relax version 1.3.15.

[Edward d'A. <ed...@do...>]

This is a major feature release focusing on more complete Mac OS X
support and prettifying all of the user interfaces (UIs).  The new
features include full Mac OS X support via fink and the Mac
application DMG file (for Leopard, Snow Leopard and Lion with PPC,
i386 and x86_64 CPUs), coloured terminal output in the prompt/script
UI modes, the ability to run the full relax test suite within the GUI
mode, general improvements throughout the GUI, support for wxPython
2.9, faster program start up, improved formatting of the HTML version
of the user manual, and expansion of the multi-processor framework.
Many additional changes are listed below.  If you are a Mac OS X user,
you are affected by one of the bugs listed below, or you would like to
use the new features, then I would recommend upgrading to this new
version.

The new relax versions can be downloaded from either
http://www.nmr-relax.com/download.html or
http://download.gna.org/relax/
.  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/).

The full list of changes is:

   Features:
       * Large improvements to the HTML user manual
(http://www.nmr-relax.com/manual/index.html).
       * The full test suite, including GUI tests, can now be run
successfully from the GUI.
       * The Mac OS X binary distribution file now supports Leopard,
Snow Leopard and Lion as well as the PPC, i386 and x86_64 CPU
architectures.
       * The prompt and script output to a terminal is now coloured.
       * Faster program startup by only importing the test suite and
GUI packages if they are actually needed.
       * Files selected via the GUI user functions can now be previewed.
       * Redesign of the spin loading wizard of the spin viewer
window to be more intuitive.
       * Expansion of the system information print out.
       * Advances in the multi-processor framework including the
pre-sending of data to slaves.
       * Support for wxPython 2.9.


   Changes:
       * Changed all of the maths in the HTML user manual page
titles, the latexonly and htmlonly environments are now being used to
produce different section titles with and without maths respectively.
       * The latex2html configuration script now allows for more
maths in the HTML user manual with the HTML_VERSION math extension.
       * The section numbers are now removed from the HTML user
manual pages to allow for more static webpages for the user functions
which do not disappear as new user functions are added.
       * The title page of the HTML user manual has been renamed to
"The relax user manual".
       * Updated the ancient COMMITTERS file which has not been
changed in over 4 years!
       * The pipe editor window is no longer centred, now matching
the behaviour all other windows.
       * All open relax windows are now closed prior to running the
test suite within the GUI.
       * Exiting the GUI now only warns about data loss only if there
is data to loose.
       * The relax controller can now not be closed while the test
suite is running.
       * During the GUI tests from the GUI, the relax controller is
now modal preventing users from interfering with the tests.
       * The relax controller now stays on top of all windows when
the GUI tests are being run improving the running of the tests on Mac
OS X and MS Windows.
       * The GUI tests now work in the GUI thanks to a lot of GUI
black magic.  The tests' tearDown() method now carefully deconstructs
the GUI element prior to the next test being run.  In the normal
'relax --gui-test' mode, the GUI object is destroyed and recreated for
each test however, when run from the GUI, the GUI object is always
there and must remain intact.  The deconstruction includes deletion of
each analysis tab and selective destruction of all non-main windows
(excluding the controller which shows the test suite progress).  The
relax data store GUI object is also reconstructed in the tearDown()
method, and all wx events flushed at the very end to prevent clashes
with the next GUI test.
       * The relax mode (i.e. prompt, script, GUI, test suite, etc.)
is now stored in the status object - this is used to activate and
deactivate certain parts of the GUI tests within the GUI and normal
test suite modes.
       * The ds.relax_gui GUI data object is now a permanent feature
of the relax data store.
       * The 'Tools->Test suite' menu item has been converted into a
sub-menu with entries for running all tests or the individual test
categories.
       * Created the _det_install_path() status singleton method for
better determining the install path - this is used for the Mac OS X
applications whereby the current logic of using sys.path[0] fails
miserably!
       * Prepared the multi-processor package for the import
mechanisms of Python 3 - this new mechanism is present in Python 2.7
now, and the code falls back to the old method when not present.
       * Complete redesign of the py2app setup.py script for building
Mac OS X applications.  The script has been converted into a class
called Setup which performs all the actions.  All files, source or
otherwise, are now stated as data files to be included in
relax.app/Contents/Resources.  All relax modules are specified by the
py2app 'includes' option so that they are forced to all be included
within the relax.app/Contents/Resources/lib/python2.X/site-packages.zip
file as *.pyc files.
       * The py2app part of the setup.py script now throws a
RelaxError if the setuptools module is missing.
       * Added the relax prompt icon to the main GUI window toolbar.
       * Added the larger sized application-x-executable-script Oxygen
icons.
       * Created the 'ansi' module containing the terminal colouring
ANSI escape sequences.
       * The test suite is now only imported in the test modes of
operation - this should speed up program initialisation.
       * The import of the gui package now only occurs in GUI mode -
this will speed up the program start up.
       * The script print out in scripting mode is now in cyan if
sys.stdout is a TTY.
       * ANSI escape characters are now turned off forcibly when in GUI
mode.
       * The sys.std*.isatty() methods are being used to determine if
text output should be coloured.
       * All RelaxWarnings are now coloured yellow when printed to a TTY.
       * All RelaxErrors are now coloured red when printed to a TTY.
       * The relax prompts will be coloured blue when printed to a TTY.
       * The GUI analyses delete_all() method now unregisters all
observer methods prior to deletion.
       * Created observer_register() for all GUI analyses for method
registration and unregistration - this method allows for external
calls to observer_register() to pre-remove the methods from the
observer objects.
       * Added debugging printouts to the delete_all() analysis method.
       * More advanced debugging printouts for the delete_analysis() method.
       * Added some heavy debugging code to the GUI analysis
delete_analysis() method.
       * Increased the size of the model-free model change warning
dialog for wxPython 2.9 on GNU/Linux.
       * The file selection wizard GUI element now has the preview
button turned on by default.
       * Double clicking on a file in the results view window now opens it.
       * Added a file preview button for the
spectrum.read_intensities user function GUI page.
       * Added a file preview button to the file selection GUI
element of the wizards.
       * Increased the size of the incomplete set up dialogs for
wxPython 2.9 on GNU/Linux.
       * Added the document-preview.png Oxygen icons.
       * Increased the loading state warning dialog size - this is to
accommodate for larger text on wxPython 2.9 on GNU/Linux with GTK.
       * Improved the spin data deletion messages from the spin viewer
window.
       * Increased the dialog heights for the deletion of spin data
via the spin viewer window.
       * Improved the user feedback during a state save by just
sleeping a little to show the busy cursor.
       * Modified the spin loading wizard so that preloaded
structures are the default.
       * The maths_fns.relax_fit module is now stored in the
dep_check module for the info print out.
       * Added the structure.read_xyz user function to the menus.
       * Created the Tools->System Information menu entry, which is
simply the sys_info user function front end.
       * Created the GUI front end to the structure.read_xyz user function.
       * The relax controller now accepts Ctrl-A to select all text.
       * The relax controller now shows the relax intro text to mimic
the prompt/scripting modes.
       * Introduced the empty() method into the structure API to
check if structural data is loaded - this will be used in the spin
loading wizard of the spin viewer window.
       * Converted the structure.read_xyz user function front end to
the new design.
       * Improved details of relax and the compiled C modules from
the info print out.
       * Created a dictionary object containing wxPython version info
within the status singleton object - this is being used to construct
the Mac dock icon, when the Carbon and Cocoa builds and not GTK are
being used.
       * Updated the multi-processor package __all__ list to allow
the relax unit tests to pass.
       * Added a document describing how to build a 3-way (i386, pcc,
x86_64) Mac OS X Python framework.
       * Added a script which is used to validate the binary
architecture of Mac OS X Frameworks.
       * Improved the relax info print out for the installed python
packages - this now shows more information for the wxPython version,
and formats the output based on maximum widths to handle different
situations.
       * Removed the ppc64 build target for the relax C modules on
Mac OS X - this architecture is not supported by the recent Xcode
frameworks, so it has been dropped.
       * The scons binary_dist target on Mac OS X can now overwrite a
pre-existing DMG file.
       * Added some epydoc @attention fields to the multi-processor API.
       * Created the fetch_data_store() multi-processor API function
- this simply returns the data store of the same processor as the
calling code.
       * The 2nd test implementation's slave command now uses the
fetch_data() API function - this is to obtain the invariant data
pre-sent by the master to the slaves.
       * Renamed the multi-processor API data_fetch() function to
fetch_data(), and implemented it.
       * Renamed data_upload() to send_data_to_slaves() and made it
more specific.
       * The multi-processor data_fetch() API function is now used to
obtain the total_length variable.
       * Shifted the self.threaded_result_processing flag into the
base Processor class where it belongs.
       * Clean up and completion of the TODO for the
Processor.assert_on_master() method.  The Processor.assert_on_master()
method has been created and calls raise_unimplemented().  The
Multi_processor.assert_on_master() method has been shifted to
Mpi4py_processor.assert_on_master(), as that method's error message is
MPI specific.  The empty Uni_processor.assert_on_master() method has
been added to allow that fabric to work.
       * Spun out all of the results queue objects into their own
module.  This completes another set of TODOs by removing these queue
objects from any fabric level.  They can now be imported and used by
any fabric level (Processor, Multi_processor, Mpi4py_processor,
Uni_processor, etc.).
       * Shifted the run_command_queue() and run_queue() methods from
the Multi_processor to Processor class.
       * The multi/test_implementation2.py script can now be run in
uni-processor mode.
       * The multi/test_implementation2.py script now properly uses
pre-send data in the slave calculations.
       * Partially implemented the Processor.data_update() method.
       * Created the special command object Slave_storage_command for
transferring data to slaves - this command currently has two special
methods:  add(), used by the master processor to add data to the
command for transfer; and clear(), used by the slave (via run()) or
the master to clear out all data.
       * Split the multi.commands module into two - the slave
commands and result commands.
       * Removed the Mpi_processor.data_upload() method as this will
be performed at the Processor level.
       * Shifted all of the processor command objects into the
multi.commands module.  The other multi.api module objects have been
shifted into the multi.misc module.
       * The multi-processor package now allows sys.exit() calls
within the master processor.
       * Removed a number of sys.exit() calls from different relax
modes.  The return call is used rather than sys.exit() to exit the
main run() method.  These were not needed and it allows the 'version',
'info', and 'gui' modes to play better with the multi-processor
package when using mpi4py.
       * Shifted the mpi4py processor module functions
broadcast_command() and ditch_all_results() into the class - these
have been turned into private methods.
       * Redesigned how the multi-processor package terminates
program execution - the Processor.exit() method has been introduced to
perform this action.
       * Spelling fix for a number of the processor method names.
       * Fully documented the Processor.run() method via comments.
       * Eliminated the unused Set_processor_property_command
multi-processor class.
       * Eliminated the unused Get_name_command multi-processor class.
       * Shifted the Multi_processor.run() method up a level to
Processor.run() - this completes one of the TODOs, and will be needed
to avoid code duplication for handling the new data_upload() and
data_fetch() API methods.
       * Eliminated the completely unused create_slaves() Processor method.
       * The processor instances now have a data storage container -
this will be used by the data_upload() and data_fetch() API methods.
       * Implemented the mpi4py processor fabric data_upload() method.
       * Updated the second multi-processor test implementation to
use the new data_upload() API function.
       * The multi.data_upload() API function now forwards the call
to the Processor classes.
       * Clean up of the Multi_processor.run_command_queue() method.


   Bugfixes:
       * Fix for the about dialogs in the GUI when combined with a
scrolling window (this is only a problem for the wxPython 2.9 series).
       * Fix for the fetch_docstrings.py script used for the user
manual creation - the number of \linebreak[0] commands inserted was
far too great.
       * In generating the HTML user manual, the ignore_commands
function is now being used to force latex2html to ignore \linebreak[0]
commands as these were previously putting the text '[0]' throughout
all the HTML pages.
       * For the HTML user manual, the document splitting has been
restored to a split depth of 5 - this had been changed to make the
main chapters of the text more readable, but the user function HTML
page is now far, far too long and is a massive strain on browsers.
       * The Mf.test_write_results system test now works with the
newer Python 2.7.3 version, as from this version onwards the XML of
the relax save and results files will be differently formatted.
       * Big bug fix for the installation path for the relax Mac OS X
application.  The path to the application Resources folder, where all
the relax data files are located, is now set to the install path.  The
relax.py module was also overwriting the value set in the status
singleton and now this no longer occurs.
       * Fix for the py2app setup.py script for Mac OS X application
creation - the list of data files to include with the app is now
properly formatted.
       * The relax GUI is now robust and able to withstand a call to
the reset user function - this could have occurred if the user ran a
script with a reset() call, or if reset() was typed at the GUI version
of the relax prompt.
       * Added isatty() methods to all of the dummy file objects
within relax - this fixes a number of errors caused by the recent
introduction of coloured text.
       * Fix for the initialisation of the Exec_info class for the
prompt/script output.
       * Fix for the residue.create user function GUI front end - the
unnamed molecules are now properly handled, and the gui_to_*() methods
are now used for data conversion.
       * Fix for the gui_to_int() function for when text instead of
an integer is given by the user.
       * Bug fix for the spin.create user function GUI interface for
when molecules or residues are not named - unnamed molecules are now
properly handled in the GUI page, and the residue name of None is
properly converted into a NoneType prior to executing the back end.
       * Big bug fix for the deletion of analyses tabs from the GUI -
this affects wxGTK users on Macs and Linux.  Now the spectrum and
relaxation data list GUI elements have observer_register() methods,
allowing the analysis delete_all() method to unregister all analysis
specific methods from the observer objects.
       * Multiple unregistrations of observer methods are now
possible without a RelaxError - this allows multiple code paths to
unregister methods to allow for pre-removal of methods to avoid queued
wx events in wxGTK from occurring on dead or missing objects.
       * Bug fix for the GUI when deleting analysis tabs - the
deletion of analysis tabs was previously failing in certain cases.
       * Fix for a bug triggered by wxPython 2.9 when deleting the
last analysis tab - the self.notebook object is now deleted when the
set_init_state() method is called, allowing it to be properly accessed
and recreated.
       * Converted the pipe switching with GUI tab switching to
synchronous to avoid rare races (triggered by wxPython 2.9).
       * The analysis deletion buttons now do nothing if the notebook
is not created yet - this avoids problems on the new wxPython 2.9
versions.
       * Fix for the radiobutton group in the
Spectral_error_type_page of the peak intensity wizard.
       * Fix for the spin loading wizard of the spin window - the
RadioButtons of the first page for selecting the spin loading method
are now fixed.
       * Fix for the about relax window size for wxPython 2.9.
       * Fix for the relax controller find dialog on Mac OS X with
wxPython 2.9.
       * wxPython 2.9 fix for the spin viewer window (at least for Mac OS
X).
       * The maximize calls for the spin viewer window are now turned
off for Mac OS X systems (this is a fix for the fink versions of
relax).
       * Bug fix for Mac OS X - the main window is no longer started
maximised (a fix for the fink version of relax).
       * Fix for the spin viewer window for wxPython 2.9 - this is
for when you right click in the tree view panel on nothing.
       * Fix for the text on the 'finish' button of the GUI wizard -
this was accidentally changed to 'apply'.
       * Bug fix for the spectrum.replicated user function for when
it is called twice with the same IDs.
       * Bug fix for the relax GUI spin viewer window.  When right
clicking on nothing in the tree view, an error would occur.  Now,
instead, a special menu pops up with a single entry for loading spins.
       * Fix for the building of the relax C modules as universal
binaries on Mac OS X - the linking was not functioning correctly, and
the resultant module was build only for i386.
       * The relax Mac OS X dock icon is now turned off when using
the wxGTK build of wxPython from fink - this prevents a little grey
frameless window appearing with the largest of the relax Ulysses
butterfly icons in the centre.
       * Bug fix for Mac OS X - attempt at killing the
Carbon.Evt.TickCount problem by removing argv emulation.
       * Fix for the scons binary_dist target on Mac OS X systems
with multiple Python versions - now the py2app program is called with
the same python version as used by scons.
       * Fix for the Processor.data_upload() method.  The
self.run_command_queue() method is no longer being used.  Instead the
add_to_queue() method is being used to queue up the slave commands,
and the run_queue() method is being called at the end to flush the
queue.
       * Fixes and clean up of the slave to master transfer mechanism
for result commands.
       * Fix for the relax info print out on Python 2.5 or below.