earlier sections, have been eliminated.   * Replicated titles in the HTML version of the relax manual (http://www.nmr-relax.com/manual/index.html), and hence replicated HTML file names overwriting earlier sections, have been eliminated.
  * Fix for [https://gna.org/bugs/?23933 bug #23933].  This is the "NameError: global name 'ids' is not defined" problem when loading relaxation data.  The bug was introduced back in November 2014, and is due to some incomplete error handling code.  The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not been specified.  Now the correct RelaxMultiSpinIDError is raised.  The 'ids' variable did not exist - it was code that was planned to be added, but never was and was forgotten.   * Fix for [https://gna.org/bugs/?23933 bug #23933].  This is the "NameError: global name 'ids' is not defined" problem when loading relaxation data.  The bug was introduced back in November 2014, and is due to some incomplete error handling code.  The problem is that the spin type that the relaxation data belongs to (@N vs. @H) has not been specified.  Now the correct RelaxMultiSpinIDError is raised.  The 'ids' variable did not exist - it was code that was planned to be added, but never was and was forgotten.
− * Fix for the CSA constant equation in the model-free chapter of the manual.  This was spotted by Christina Möller and reported on the relax-users mailing list at https://mail-archive.com/relax-users%40gna.org/msg01776.html . + * Fix for the CSA constant equation in the model-free chapter of the manual.  This was spotted by [https://mail-archive.com/relax-users%40gna.org/msg01776.html  Christina Möller and reported on the relax-users mailing list].
  * Bug fix for the storage of the XML structural object in the state and results files.  Previously any objects added to cdp.structure (or any structure object) would not be saved by the structural object to_xml() method unless the function is explicitly modified to store that object.  Now all objects present will be converted to XML.   * Bug fix for the storage of the XML structural object in the state and results files.  Previously any objects added to cdp.structure (or any structure object) would not be saved by the structural object to_xml() method unless the function is explicitly modified to store that object.  Now all objects present will be converted to XML.
  * Fix for the relaxation dispersion analysis in the GUI, as caught by the Relax_disp.test_paul_schanda_nov_2015 GUI test.  When loading from a script state file, the value of "None" can be present.  This is now set to the standard values.   * Fix for the relaxation dispersion analysis in the GUI, as caught by the Relax_disp.test_paul_schanda_nov_2015 GUI test.  When loading from a script state file, the value of "None" can be present.  This is now set to the standard values.
− * Fix for running relax at a server with no graphical display and using matplotlib.  The error was found with the Relax_disp.test_repeat_cpmg system test.  And the error generated was: "QXcbConnection: Could not connect to display. Aborted (core dumped)".  The backend of matplotlib has to be changed.  This is for example described in: http://stackoverflow.com/questions/2766149/possible-to-use-pyplot-without-display http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib. + * Fix for running relax at a server with no graphical display and using matplotlib.  The error was found with the Relax_disp.test_repeat_cpmg system test.  And the error generated was: "QXcbConnection: Could not connect to display. Aborted (core dumped)".  The backend of matplotlib has to be changed.  This is for example described in: http://stackoverflow.com/questions/2766149/possible-to-use-pyplot-without-display and http://stackoverflow.com/questions/8257385/automatic-detection-of-display-availability-with-matplotlib.
  * Modified the behaviour of the [http://www.nmr-relax.com/manual/bmrb_write.html bmrb.write user function] backend for a model-free analysis (fix for [https://gna.org/bugs/?24131 bug #24131]).  This is in the bmrb_write() method of the model-free analysis API.  Deselected spins are now skipped and a check has been added to be sure that spin data has been assembled.   * Modified the behaviour of the [http://www.nmr-relax.com/manual/bmrb_write.html bmrb.write user function] backend for a model-free analysis (fix for [https://gna.org/bugs/?24131 bug #24131]).  This is in the bmrb_write() method of the model-free analysis API.  Deselected spins are now skipped and a check has been added to be sure that spin data has been assembled.
  * Another fix for [https://gna.org/bugs/?24131 bug #24131].  This is the BMRB export failure when the SpinContainer object has no {{:S2}} attribute.  Now no data is stored in the BMRB file if a model-free model has not been set up for the spin.  This allows the test suite to pass.   * Another fix for [https://gna.org/bugs/?24131 bug #24131].  This is the BMRB export failure when the SpinContainer object has no {{:S2}} attribute.  Now no data is stored in the BMRB file if a model-free model has not been set up for the spin.  This allows the test suite to pass.

@@ Line 150: / Line 150: @@
 * [http://wiki.nmr-relax.com/Relax_4.0.1 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2519 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2519|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/69 Gmane mailing list archive].
 * [https://www.mail-archive.com/relax-announce@gna.org/msg00059.html Mail Archive]

@@ Line 4: / Line 4: @@
 | version  = 4.0.1
 | prev     = 4.0.0
 | keywords = Google Cloud Computing, Numpy, PDB, Principle component analysis, relaxation dispersion
 | type     = Major feature and bugfix

@@ Line 151: / Line 151: @@
 * [https://gna.org/forum/forum.php?forum_id=2519 Gna! news item].
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/69 Gmane mailing list archive].
 * [https://mail.gna.org/public/relax-announce/2015-12/msg00000.html Local archives].
 * [https://marc.info/?l=relax-announce&m=145021808817686&w=2 Mailing list ARChives (MARC)].

@@ Line 151: / Line 151: @@
 * [https://gna.org/forum/forum.php?forum_id=2519 Gna! news item].
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/69 Gmane mailing list archive].
-* [https://mail.gna.org/public/relax-announce/2015-12/msg00001.html Local archives].
+* [https://mail.gna.org/public/relax-announce/2015-12/msg00000.html Local archives].
-* [https://marc.info/?l=relax-announce&m=144485916126262&w=2 Mailing list ARChives (MARC)].
+* [https://marc.info/?l=relax-announce&m=145021808817686&w=2 Mailing list ARChives (MARC)].
 {{:Softpedia}}

@@ Line 104: / Line 104: @@
 * Modified the [http://www.nmr-relax.com/api/4.0/pipe_control.structure.main-module.html#assemble_structural_coordinates assemble_structural_coordinates() method] to return more information.  This is from the [http://www.nmr-relax.com/api/4.0/pipe_control.structure.main-module.html pipe_control.structure.main module].  The <code>lists</code> boolean argument is now accepted which will cause the function to additionally return the object ID list per molecule, the model number list per molecule, and the molecule name list per molecule.
 * The [http://www.nmr-relax.com/manual/structure_pca.html structure.pca user function] now creates graphs of the PC projections.  This includes PC1 vs. PC2, PC2 vs. PC3, etc.
-* Added the Gromacs PCA results for the distribution.pdb file.  This includes a script used to execute all parts of Gromacs and all output files.
+* Added the [http://www.gromacs.org/ Gromacs] PCA results for the distribution.pdb file.  This includes a script used to execute all parts of Gromacs and all output files.
-* Updated the Gromacs PCA results for the newest Gromacs version (5.1.1).
+* Updated the Gromacs PCA results for the [http://manual.gromacs.org/documentation/5.1.1/ReleaseNotes/index.html newest 5.1.1 Gromacs version].
 * Created an initial [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca system test].  This executes the new [http://www.nmr-relax.com/manual/structure_pca.html structure.pca user function], and checks if data is stored in <code>cdp.structure</code>.
 * Improved the graphs in the backend of the [http://www.nmr-relax.com/manual/structure_pca.html structure.pca user function].  The graphs are now clustered so that different models of the same structure in the same data pipe are within one graph set.  The graph header has also been improved.
-* Expanded the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca system test] checks to compare to the values from Gromacs.
+* Expanded the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca system test] checks to compare to the values from [http://www.gromacs.org/ Gromacs].
 * A weighted mean structure can now be calculated.  This is for the [http://www.nmr-relax.com/api/4.0/lib.structure.statistics-module.html#calc_mean_structure calc_mean_structure() function] of the [http://www.nmr-relax.com/api/4.0/lib.structure.statistics-module.html relax library module lib.structure.statistics].  Weights can now be supplied for each structure to allow for a weighted mean to be calculated and returned.
 * Added support for <code>observer</code> structures in the [http://www.nmr-relax.com/manual/structure_pca.html structure.pca user function].  This allows a subset of the structures used in the PC analysis to have zero weight so that these structures can be used for comparison purposes.  The <code>obs_pipes</code>, <code>obs_models</code>, and <code>obs_molecules</code> arguments have been added to the user function front end.  The backend uses this to create an array of weights for each structure.  And the [http://www.nmr-relax.com/api/4.0/lib.structure.pca-module.html lib.structure.pca functions] use the zero weights to remove the observer structures from the PC mode calculations.

Relax 4.0.1 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Added relax 4.0.2 to the infobox.

Bugman: /* Links */ Added the Mail Archive release message link.

Bugman: /* Links */ Fixes for the links.

Bugman: Added Gromacs links.

Bugman: Added tags throughout.

Bugman: The bug report summary is now included in the link.

Bugman: Links to the API documentation.

Bugman: HTML formatting fix by converting -> to →.

Bugman: Link formatting.

Bugman: Added `tags throughout.`