Difference between revisions of "Relax 4.0.2"
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<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 | + | * 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 | + | * 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 | + | * 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/> | ||
Revision as of 16:46, 13 May 2016
 | |||||
| relax version 4.0.2 | |||||
| |||||
| Release type | Minor feature and bugfix | ||||
|---|---|---|---|---|---|
| Release date | 13 May 2016 | ||||
|
| |||||
 The relax 4.0.2 user manual | |||||
Contents
Description
This is a minor feature and bugfix release. The new user functions system.cd and system.pwd have been added to allow the working directory to be changed and displayed. The time and sys_info user functions have been renamed to system.time and system.sys_info. The structure.delete_ss user function has been created to remove the helix and sheet information from the internal structural object. For bugs, the 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.
Download
The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).
CHANGES file
Version 4.0.2
(13 May 2016, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.2
Features
- Addition of the new user functions system.cd and system.pwd to allow the working directory to be changed and displayed.
- Addition of the structure.delete_ss user function to remove the helix and sheet information from the internal structural object.
Changes
- Improved formatting for the
\yesLaTeX command for the 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.
- Avoidance of a replicated title in the frame order chapter of the manual.
- Added some unicode characters for improved formatting of the
CHANGESfile. - 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.
- Added a check for the total argument for the frame_order.distribute user function. The maximum value is 9999, as the PDB format cannot accept more models.
- Creation of the 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.
- Created a short Info_box copyright string for displaying in the main GUI window. This shows the full range of copyright dates.
- Added the
spin_numboolean argument to the structure.load_spins user function. Setting this flag toFalsewill 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 isTrue, preserving the old behaviour. - Added support for concatenating atomic positions in the structure.load_spins user function. Together with the
spin_numflag set toFalse, 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 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
systemsubclass. This is to prepare for other system related functions. - 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 Pythonosandsystemrelated functions. For example changing directory or printing working directory. - In
lib.__init__, adding the filename forsystem.py. - Renaming the 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 the new user function 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 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 user function 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 a relax GUI menu for changing the current working directory.
- Adding a menu item for changing the current working directory.
- Adding a verbose
True/Falsefor the lib.system.pwd() function. - Storing the current working directory as a GUI variable.
- Adding a toolbar button for changing the current working directory.
- Adding a verbose flag to lib.system.pwd() function.
- Changing to a filedialog for the user function system.cd.
- Adding an observer for current working directory.
- Modifying the user function system.cd not to show the result to STDOUT.
- Letting the lib.system.cd function notify the observer, when changing directory.
- Letting the current working directory be printed in the statusbar in the bottom.
- Updating
self.system_cwd_pathwhen 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.
- Changing the keyboard shortcut for changing the working directory to
Ctrl+W. SinceCtrl+Cis 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.
- Added a newline character after printing the script.
- Optimising the width of the statusbar.
- When the user function script is called, a notification of
pipe_alterationis 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 time → 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.
- Created a system test for catching 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 bug #24601 to complete in a reasonable time (2 seconds on one system).
- Fix for the independence of the relax library. As
lib.systemwas using the status object, the library independence was broken. To work around this, the module has simply been shifted into the 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.pngandplaces/folder-favorites.pngOxygen 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.gzfile creation. - Some more details for the
*.eps.gzicon 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.
Bugfixes
- Fix for 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 structure.read_pdb user function 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 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 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.
Links
For reference, the announcement for this release can also be found at following links:
- Official release notes on the relax wiki.
- Gna! news item.
- Gmane mailing list archive.
- Mail Archive
- Local archives.
- Mailing list ARChives (MARC).
Softpedia also has information about the newest relax releases:
- Softpedia page for relax on GNU/Linux.
- Softpedia page for relax on MS Windows.
- Softpedia page for relax on Mac OS X.
Announcements
If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.
See also
- The combined release notes for all relax versions (warning, this is very large).
- The combined release descriptions for all relax versions.
- The combined release metadata for all relax versions.
- The combined release features for all relax versions.
- The combined release changes for all relax versions (warning, this is very large).
- The combined release bugfixes for all relax versions.
- The combined release announcement links for all relax versions.
