Relax 4.0.2 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link.

2020-10-08T20:20:48Z

Links: Fix the broken Gna! forum link.

Bugman: /* Bugfixes */ Switch to the {{gna bug link}} template to fix the broken links.

2020-10-08T20:17:58Z

Bugfixes: Switch to the {{gna bug link}} template to fix the broken links.

Bugman: Added relax 4.0.3 to the infobox.

2016-10-28T15:52:07Z

Added relax 4.0.3 to the infobox.

Bugman: /* Links */ Updated the MARC link.

2016-05-17T12:29:00Z

Links: Updated the MARC link.

Bugman: Fix for the Gna! news link.

2016-05-13T17:03:39Z

Fix for the Gna! news link.

Bugman: Added `tags throughout.`


2016-05-13T16:46:37Z
Added <code> tags throughout.

				
				
				
				
				
				← Older revision
				Revision as of 16:46, 13 May 2016
				
Line 40:
Line 40:
    
  <section begin=changes/>   <section begin=changes/>
− * Improved formatting for the \yes LaTeX command for the [http://www.nmr-relax.com/manual/ HTML manual].  This now inputs the raw HTML character for a tick. + * Improved formatting for the <code>\yes</code> LaTeX command for the [http://www.nmr-relax.com/manual/ HTML manual].  This now inputs the raw HTML character for a tick.
  * The replicate title finding script now processes short titles as well.  This shows that the Frame_order.html file will be conflicting and overwritten.   * The replicate title finding script now processes short titles as well.  This shows that the Frame_order.html file will be conflicting and overwritten.
  * Avoidance of a replicated title in the frame order chapter of the manual.   * Avoidance of a replicated title in the frame order chapter of the manual.
− * Added some unicode characters for improved formatting of the CHANGES file. + * Added some unicode characters for improved formatting of the <code>CHANGES</code> file.
  * A number of updates for the release checklist document.  This should make it easier to replicate the full release process.   * A number of updates for the release checklist document.  This should make it easier to replicate the full release process.
  * Update the release checklist document.  The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release.   * Update the release checklist document.  The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release.
  * Added a check for the total argument for the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function].  The maximum value is 9999, as the PDB format cannot accept more models.   * Added a check for the total argument for the [http://www.nmr-relax.com/manual/frame_order_distribute.html frame_order.distribute user function].  The maximum value is 9999, as the PDB format cannot accept more models.
− * Creation of the [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function].  This simply resets the helices and sheets data structures in the internal structural object to []. + * Creation of the [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function].  This simply resets the helices and sheets data structures in the internal structural object to <code>[]</code>.
  * Updated the copyright notices for 2016.   * Updated the copyright notices for 2016.
  * Created a short [http://www.nmr-relax.com/api/4.0/info.Info_box-class.html Info_box] copyright string for displaying in the main GUI window.  This shows the full range of copyright dates.   * Created a short [http://www.nmr-relax.com/api/4.0/info.Info_box-class.html Info_box] copyright string for displaying in the main GUI window.  This shows the full range of copyright dates.
− * Added the spin_num boolean argument to the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Setting this flag to False will cause the spin number information to be ignored when creating the spin containers.  This allows for better support of homologous structures but with different PDB atom numbering.  The default flag value is True, preserving the old behaviour. + * Added the <code>spin_num</code> boolean argument to the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Setting this flag to <code>False</code> will cause the spin number information to be ignored when creating the spin containers.  This allows for better support of homologous structures but with different PDB atom numbering.  The default flag value is <code>True</code>, preserving the old behaviour.
− * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions. + * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the <code>spin_num</code> flag set to <code>False</code>, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.
  * Fix for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_read_pdb_internal3 Structure.test_read_pdb_internal3 system test].  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument.   * Fix for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_read_pdb_internal3 Structure.test_read_pdb_internal3 system test].  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument.
− * In the GUI the user functions [http://www.nmr-relax.com/manual/sys_info.html sys_info] and [http://www.nmr-relax.com/manual/time.html time] are now grouped into a "system" subclass.  This is to prepare for other system related functions. + * In the GUI the user functions [http://www.nmr-relax.com/manual/sys_info.html sys_info] and [http://www.nmr-relax.com/manual/time.html time] are now grouped into a <code>system</code> subclass.  This is to prepare for other system related functions.
  * Added a new 16x16 icon for the oxygen folder-favorites icon.   * Added a new 16x16 icon for the oxygen folder-favorites icon.
− * Adding a new file at lib.system.  This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. + * Adding a new file at <code>lib.system</code>.  This file will contain different functions related to Python <code>os</code> and <code>system</code> related functions.  For example changing directory or printing working directory.
− * In lib.__init__, adding the filename for system.py. + * In <code>lib.__init__</code>, adding the filename for <code>system.py</code>.
  * Renaming the folder-favorites icon.   * Renaming the folder-favorites icon.
  * Deleting the old folder-favorites icon.   * Deleting the old folder-favorites icon.
− * Adding a new graphics variable: WIZARD_OXYGEN_PATH, to use oxygen icons with size of 200px. + * Adding a new graphics variable: <code>WIZARD_OXYGEN_PATH</code>, to use oxygen icons with size of 200px.
  * Adding the new user function [http://www.nmr-relax.com/manual/system_cd.html system.cd].  This is to change the current working directory.   * Adding the new user function [http://www.nmr-relax.com/manual/system_cd.html system.cd].  This is to change the current working directory.
  * Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image.   * Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image.
Line 68:
Line 68:
  * Adding a relax GUI menu for changing the current working directory.   * Adding a relax GUI menu for changing the current working directory.
  * Adding a menu item for changing the current working directory.   * Adding a menu item for changing the current working directory.
− * Adding a verbose True/False for the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#pwd lib.system.pwd() function]. + * Adding a verbose <code>True</code>/<code>False</code> for the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#pwd lib.system.pwd() function].
  * Storing the current working directory as a GUI variable.   * Storing the current working directory as a GUI variable.
  * Adding a toolbar button for changing the current working directory.   * Adding a toolbar button for changing the current working directory.
Line 77:
Line 77:
  * Letting the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#cd lib.system.cd function] notify the observer, when changing directory.   * Letting the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#cd lib.system.cd function] notify the observer, when changing directory.
  * Letting the current working directory be printed in the statusbar in the bottom.   * Letting the current working directory be printed in the statusbar in the bottom.
− * Updating self.system_cwd_path when a directory change is observed. + * Updating <code>self.system_cwd_path</code> when a directory change is observed.
  * For the four auto-analysis methods, the default results directory is now the current working directory instead of the launch directory.   * For the four auto-analysis methods, the default results directory is now the current working directory instead of the launch directory.
− * Changing the keyboard shortcut for changing the working directory to Ctrl+W.  Since Ctrl+C is often used for copying (from the terminal). + * Changing the keyboard shortcut for changing the working directory to <code>Ctrl+W</code>.  Since <code>Ctrl+C</code> is often used for copying (from the terminal).
  * Fix for GUI prompt bug, where ANSI escape characters should not be printed when interpreter is inherited from wxPython.   * Fix for GUI prompt bug, where ANSI escape characters should not be printed when interpreter is inherited from wxPython.
  * Added a newline character after printing the script.   * Added a newline character after printing the script.
  * Optimising the width of the statusbar.   * Optimising the width of the statusbar.
− * When the user function script is called, a notification of pipe_alteration is made.  This will force the GUI to update, and make sure that it is up to-date. + * When the user function script is called, a notification of <code>pipe_alteration</code> is made.  This will force the GUI to update, and make sure that it is up to date.
  * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] → [http://www.nmr-relax.com/manual/system_time.html system.time] user function change.   * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] → [http://www.nmr-relax.com/manual/system_time.html system.time] user function change.
  * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.   * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.
  * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  The test uses his data and script to trigger the bug.   * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  The test uses his data and script to trigger the bug.
  * Simplified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_bug_24601_r2eff_missing_data Relax_disp.test_bug_24601_r2eff_missing_data system test].  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system).   * Simplified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_bug_24601_r2eff_missing_data Relax_disp.test_bug_24601_r2eff_missing_data system test].  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system).
− * Fix for the independence of the relax library.  As lib.system was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the [http://www.nmr-relax.com/api/4.0/pipe_control-module.html pipe_control package]. + * Fix for the independence of the relax library.  As <code>lib.system</code> was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the [http://www.nmr-relax.com/api/4.0/pipe_control-module.html pipe_control package].
− * Added some missing oxygen icons to allow the relax manual to compile.  These are the 128x128 EPS versions of the places/folder-development.png and places/folder-favorites.png Oxygen icons recently introduced.  For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added.  To help create these EPS icons in the future, the graphics/README file has been added with a description of the *.eps.gz file creation. + * Added some missing oxygen icons to allow the relax manual to compile.  These are the 128x128 EPS versions of the <code>places/folder-development.png</code> and <code>places/folder-favorites.png</code> Oxygen icons recently introduced.  For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added.  To help create these EPS icons in the future, the graphics/README file has been added with a description of the <code>*.eps.gz</code> file creation.
− * Some more details for the *.eps.gz icon creation process. + * Some more details for the <code>*.eps.gz</code> icon creation process.
  * Mac OS X fixes for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca] and [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca_observers Structure.test_pca_observers] system tests.  The eigenvectors on this OS are sometimes inverted.  As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required.   * Mac OS X fixes for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca] and [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca_observers Structure.test_pca_observers] system tests.  The eigenvectors on this OS are sometimes inverted.  As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required.
  <section end=changes/>   <section end=changes/>



Bugman: Links to the API documentation.
2016-05-13T16:40:55Z
Links to the API documentation.

				
				
				
				
				
				← Older revision
				Revision as of 16:40, 13 May 2016
				
Line 49:
Line 49:
  * Creation of the [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function].  This simply resets the helices and sheets data structures in the internal structural object to [].   * Creation of the [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function].  This simply resets the helices and sheets data structures in the internal structural object to [].
  * Updated the copyright notices for 2016.   * Updated the copyright notices for 2016.
− * Created a short Info_box copyright string for displaying in the main GUI window.  This shows the full range of copyright dates. + * Created a short [http://www.nmr-relax.com/api/4.0/info.Info_box-class.html Info_box] copyright string for displaying in the main GUI window.  This shows the full range of copyright dates.
  * Added the spin_num boolean argument to the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Setting this flag to False will cause the spin number information to be ignored when creating the spin containers.  This allows for better support of homologous structures but with different PDB atom numbering.  The default flag value is True, preserving the old behaviour.   * Added the spin_num boolean argument to the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Setting this flag to False will cause the spin number information to be ignored when creating the spin containers.  This allows for better support of homologous structures but with different PDB atom numbering.  The default flag value is True, preserving the old behaviour.
  * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.   * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.
− * Fix for the Structure.test_read_pdb_internal3 system test.  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument. + * Fix for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_read_pdb_internal3 Structure.test_read_pdb_internal3 system test].  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument.
  * In the GUI the user functions [http://www.nmr-relax.com/manual/sys_info.html sys_info] and [http://www.nmr-relax.com/manual/time.html time] are now grouped into a "system" subclass.  This is to prepare for other system related functions.   * In the GUI the user functions [http://www.nmr-relax.com/manual/sys_info.html sys_info] and [http://www.nmr-relax.com/manual/time.html time] are now grouped into a "system" subclass.  This is to prepare for other system related functions.
  * Added a new 16x16 icon for the oxygen folder-favorites icon.   * Added a new 16x16 icon for the oxygen folder-favorites icon.
− * Adding a new file at lib/system.py.  This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. + * Adding a new file at lib.system.  This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory.
− * In /lib/__init__.py, adding the filename for system.py. + * In lib.__init__, adding the filename for system.py.
  * Renaming the folder-favorites icon.   * Renaming the folder-favorites icon.
  * Deleting the old folder-favorites icon.   * Deleting the old folder-favorites icon.
Line 63:
Line 63:
  * Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image.   * Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image.
  * Adding a user function translation for:  This is to catch the new naming of these functions.   * Adding a user function translation for:  This is to catch the new naming of these functions.
− * Adding a new lib.system.pwd() function, to print and return the current working directory. + * Adding a new [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#pwd lib.system.pwd() function], to print and return the current working directory.
  * Adding a new user function [http://www.nmr-relax.com/manual/system_pwd.html system.pwd] to print/display the current working directory.   * Adding a new user function [http://www.nmr-relax.com/manual/system_pwd.html system.pwd] to print/display the current working directory.
  * Adding new 16x16 px and 200px of the oxygen icon folder-development.  This icon is used for displaying the current working directory.   * Adding new 16x16 px and 200px of the oxygen icon folder-development.  This icon is used for displaying the current working directory.
  * Adding a relax GUI menu for changing the current working directory.   * Adding a relax GUI menu for changing the current working directory.
  * Adding a menu item for changing the current working directory.   * Adding a menu item for changing the current working directory.
− * Adding a verbose True/False for the lib.system.pwd() function. + * Adding a verbose True/False for the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#pwd lib.system.pwd() function].
  * Storing the current working directory as a GUI variable.   * Storing the current working directory as a GUI variable.
  * Adding a toolbar button for changing the current working directory.   * Adding a toolbar button for changing the current working directory.
− * Adding a verbose flag to lib.system.pwd() function. + * Adding a verbose flag to [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#pwd lib.system.pwd() function].
  * Changing to a filedialog for the user function [http://www.nmr-relax.com/manual/system_cd.html system.cd].   * Changing to a filedialog for the user function [http://www.nmr-relax.com/manual/system_cd.html system.cd].
  * Adding an observer for current working directory.   * Adding an observer for current working directory.
  * Modifying the user function [http://www.nmr-relax.com/manual/system_cd.html system.cd] not to show the result to STDOUT.   * Modifying the user function [http://www.nmr-relax.com/manual/system_cd.html system.cd] not to show the result to STDOUT.
− * Letting the lib.system.cd function notify the observer, when changing directory. + * Letting the [http://www.nmr-relax.com/api/4.0/pipe_control.system-module.html#cd lib.system.cd function] notify the observer, when changing directory.
  * Letting the current working directory be printed in the statusbar in the bottom.   * Letting the current working directory be printed in the statusbar in the bottom.
  * Updating self.system_cwd_path when a directory change is observed.   * Updating self.system_cwd_path when a directory change is observed.
Line 87:
Line 87:
  * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.   * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.
  * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  The test uses his data and script to trigger the bug.   * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  The test uses his data and script to trigger the bug.
− * Simplified the Relax_disp.test_bug_24601_r2eff_missing_data system test.  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system). + * Simplified the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_bug_24601_r2eff_missing_data Relax_disp.test_bug_24601_r2eff_missing_data system test].  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system).
− * Fix for the independence of the relax library.  As lib.system was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the pipe_control package. + * Fix for the independence of the relax library.  As lib.system was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the [http://www.nmr-relax.com/api/4.0/pipe_control-module.html pipe_control package].
  * Added some missing oxygen icons to allow the relax manual to compile.  These are the 128x128 EPS versions of the places/folder-development.png and places/folder-favorites.png Oxygen icons recently introduced.  For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added.  To help create these EPS icons in the future, the graphics/README file has been added with a description of the *.eps.gz file creation.   * Added some missing oxygen icons to allow the relax manual to compile.  These are the 128x128 EPS versions of the places/folder-development.png and places/folder-favorites.png Oxygen icons recently introduced.  For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added.  To help create these EPS icons in the future, the graphics/README file has been added with a description of the *.eps.gz file creation.
  * Some more details for the *.eps.gz icon creation process.   * Some more details for the *.eps.gz icon creation process.
− * Mac OS X fixes for the Structure.test_pca and Structure.test_pca_observers system tests.  The eigenvectors on this OS are sometimes inverted.  As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required. + * Mac OS X fixes for the [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca Structure.test_pca] and [http://www.nmr-relax.com/api/4.0/test_suite.system_tests.structure.Structure-class.html#test_pca_observers Structure.test_pca_observers] system tests.  The eigenvectors on this OS are sometimes inverted.  As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required.
  <section end=changes/>   <section end=changes/>
    
Line 99:
Line 99:
  * Fix for [https://gna.org/bugs/?24218 bug #24218, the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified].  The logic for the labels was expanded from being only for all tensors to handling subsets.   * Fix for [https://gna.org/bugs/?24218 bug #24218, the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified].  The logic for the labels was expanded from being only for all tensors to handling subsets.
  * Bug fix for the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] [https://gna.org/bugs/?24300 bug #24300, when the merge flag is True, and both multiple structures and multiple models are present, the structure.read_pdb user function would fail with a RelaxError].  The problem was that the molecule index was simply not being updated correctly.   * Bug fix for the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] [https://gna.org/bugs/?24300 bug #24300, when the merge flag is True, and both multiple structures and multiple models are present, the structure.read_pdb user function would fail with a RelaxError].  The problem was that the molecule index was simply not being updated correctly.
− * Fix for [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  To handle the missing data, the peak intensity keys are now checked for in the spin container peak_intensities data structure.  This is both for the [[R2eff model|R2eff]] model optimisation as well as the data back-calculation.  A warning is given when the key is missing.  The relaxation dispersion base_data_loop() method has been modified to now yield the spin ID string, as this is used in the warnings.  In addition, the Grace plotting code in the relax library was also modified.  When peak intensity keys are missing, some of the Grace plots will have no data.  The code will now generate a plot for that data set, but detect the missing data and allow an empty plot to be created. + * Fix for [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  To handle the missing data, the peak intensity keys are now checked for in the spin container peak_intensities data structure.  This is both for the [[R2eff model|R2eff]] model optimisation as well as the data back-calculation.  A warning is given when the key is missing.  The [http://www.nmr-relax.com/api/4.0/specific_analyses.relax_disp.api.Relax_disp-class.html#base_data_loop relaxation dispersion base_data_loop() method] has been modified to now yield the spin ID string, as this is used in the warnings.  In addition, the Grace plotting code in the relax library was also modified.  When peak intensity keys are missing, some of the Grace plots will have no data.  The code will now generate a plot for that data set, but detect the missing data and allow an empty plot to be created.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: More link fixes.
2016-05-13T16:31:14Z
More link fixes.

				
				
				
				
				
				← Older revision
				Revision as of 16:31, 13 May 2016
				
Line 40:
Line 40:
    
  <section begin=changes/>   <section begin=changes/>
− * Improved formatting for the \yes LaTeX command for the HTML manual (www.nmr-relax.com/manual/).  This now inputs the raw HTML character for a tick. + * Improved formatting for the \yes LaTeX command for the [http://www.nmr-relax.com/manual/ HTML manual].  This now inputs the raw HTML character for a tick.
  * The replicate title finding script now processes short titles as well.  This shows that the Frame_order.html file will be conflicting and overwritten.   * The replicate title finding script now processes short titles as well.  This shows that the Frame_order.html file will be conflicting and overwritten.
  * Avoidance of a replicated title in the frame order chapter of the manual.   * Avoidance of a replicated title in the frame order chapter of the manual.



Bugman: Link improvements.
2016-05-13T16:29:31Z
Link improvements.

				
				
				
				
				
				← Older revision
				Revision as of 16:29, 13 May 2016
				
Line 13:
Line 13:
    
  <section begin=description/>   <section begin=description/>
− This is a minor feature and bugfix release.  The new user functions [http://www.nmr-relax.com/manual/system_cd.html system.cd] and [http://www.nmr-relax.com/manual/system_pwd.html system.pwd] have been added to allow the working directory to be changed and displayed.  The [http://www.nmr-relax.com/manual/time.html time] and [http://www.nmr-relax.com/manual/sys_info.html sys_info] user functions have been renamed to [http://www.nmr-relax.com/manual/system_time.html system.time] and [http://www.nmr-relax.com/manual/system_sys_info.html system.sys_info].  The [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function] has been created to remove the helix and sheet information from the internal structural object.  For bugs, the [[R2eff model|R2eff]] dispersion model can now handle missing peaks in subsets of spectra, and the structure.read_pdb can now handle multiple structures and multiple models with the merge flag set. + This is a minor feature and bugfix release.  The new user functions [http://www.nmr-relax.com/manual/system_cd.html system.cd] and [http://www.nmr-relax.com/manual/system_pwd.html system.pwd] have been added to allow the working directory to be changed and displayed.  The [http://www.nmr-relax.com/manual/time.html time] and [http://www.nmr-relax.com/manual/sys_info.html sys_info] user functions have been renamed to [http://www.nmr-relax.com/manual/system_time.html system.time] and [http://www.nmr-relax.com/manual/system_sys_info.html system.sys_info].  The [http://www.nmr-relax.com/manual/structure_delete_ss.html structure.delete_ss user function] has been created to remove the helix and sheet information from the internal structural object.  For bugs, the [[R2eff model|R2eff]] dispersion model can now handle missing peaks in subsets of spectra, and the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] can now handle multiple structures and multiple models with the merge flag set.
  <section end=description/>   <section end=description/>
    
Line 53:
Line 53:
  * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.   * Added support for concatenating atomic positions in the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function].  Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering.  The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions.
  * Fix for the Structure.test_read_pdb_internal3 system test.  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument.   * Fix for the Structure.test_read_pdb_internal3 system test.  With the new atomic position concatenation support, when called sequentially the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] should always use the same value for the ave_pos argument.
− * In the GUI the user functions sys_info and time are now grouped into a "system" subclass.  This is to prepare for other system related functions. + * In the GUI the user functions [http://www.nmr-relax.com/manual/sys_info.html sys_info] and [http://www.nmr-relax.com/manual/time.html time] are now grouped into a "system" subclass.  This is to prepare for other system related functions.
  * Added a new 16x16 icon for the oxygen folder-favorites icon.   * Added a new 16x16 icon for the oxygen folder-favorites icon.
  * Adding a new file at lib/system.py.  This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory.   * Adding a new file at lib/system.py.  This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory.
Line 86:
Line 86:
  * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] → [http://www.nmr-relax.com/manual/system_time.html system.time] user function change.   * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] → [http://www.nmr-relax.com/manual/system_time.html system.time] user function change.
  * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.   * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.
− * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601].  This is the failure of the optimisation of the [[R2eff model|R2eff]] dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601.  The test uses his data and script to trigger the bug. + * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  The test uses his data and script to trigger the bug.
  * Simplified the Relax_disp.test_bug_24601_r2eff_missing_data system test.  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system).   * Simplified the Relax_disp.test_bug_24601_r2eff_missing_data system test.  This is to allow the test to catch [https://gna.org/bugs/?24601 bug #24601] to complete in a reasonable time (2 seconds on one system).
  * Fix for the independence of the relax library.  As lib.system was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the pipe_control package.   * Fix for the independence of the relax library.  As lib.system was using the status object, the library independence was broken.  To work around this, the module has simply been shifted into the pipe_control package.
Line 97:
Line 97:
    
  <section begin=bugfixes/>   <section begin=bugfixes/>
− * Fix for [https://gna.org/bugs/?24218 bug #24218].  This is the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified.  The logic for the labels was expanded from being only for all tensors to handling subsets. + * Fix for [https://gna.org/bugs/?24218 bug #24218, the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified].  The logic for the labels was expanded from being only for all tensors to handling subsets.
− * Bug fix for the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] [https://gna.org/bugs/?24300 bug #24300].  When the merge flag is True, and both multiple structures and multiple models are present, the structure.read_pdb user function would fail with a RelaxError.  The problem was that the molecule index was simply not being updated correctly. + * Bug fix for the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] [https://gna.org/bugs/?24300 bug #24300, when the merge flag is True, and both multiple structures and multiple models are present, the structure.read_pdb user function would fail with a RelaxError].  The problem was that the molecule index was simply not being updated correctly.
− * Fix for [https://gna.org/bugs/?24601 bug #24601].  This is the failure of the optimisation of the [[R2eff model|R2eff]] dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta.  To handle the missing data, the peak intensity keys are now checked for in the spin container peak_intensities data structure.  This is both for the [[R2eff model|R2eff]] model optimisation as well as the data back-calculation.  A warning is given when the key is missing.  The relaxation dispersion base_data_loop() method has been modified to now yield the spin ID string, as this is used in the warnings.  In addition, the Grace plotting code in the relax library was also modified.  When peak intensity keys are missing, some of the Grace plots will have no data.  The code will now generate a plot for that data set, but detect the missing data and allow an empty plot to be created. + * Fix for [https://gna.org/bugs/?24601 bug #24601, the failure of the optimisation of the R2eff dispersion model when peaks are missing from one spectrum], as reported by Petr Padrta.  To handle the missing data, the peak intensity keys are now checked for in the spin container peak_intensities data structure.  This is both for the [[R2eff model|R2eff]] model optimisation as well as the data back-calculation.  A warning is given when the key is missing.  The relaxation dispersion base_data_loop() method has been modified to now yield the spin ID string, as this is used in the warnings.  In addition, the Grace plotting code in the relax library was also modified.  When peak intensity keys are missing, some of the Grace plots will have no data.  The code will now generate a plot for that data set, but detect the missing data and allow an empty plot to be created.
  <section end=bugfixes/>   <section end=bugfixes/>
    



Bugman: HTML formatting fix by converting -> to →.
2016-05-13T16:24:29Z
HTML formatting fix by converting -> to →.

				
				
				
				
				
				← Older revision
				Revision as of 16:24, 13 May 2016
				
Line 84:
Line 84:
  * Optimising the width of the statusbar.   * Optimising the width of the statusbar.
  * When the user function script is called, a notification of pipe_alteration is made.  This will force the GUI to update, and make sure that it is up to-date.   * When the user function script is called, a notification of pipe_alteration is made.  This will force the GUI to update, and make sure that it is up to-date.
− * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] -> [http://www.nmr-relax.com/manual/system_time.html system.time] user function change. + * Updated the frame order auto-analysis for the [http://www.nmr-relax.com/manual/time.html time] → [http://www.nmr-relax.com/manual/system_time.html system.time] user function change.
  * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.   * Fix for the GUI status bar element widths.  Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window.  Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation.
  * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601].  This is the failure of the optimisation of the [[R2eff model|R2eff]] dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601.  The test uses his data and script to trigger the bug.   * Created a system test for catching [https://gna.org/bugs/?24601 bug #24601].  This is the failure of the optimisation of the [[R2eff model|R2eff]] dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601.  The test uses his data and script to trigger the bug.

@@ Line 109: / Line 109: @@
 * [http://wiki.nmr-relax.com/Relax_4.0.2 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2533 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2533|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/70 Gmane mailing list archive].
 * [https://www.mail-archive.com/relax-announce@gna.org/msg00060.html Mail Archive]

@@ Line 4: / Line 4: @@
 | version  = 4.0.2
 | prev     = 4.0.1
 | keywords =
 | type     = Minor feature and bugfix

@@ Line 112: / Line 112: @@
 * [https://www.mail-archive.com/relax-announce@gna.org/msg00060.html Mail Archive]
 * [https://mail.gna.org/public/relax-announce/2016-05/msg00000.html Local archives].
-* [https://marc.info/?l=relax-announce&m=145021808817686&w=2 Mailing list ARChives (MARC)].
+* [https://marc.info/?l=relax-announce&m=146335793029456&w=2 Mailing list ARChives (MARC)].
 {{:Softpedia}}

@@ Line 108: / Line 108: @@
 * [http://wiki.nmr-relax.com/Relax_4.0.2 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2532 Gna! news item].
+* [https://gna.org/forum/forum.php?forum_id=2533 Gna! news item].
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/70 Gmane mailing list archive].
 * [https://www.mail-archive.com/relax-announce@gna.org/msg00060.html Mail Archive]

Relax 4.0.2 - Revision history

Bugman: /* Links */ Fix the broken Gna! forum link.

Bugman: /* Bugfixes */ Switch to the {{gna bug link}} template to fix the broken links.

Bugman: Added relax 4.0.3 to the infobox.

Bugman: /* Links */ Updated the MARC link.

Bugman: Fix for the Gna! news link.

Bugman: Added tags throughout.

Bugman: Links to the API documentation.

Bugman: More link fixes.

Bugman: Link improvements.

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

Bugman: Added `tags throughout.`