Author: bugman
Date: Fri May 13 16:43:15 2016
New Revision: 28213
URL: http://svn.gna.org/viewcvs/relax?rev=28213&view=rev
Log:
Backported the relax 4.0.2 CHANGES file changes to trunk.
The command used was:
svn merge -r28211:28212 svn+ssh://bug...@svn.gna.org/svn/relax/tags/4.0.2 .
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28213&r1=28212&r2=28213&view=diff
==============================================================================
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Fri May 13 16:43:15 2016
@@ -1,3 +1,74 @@
+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 \yes LaTeX command for the HTML manual
(www.nmr-relax.com/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 CHANGES
file.
+ * 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_num boolean argument to the 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
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
structure.load_spins user function should always use the same value for the
ave_pos argument.
+ * In the GUI the userfunctions sys_info() and 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.
+ * 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.
+ * In /lib/__init__.py, adding the filename for system.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/False for 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_path 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.
+ * Changing the keyboard shortcut for changing the working directory to
Ctrl+W. Since Ctrl+C 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.
+ * 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_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 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. This is the failure
of the optimisation of the '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.
+ * 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.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.
+ * 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.
+ * 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 (https://gna.org/bugs/?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.
+ * Bug fix for the structure.read_pdb user function (bug #24300,
https://gna.org/bugs/?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. This is the failure of the optimisation of the
'R2eff' dispersion model when peaks are missing from one spectrum, as reported
by Petr Padrta at https://gna.org/bugs/?24601. 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.
+
+
+
Version 4.0.1
(14 December 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/4.0.1
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