This major release introduces the second version of the relax
graphical user interface (GUI). This is a major rewrite of the entire
GUI code base. The GUI should now be much more flexible, being able
to handle all the different ways NMR data is collected and errors are
measured. It now has the much of the flexibility of the prompt /
scripting interface by the implementation of GUI versions of many of
the user functions, and the GUI now has support for small organic
molecules, RNA, DNA, sugars, etc. This flexibility will allow all
other analysis types (reduced spectral density mapping, N-state model,
the frame order theory, consistency testing, etc.) to be added to the
GUI in the future. The GUI is now fully tested and functional on the
three major platforms of GNU/Linux, Mac OS X and MS Windows.
In addition, there have been significant bugs fixed throughout the
program in both the GUI and the rest of the code base. There are a
number of improvements to the frame order theory. A number of new
structure user functions have been added for structure creation and
structure displacement and superimposition. There have been
improvements to the N-state model analysis and to the handling of RDC
and PCS values. New user functions have been added for visual
representation of model-free results in PyMOL. And finally, the
auto-analyses have been redesigned to have all input data pre-loaded
into a relax data pipe and that data pipe passed into the the
analysis. This grants more flexibility, specifically for non-protein
organic molecules which can now be used with the dauvergne_protocol
auto-analysis (http://www.nmr-relax.com/refs.html#dAuvergneGooley08b).
Due to the incredible number of changes and fixes which are part of
this release (see below), all users are recommended to upgrade to this
newest version. The new relax versions can be downloaded from either
http://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).
The full list of changes is:
Features:
* The positive and negative cones from the frame order theory
are now different PDB models.
* Monte Carlo simulations are now implemented for the frame
order analysis.
* Created the structure.connect_atom user function to expose
the back-end functionality.
* Created the structure.add_atom user function to expose the
back-end functionality.
* Created the structure.translate user function to translate
structural components.
* Created the structure.superimpose user function which uses
the Kabsch algorithm to implement the direct fit-to-first algorithm
and the iterative fit-to-mean algorithm.
* Created the structure.displacement user function to
calculate the rotational and translational displacement between two
models via the Kabsch algorithm.
* Extended the N-state model analysis to allow a separate
paramagnetic centre per state.
* The structure.read_pdb user function can now handle bzip2 or
gzip compressed PDB files.
* The structure.write_pdb user function can now create
compressed (bzip2 or gzip) PDB files.
* Created the structure.rotate user function to allow the
application of arbitrary rotations to the structures loaded into relax
about a given origin.
* Added the bc flag to the RDC and PCS display and write user
functions to allow the back-calculated data to be displayed or written
rather than the measured values.
* Increased the efficiency of the relax data store spin system
creation, this becomes noticeable when large numbers of structures are
read into relax.
* The N-state model can now be optimised with a subset of the
alignment tensors fixed.
* The alignment_tensor.fix user function is now tensor
specific, allowing a subset of tensors to be optimised while the
others are kept fixed.
* Added the ability to specify J+D verses J+2D measured RDCs.
* Addition of many new oxygen icons for the GUI.
* Implemented the sys_info user function in all UI modes
(prompt/script/GUI).
* Implemented the spectrum.delete user function in all UI
modes (prompt/script/GUI).
* Addition of the pymol.macro_apply, pymol.macro_create, and
pymol.macro_run user functions for the visualisation of model-free
parameters mapped to a structure. This matches the equivalent Molmol
user functions and styles.
* A complete redesign of the GUI where any number of analyses
can be created and closed as needed.
* The GUI is now fully functional on Mac OS X and MS Windows.
* The elimination of many race conditions causing the GUI to crash.
* Implementation within the GUI of many of the relax user
functions available in the prompt and scripting UI modes.
* Creation of the test suite GUI test category to complement
the system and unit tests.
* Added a toolbar to the main relax window with some of the
most important menu entries as icons.
* Most parts of the GUI are now deactivated when execution is
in progress (via the execution lock) to prevent fatal race conditions.
* Redesigned the dauvergne_protocol, NOE and Rx auto-analyses
to use a pre-prepared data pipe for data input. This allows greater
support for the GUI and for analyses of RNA, DNA, and small molecules.
Changes:
* Changed the name of the model_num argument to model in the
centre_of_mass() function.
* The generic_fns.structure.mass.centre_of_mass() function now
accepts the model number argument, allowing specific models to be
isolated.
* The generic_fns.structure.mass.centre_of_mass() function now
accepts the atom ID argument, allowing the centre of mass of subsets
of the structure to be calculated.
* Addition of a number of frame order test data and system
tests for the simpler models (Frame_order.test_cam_rigid,
Frame_order.test_cam_free_rotor, Frame_order.test_cam_free_rotor2,
Frame_order.test_cam_rotor, Frame_order.test_cam_rotor2,
Frame_order.test_cam_iso_cone_free_rotor,
Frame_order.test_cam_iso_cone_free_rotor2).
* More use of the structural API in the
create_diff_tensor_pdb() function.
* Created the add_model() structural API method.
* Eliminated one of the eigenframe parameters from the rotor
frame order model. In the rotor frame order model, the x and y axes
of the eigenframe of the motion are not defined. Therefore the 3
eigenframe Euler angles have been replaced by 2 spherical angles
defining the rotation axis removing a lot of optimisation issues with
this model.
* The frame order torsion angle cone_sigma_max is now forced
to be positive. Optimisation sometimes comes up with the negative of
the angle but, as both the negative and positive angles are the same
result, the angle is always unpacked after optimisation as the
absolute value.
* Added a check to prevent the frame order grid search from
being too big causing out of memory errors.
* The internal structural object no longer requires the 'ATOM'
PDB record for creating PDB files. This affects the
structure.write_pdb user function.
* Added the translate method to the structural API.
* Created the Structure.test_superimpose_fit_to_mean system
test to test the 'fit to mean' algorithm of the structure.superimpose
user function.
* Shifted the structural API calc_displacement() method into
the main module.
* Created the arg_check.is_int_list() function for checking
for lists of integers.
* Created the Structure.test_superimpose_fit_to_first system
test to test the 'fit to first' algorithm of the structure.superimpose
user function.
* Added the centroid argument to the structure.displacement
user function for pivoted motions. By specifying the centroid
position for all structures, a pivoted motion is assumed. All
displacements will be zero, and the angles will be that of the
pivoting motion.
* Created the Structure.test_displacement system test for
checking the structure.displacement user function.
* Added checks for the n_state_model.cone_pdb user function in
the N_state_model.test_5_state_xz system test.
* Added a few new argument checks for arrays and matrices of
floats including arg_check.is_float_array() and
arg_check.is_float_matrix().
* Added a few new RelaxError classes (RelaxNoneListFloatError,
RelaxMatrixFloatError, RelaxNoneMatrixFloatError) and the BaseArgError
class was also modified to handle the length argument (now the size
arg) being a tuple for matrix sizes.
* The N-state model Monte Carlo simulations can now handle
fixed alignment tensors.
* Created the alignment tensor module return_tensor() function
for returning tensors. This takes fixed tensors into account,
skipping them if the skip_fixed flag is set.
* Created the alignment tensor module num_tensors() method for
counting tensors. This excludes fixed tensors by default.
* The RDC and PCS display and write user functions now output
molecule name, residue name, residue number, spin name and spin number
columns instead of the spin ID column. This is better to read back
into relax as info such as the spin number can be ignored, allowing
different PDB files to be used.
* Created a system test for loading RDCs from a file with spin
ID strings at the start.
* Created the N_state_model.test_metal_pos_opt N-state model
system test.
* The RDC and PCS Q factors for each alignment is now stored
as a dictionary in the relax data store.
* Updated the N-state model analysis code to handle the
per-alignment tensor fixed flag.
* Updated the relax data store alignment tensor objects to
allow for the per-tensor fixed flag.
* Created the generic_fns.align_tensor.all_fixed() function
for determining if all tensors are fixed.
* Created the Grace.test_cam_kkalpha_plot1 system test for
checking the grace plotting of mixed data.
* Created the N_state_model.test_monte_carlo_sims system test
for checking MC sims with alignment data.
* Updates for Python 3.0 using the Python 2to3 script.
* Created the N_state_model.test_rdc_tensor system test for
catching a strange RDC back calculation bug.
* Created the Mf.test_bug_18790 system test for catching bug
#18790 (https://gna.org/bugs/?18790).
* Created the Relax_fit.test_bug_18789 system test for
catching bug #18789 (https://gna.org/bugs/?18789). The Grace file is
written out, re-opened, and then the numbers checked.
* The GUI test result classes are now being used by the GUI
test suite code path.
* Implemented some new classes to allow better control of the
test suite from the GUI. The GuiTestResult and GuiTestRunner classes
have been added to the relax_test_runner module, and these are used
rather than RelaxTestResult and RelaxTestRunner if the from_gui flag
is sent to the main Test_suite_runner class.
* The test result handling is now performed 100% in
test_suite_runner. Previously each class of test (system, unit, and
GUI) were managing a separate instance of RelaxTestRunner. Now it is
all controlled from one spot. This will allow better management of
the tests from the GUI.
* The results of the unit tests are now going to the proper
sys.stdout stream. The text was previously sent to the initial stream
that sys.stderr is set to. This is overwritten by relax though to be
able to send it to the relax controller. This allows the results to
be captured.
* Added the 'Tools->Test suite' menu entry.
* The checks in the model-free analyses for correct relaxation
data errors now prints out the spin ID string.
* The test suite runner 'tests' argument now defaults to []
which is the proper null value.
* Renamed the 'Settings' menu to 'Tools'.
* The results viewer window now only executes one user
function for the diffusion tensor if PyMOL is missing, preventing 3
errors (with windows) from appearing.
* Modified the GUI interpreter apply() method to catch
RelaxErrors. Now gui_raise() is used to raise the error and show a
dialog, and the method returns the execution status.
* The diffusion tensor PDB in the results viewer is now
launched by synchronous pymol user function calls.
* The C modules are now compiled as universal binaries on Mac
OS X. This includes the targets i386, x86_64 and ppc64 by default.
* The relax information print out now includes the version and
path info for the mpi4py and wx modules.
* The spectrum ID is no longer stored if
spectrum.read_intensities fails to load any data. A call to the
delete() function has been added to remove all data loading prior to
the error.
* Redesigned the gui_raise() function so that it is more user
friendly. The relax controller window with error message is shown
first, followed by the modal RelaxError message dialog on top of all
other windows.
* The spectrum.read_intensities user function now throws a
RelaxError if no data was loaded. This is to tell the user that
something went wrong, and makes more sense in the GUI mode.
* With debugging turned on, the relax test suite no longer
captures the IO streams. This will allow for better debugging of
racing in the GUI tests on MS Windows.
* Removed the brackets from the user function names in the
RelaxError system as these make no sense in the GUI version of the
user functions.
* Clicking on 'Execute relax' now raises the relax controller
to the front, if already shown.
* The GUI prompt window is now also deactivated with the
execution lock. This will prevent race conditions as previously the
user was able to execute any user function or manipulate any of the
data in the relax data store while execution was in progress
* More of the main menu entries have been disabled with the
execution lock to prevent racing.
* The spin loader toolbar button in the spin viewer window is
now properly disabled with the execution lock.
* The spin loader button in the spin viewer window is now
deactivated with the execution lock.
* The wizard page base method on_apply() now does nothing.
This should help eliminate Mac OS X bugs.
* The scipy python package is now listed with the relax info (-i
flag).
* The peak list and relaxation data GUI element pop up menus
are now disabled with the execution lock. This will prevent weird
bugs.
* The spin viewer window is now properly maximised on MS Windows.
* Improvements to the showing of the relax controller on
errors and warnings. The Show() call is no longer made if already
shown, and if not shown, the LogCtrl is scrolled to the position of
the error message.
* The relax controller is now shown on all errors and warning
(or raised if below other windows).
* The View menu entries now raise the window to the front if
already open, this is useful when too many windows are open.
* The spin.name page is now added to the front of the Rx peak
list wizard.
* The spin.name GUI page is now added to the front of the NOE
peak list wizard if spins are not named.
* Expanded the spin.name user function docstring.
* Shifted the spin ID field to the end of the spin.name user
function GUI page, this is to make it easier for users as it is often
assumed that the first field is the important one.
* The proceed_on_error flag is now taken into account by the
wizard's finish button.
* The Rx peak list wizard now no longer skips to the next page
when an error occurs.
* All GUI user functions now use the base page execute()
method instead of the interpreter directly.
* Created the user function base page execute() method for
running the user functions. This will launch the interpreter in
either asynchronous or synchronous mode dependent on the sync flag.
* The sync flag is now set for all of the pages of the NOE
peak list wizard.
* The UF_page base class now accepts the 'sync' argument, this
will be used to allow for asynchronous or synchronous operation.
* The NOE peak list wizard should now stop proceeding on all errors.
* Modified all of the gui_to_*() functions to catch a real
None input value.
* Created the gui.misc.gui_to_str_or_list() conversion function.
* Created the gui.misc.gui_to_int_or_list() conversion function.
* The relax controller menu now has icons.
* The relaxation data list GUI element now has a pop up menu
with a 'Delete' entry.
* The relax data list delete button now opens with the first
selected item in the list.
* The relax_data.delete GUI user function can now have a
starting ID string value.
* The peak list GUI element ListCtrl now has a pop up menu
with a 'Delete' entry.
* The peak list GUI element now has a delete button which
launches the spectrum.delete user function.
* The spectrum.delete user function can now be started with an
initial ID string.
* Created the RelaxSpectraError and RelaxNoSpectraError error
classes for spectral data.
* Improvements to the wizard _display_page() method.
* The user function class is no longer stored in self.gui.
* Elimination of the self.gui class object.
* Converted the results viewer window to handle the new user
function GUI page design.
* Better support for running a script and the GUI from the
command line, the script is now run at the very end, after all of the
GUI is set up, and is run with a wx.CallAfter call.
* The spin loading wizard is now accessible from the tree's
root menu in the spin viewer window.
* Added a toolbar button to the spin viewer window to launch a
wizard for loading spins. A simple wizard has been created for the
spin viewer window for loading spins which directs the user to either
the sequence.read user function or the structure.read_pdb and
structure.load_spins user functions. The wizard page Load_method_page
has been added at the start to allow the user to choose the method,
and the last page Finish_page has been added so that the wizard can
have a finish button and terminal page.
* Converted all of the user function GUI pages to use the new
create_wizard() base method. This significantly simplifies the code.
The functions also no longer expect a wx event.
* The deselect user function GUI pages no longer expect the
user function page to be returned.
* Added the return_page argument to create_wizard() so that
the user function page can be selectively returned.
* Complete redesign of the user function menu system, this is
now more flexible and should be more compatible with window ordering
under MS Windows.
* Simplified the deselect user functions using the new GUI
user function design.
* The create_wizard() method now returns the user function
page, this will be needed as sometimes the fields have to be changed.
* Removed the now useless UF_base.__init__() method.
* The User_functions class no longer takes any arguments.
* The interpreter singleton is now being used by the user
function GUI pages (part of the elimination of self.gui).
* The relax GUI no longer starts maximised if debugging is on.
* The script GUI user function is now operational again, the
interpreter object is now imported and the synchronous apply() rather
asynchonous queue() method is now used. This allows the execution
lock to be released by the script at the end.
* The script user function GUI element now uses wx.GetApp() to
access to the relax controller window.
* The GUI Main instance is now stored in the wx.App as
self.gui, this will allow access to the GUI class via wx.GetApp()
calls, avoiding the need to pass the instance around (part of the
elimination of self.gui).
* The screen is no longer cleared prior to relax execution on
MS Windows preventing the Windows PowerShell history from being wiped
out.
* Improved the RelaxError messages in validate_sequence(), the
invalid data is now printed so that the user can see why it is
invalid.
* Improved the print outs of the scons 'binary_dist' target
for Mac OS X.
* Modified the 'clean' scons target to remove the py2app build
and dist directories (for Mac OS X).
* Created the 'scons binary_dist' target for Mac OS X. Typing
'scons binary_dist' on a Mac will now create a DMG image of a
universal Mac OS X application.
* Added the Mac OS X DMG distribution file names to the scons script.
* Modified the setup.py file so that the Mac OS X .app
creation code is in the mac_setup() function.
* Updated the hdiutil command options for the Mac OS X DMG
file creation.
* Added instructions to the setup.py file for creating a Mac
OS X DMG distribution file.
* Removed the GUI wait_for_interpreter() method as this is
replaced by the interpreter flush() method.
* Text files in the results viewer window are now opened with
a text editor on Mac OS X and MS Windows. On a Mac, the text file of
NOE values was being opened up in 'Saturn', as the file ending '*.out'
is associated with that software.
* The gui_error() window caption is now simply 'RelaxError'
rather than the specific relax error name, this now matches the
prompt/script print outs which only have RelaxError (unless debugging
is turned on).
* The GUI tests in the test suite no longer have IO redirected
to a window in Mac OS X and MS Windows.
* Deleted the old gui.filedialog.opendir function and replaced
it with a specialised RelaxDirDialog class. This class is more
advanced in that it changes the Python working directory so that the
user does not have to always navigate back to the same place if relax
is launched from a different directory.
* The RelaxFileDialog object now changes the relax working
directory as the user changes directories.
* The Rx spectra list wizard now uses the on_init() wizard
page method for the page updates. This prevents the values in the
pages being reset when the apply button is clicked.
* Created the GUI wizard page method on_init(), this is
executed each time a wizard page is newly displayed.
* Removed the check for Monte Carlo simulations from the
monte_carlo.setup user function allowing MC simulations to be run more
than once.
* The results viewer window no longer shows 1 warning dialog
per results file. At the end of the analysis, one warning dialog per
results file was being shown as the execution lock was on. Now a
special method for the 'result_file' observer object has been added
which skips this dialog.
* The Monte Carlo simulation state is now turned off after the
MC analysis is complete. This allows the user to make slight
modifications and rerun the analysis and optimisation. The
monte_carlo.error_analysis user function switches the state at the
very end, just as monte_carlo.setup switches the state to on.
* The relax execution lock now has debugging print outs.
* The status container instance is now private in the
Relax_lock objects.
* The fake_lock variable in the status module classes is now private.
* The spin_id_to_data_list error messages are now more informative.
* The RelaxInvalidSeqError now prints out a more detailed
message for the validate_sequence() function.
* The flush flag is set for the first page of the Rx peak
height loading wizard.
* Added the ability to flush the GUI interpreter thread in the
wizard prior to changing to the next page, this will help in solving
races when a series of user functions are strung one after the other.
* The notification of observers in status.observers.gui_uf has
been modified. The GUI user function pages no longer perform this as
the calls to the interpreter are via the interpreter thread, hence the
completion of the page does not signal the completion of the user
function. Instead the interpreter thread (and the synchronous apply()
call as well) perform the notification once complete.
* The GUI auto-analyses now initialise with a synchronous call
to pipe.create(), this uses the GUI interpreter object apply() method
to prevent race conditions. This is important as the pipe creation
needs to be completed prior to the setting up of the GUI elements.
* Created the GUI interpreter object apply() for synchronous
calls to the user functions.
* Redesigned the GUI interpreter object so that the thread is
a separate object, this is to allow both synchronous and asynchronous
calls to the interpreter.
* Added the _get_uf() method to the GUI interpreter object for
abstracting the code.
* All the model-free macro methods are no longer private, the
class will not be used as a base class for the model-free specific
class.
* Abstracted the model-free 'classic' Molmol and PyMOL
creation in to a base class. As most of the code between the
specific_fns.model_free.molmol and specific_fns.model_free.pymol
modules is identical, significantly simplifying the code base.
* The results viewer window can now open Molmol macro files.
* The results viewer will now open PyMOL files in PyMOL via
pymol.macro_run.
* Modified the Molmol macro related user function front end to
match those of PyMOL, there are: molmol.macro_exec is now
molmol.macro_apply; molmol.write is now molmol.macro_write;
molmol.macro.run has been added to execute macros from text files.
* The GUI interpreter thread is now flushed prior to execution
of the auto-analyses.
* Created the GUI interpreter thread flush() method for
blocking until the queue is empty.
* Added a join() wrapper method for the GUI interpreter thread
internal queue.
* Added the empty() method to the GUI interpreter thread to
determine if the internal queue is empty.
* Some cleaning up of the mpi4py processor module.
* Removed a pile of unused code from the mpi4py processor module.
* Removed the _sys_exit module variable from the mpi4py
processor as it is unnecessary.
* Eliminated the restore_stdio() method from the multi
package, the redirection of IO streams is totally incompatible with an
IO redirection performed by the underlying Python program.
* Removed the IO redirection from the uni-processor
return_object() method. The IO redirection in the 'multi' package
overwrites all IO redirection any Python program is attempting to
perform.
* The uni-processor call to capture_stdio() has been removed,
no IO redirection will be performed in uni-processor mode.
* Deleted the STDOUT and STDERR capture in MF_minimise_command
multi-processor class as it was breaking both the GUI and the test
suite.
* Removed the multi_processor module as this is now called
multi_processor_base. This was deleted a long time ago but somehow
survived in one of the branches and was merged back in.
* Renamed the PrependOut class to IO_filter in multi/processor_io.py.
* Renamed the prependStringIO module to processor_io in
preparation for a redesign.
* Clean up of the multi-processor IO module. The
Multiplex_stdout class has been deleted as this is the wrong way of
handling the IO streams and is unused anyway. The PrependStringIO
class has had the getvalue() and truncate() methods removed as these
need not be implemented as it is provided by StringIO.
* Created Redirect_text.flush() for the relax controller for
compatibility with the multi-processor code.
* All calls to user functions in self.gui.interpreter now pass
through the queue() method.
* The 'relax_gui_mode' module is blacklisted from the epydoc
documentation generation. Without this, the relax GUI launches when
executing 'scons api_manual_html'.
* The dauvergne_protocol auto-analysis now creates the PyMOL
macros for the model-free data.
* The molmol.write and pymol.write now add the macro files to
the result files list.
* The dauvergne_protocol auto-analysis now generates MOLMOL
macros and text files with the parameters.
* The interpreter thread no longer dies when an error occurs.
This has been redesigned so that the error catching occurs within the
infinite loop. Without this the user functions are completely useless
after an error and do nothing.
* RelaxErrors are handled as in the auto-analyses and
prompt/scripting mode in the GUI user functions. The traceback is now
suppressed and a dialog with the error is show.
* The print outs for catching exceptions in threads is now
going to STDERR rather than STDOUT.
* sys.__stdout__ and sys.__stderr__ are no longer being written to.
* Saving the relax state from the GUI now shows the busy
cursor for user feedback. After MC sims saving the state can take a
few seconds with the GUI frozen, so this feedback is necessary.
* Errors are now handled properly in the interpreter thread
for GUI user functions.
* The GUI analysis execution threads are now daemonic to allow
relax to exit.
* Redesigned how user functions are executed in the GUI so
they are queued and launched in a thread. This allows the GUI to be
responsive while the user functions execute. This is only at the
level of the GUI and not the relax interpreter. The execution lock is
also acquired to lock up the GUI while the user function executes. A
special daemon thread called self.gui.interpreter has a queue object
so that a series of user functions can be queued up if needed. The
program now also exists with wx.Exit() call to prevent unhandled
exceptions occurring in this daemon thread.
* The pipe.create user function page is now using PIPE_DESC to
present a list of pipe types for the user. This gives the descriptive
name of the data pipe type rather than the keyword argument values.
* Created the PIPE_DESC dictionary to provide descriptions of
the data pipes.
* The consistency testing and hybrid data pipes are now listed
in the pipe.create user function docstring.
* The GUI now returns to normal when opening an invalid or
incompatible save file.
* Molmol is now properly launched from relax to read commands
from STDIN.
* Synchronised the code for handling Molmol and PyMOL. The
Molmol code is now very similar to that of PyMOL, using
subprocess.Popen rather than os.popen. There is now a Molmol
execution object that is used by the molmol user functions.
* The GUI tests are now skipped when the wx module is not
present (or is broken). This allows relax to operate without having
wx installed.
* Modified the dauvergne_protocol auto-analysis to be able to
loop over all the global models. The diff_model argument can now be a
list of global model names, allowing the protocol to loop over each
diffusion model.
* The results viewer window also updates via the result_file observer.
* The result_file observer object has been created and is
being used throughout relax.
* PyMOL is now always launched as an external program as the
pymol module loading method was causing huge problems for the GUI.
* Diffusion tensor PDB files are now opened in PyMOL from the
results viewer window.
* The cdp.result_file structure has been modified to include a
type, a label, and the file path.
* The results viewer window presents the results files in a
wx.TextCtrl.
* The results viewer window is deactivated with the execution lock.
* Modified the results viewer to operate like the spin viewer
with respect to pipe changing.
* The results viewing code (the viewer window) has now been
separated from the analysis GUI code.
* A diffusion tensor representation of the final results is
created for dauvergne_protocol.
* Grace plots of the final model-free results are now produced
by the dauvergne_protocol auto-analysis.
* Deleted the status_reset() method from the
dauvergne_protocol auto-analysis as it served no purpose.
* All the data pipes are cleared out in the final stage of the
dauvergne_protocol. This is to remove many of the temporary data
pipes from view of the user in the GUI.
* Removal of the unused gui.execution.calc_modelfree module.
This was a direct copy of the auto_analyses.dauvergne_protocol module,
but is unmaintainable and of no use in the GUI anymore.
* Modified the pipe editor window design to be closer to that
of the spin viewer. The observer methods are now unregistered on
closing the window, which should speed up relax.
* The data pipe and spin viewer window Show() methods are now
only called if IsShown() is False.
* Warning dialogs are shown if the pipe editor or spin viewer
windows are opened during the execution lock.
* Improvements to the user warning dialog about closing
windows, the dialog is now only shown once at the start and it blocks
the auto-analysis.
* Added a message dialog to warn the user to close the spin
viewer and pipe editor windows to speed up calculations.
* Deleted the unused dir_message(), exec_relax() and
relax_run_ok() message functions.
* The pipe_lock and spin_lock (via Relax_lock) locks are now
reentrant locks. This allows nested locking via one thread, which is
necessary as the functions of generic_fns.pipes and
generic_fns.mol_res_spin often call functions of the same module in a
nested way.
* Created an object called Relax_lock to help debug locking
issues in relax. The status.spin_lock lock is now using Relax_lock.
* All of the generic_fns.mol_res_spin fns which modify the
data structure are now using the new lock.
* Created the status.reset() method to resetting the status object.
* Created a lock object for the molecule, residue and spin
data structures. This will be used to prevent races when spin data is
being accessed and changed at the same time. This affects the spin
viewer window which is very sensitive to races.
* The relax controller window is calling Layout() after
updating to show all panels properly. This is needed when showing the
model-free or Rx panels.
* Clean up of the showing and hiding of spin viewer window,
all observers and registered now in the Show() method and unregistered
in handler_close().
* The R1 and R2 curve-fitting tabs are completely deactivated
by the execution lock.
* The NOE auto-analysis tab is completely deactivated with the
execution lock.
* The execute relax button is now turned off by the execution
lock in the model-free auto-analysis tab.
* The GUI analysis base class add_execute_relax() method now
returns the button.
* The add_spin_systems() base class method now returns the
Text_ctrl instance it creates.
* Converted the analysis base class add_text_sel_element()
method to the object Text_ctrl. This has the Enable(), SetValue(),
and GetValue() methods implemented as a wx object.
* Renamed the 'spin_ctrl' module to 'elements' to store all of
the special GUI analysis elements.
* More enabling/disabling of the model-free auto-analysis GUI element.
* The spectrum list GUI element can also now be
enabled/disabled via Enable().
* The relaxation data list GUI element can now be
enabled/disabled via Enable().
* All the model-free auto-analysis activation and deactivation
calls now pass through wx.CallAfter.
* The model-free model fields are now activated/deactivated
with the execution lock.
* Created the Spin_control object for the analysis GUI
elements from the base add_spin_element() method. This class
implements the Enable(), GetValue(), and SetValue() methods to mimic a
wx control.
* Tooltips are now given for the relax controller gauges and
text fields.
* The spin viewer tree pop up menus are now disabled when the
execution lock is on.
* All the spin viewer tree pop up menus now have IDs as class
variables via wx.NewId().
* The spin viewer menus and pipe switching elements are now
disabled when the execution lock is on.
* Many of the 'File' menu entries are now disabled when the
execution lock is on.
* The main menu IDs are now all class variables called
self.MENU_* and are given by wx.NewId().
* The pipe editor window is starting inactive if the execution
lock is on.
* Most of the data pipe functions are now using the data pipe
locking object status.pipe_lock. The functions which acquire the lock
object and which modify the pipe state include: copy(), create(),
delete(), switch(). The functions which acquire the lock object to
prevent changes while they execute include: display(), pipe_loop().
* Created a lock object for the relax data pipes. This will
be used to prevent races in the GUI when data pipe info is accessed,
but when a thread is changing the data pipes at the same time.
* The pipe editor window methods are now deactivated when the
execution lock is on.
* The original zoom level is available in the relax controller
log control pop up menu.
* Zooming can now be changed with Ctrl-+, Ctrl-- and Ctrl-0 in
the relax controller, enabling zoom in, zoom out, and the original
zoom to be accessed by the keyboard.
* Created a replacement pop up menu for the relax controller
log control. This has functions for finding text, copying text,
selecting all, and zooming in or out.
* The relax controller log control can no longer have text
inserted. This was happening with the middle mouse button click on
GNU/Linux.
* A find dialog is now available for the relax controller log
control to find text in the messages, this is available with Ctrl-F.
* Deleted the now unused gui.execution.calc_rx module.
* The GUI dauvergne_protocol test now uses the same
optimisation settings as the system test.
* The diff_tensor_grid_inc dauvergne_protocol argument is now
available in the auto-analysis GUI tab. This is not exposed to the
user though.
* The dauvergne_protocol GUI test is now checking the same
data as the equivalent system test.
* The solution for the dauvergne_protocol system test is
reached after 1 iteration, so the test is shortened.
* Better testing of the new diff_tensor_grid_inc argument to
the dauvergne_protocol auto-analysis.
* The dauvergne_protocol system test script can now run stand-alone.
* Re-activated and redesigned the system test of the
dauvergne_protocol.
* The unit vector loading wizard is now stored in the base
model-free auto-analysis class. This is for access to the GUI element
from the test-suite.
* Fix for the unit vector check in the model-free auto-analysis GUI
tab.
* Added a button and created a wizard for loading unit vectors
from PDB files. This has been added to the model-free GUI
auto-analysis tab.
* Unit vectors are now only checked for in the model-free GUI
auto-analysis when needed.
* Full errors are raised in the protected_exec() function if
in debugging mode.
* Improvements to the structure.vector user function docstring.
* Created the wizard page spin_control() method for adding a
spin control.
* The results file viewer is now executing the grace.view user
function to display Grace files.
* Fix for the protected_exec() method - the error is no longer
raised so it can return False.
* Implemented the NOE data_names() and return_data_desc()
specific API methods.
* The gui_raise() method now turns off the busy cursor if needed.
* Added the 'Help->Licence' menu entry (this is a simple copy
of 'User functions->gpl').
* The results viewer window now uses cdp.result_files. This
decouples the files and their creation from the GUI.
* The grid search increments default to 21 now in the Rx
fitting auto-analysis GUI tab, the MC simulation tooltip now also
recommends a min of 500 sims.
* In debugging and test mode, the relax controller now writes
back to the original IO streams instead of sys.__stdout__ and
sys.__stderr__.
* The relax controller log control styles are now set to the
'modern_small' fonts.
* Expanded and renamed the 'modern' fonts.
* RelaxWarnings are now coloured 'orange red' in the log
control of the relax controller.
* The Monte Carlo simulation number is now stored in the
auto-analysis part of the status object. This is only when an
auto-analysis is running.
* The relax prompt is now coloured blue in the relax
controller log element.
* The STDOUT and STDERR streams are segregated in the relax
controller LogCtrl and STDERR messages coloured red.
* The relax controller log window can now distinguish between
STDOUT and STDERR messages. STDOUT and STDERR are now being sent to
separate instances of Redirect_text, and added to the log queue with a
flag specifying which is which.
* The relax controller and auto-analysis threads are now
active in debugging mode.
* The relax controller Redirect_text object is now placing all
messages onto a log queue and the LogCtrl is reading from this queue.
The log_queue Queue object is now used to store messages so that not
every write() event to STDOUT and STDERR results in the relax
controller log window updating. This allows the controller and the
GUI to remain responsive as masses of messages are produced.
* The new relax controller now appears to be thread safe.
* The relax controller window now can move behind the other windows.
* Key events are now controlled in the relax controller log
element, this prevents text insertion and deletion.
* Scrolling now follows the end, if at the end, in the relax
controller log window.
* Implemented limited scroll back on the LogCtrl relax
controller log element. This will prevent the computer from running
out of memory. The maximum number of lines is now stored in the
status singleton.
* Created a custom control for the relax controller log
element. This is derived from wx.stc.StyledTextCtrl and will allow
much greater control.
* Renamed the relax controller IO redirection append_text()
method to add_text().
* The gui_raise() function now only shows the dialog if the
status.show_gui flag is set.
* Shifted the exception_queue object into the base of the status
object.
* The spectrum.error_analysis can now be repetitively
performed, this allows changes such as addition of new spectra to
occur.
* A timer is now being used to update the gauges of the relax
controller, the gauges were previously not pulsing correctly.
* The Question message dialog answer is now set to 'No' if the
window close icon is clicked.
* The Missing_data and Question message dialogs are now always
on top, this prevents them from being hidden by other windows.
* The gui_to_float() and gui_to_int() functions can now handle
float or int inputs.
* All of the gui_to_*() functions now check for empty unicode
strings u'' as well.
* Modified the gui_to_float() and gui_to_int() functions to
handle expressions, this means that the float '1.23 * 1e-6' or '1.234
* 4 - 0.06' can input by the user.
* The font is now set on the text of the Question message box.
* Added checks for sequence and spectral data for the Rx
curve-fitting and NOE auto-analysis GUI tabs.
* All buttons in the GUI now have their fonts set. This is
for GUI consistency between GNU/Linux, Mac OS X and MS Windows.
* The about relax dialog is now resized dependent on the
extent of the text, fixing the dialog on MS Windows.
* The wx.lib.wordwrap module is now used for wrapping the text
in the about GUI dialogs.
* Shifted the font initialisation to the very start of the GUI
launching.
* The results files lists are only updated if the files are
not already there.
* Complete redesign of the relax controller. The new features
include: A dynamically updated analysis specific status update;
Analysis specific GUI elements, dynamically hidden or shown; A display
of the current analysis and current data pipe; Correct updating of the
gauges in all analyses; Separation of the text redirection and the
progress updating; Text scroll back limited by default to 100000
lines; Text scroll back cleared as a user would expect with removal of
lines from the start; Cleaner layout of all elements.
* The dauvergne_protocol auto-analysis now stores the maximum
number of iterations value.
* Created the GUI analysis current_data() method for returning
the data store container.
* The auto-analysis status objects are now set up for all
auto-analyses.
* The auto-analyses status objects now have a completion flag
'fin' to indicate if the analysis is complete.
* Added a new analysis method current_analysis_type() for
determining the current analysis type.
* The opening of the results viewer window after an analysis
is now thread safe.
* There is now an observer object for the execution lock.
* The text redirection to the relax controller is set up in
the controller removing repetition. The redirection was happening in
the controller first and then again in each analysis.
* Modified how the auto_analysis status object behaves so
setting values causes an observer to be notified.
* The fonts are now set for all parts of the wizard pages for
OS consistency.
* The results display window is now shown at the end of the
auto-analysis execution.
* A busy cursor is now shown while waiting for the new analysis
wizard.
* The save_state flag has been added to the NOE auto-analysis
so that the save state can be turned off.
* Removed the no longer used GUI NOE calculation module
(gui.execution.calc_noe).
* The status bar is properly updated to show nothing if all
data pipes have been deleted.
* The setting up of a new analysis tab now uses freezing and
thawing and the busy cursor.
* The new_analysis method now checks that the C modules are
compiled, and returns cleanly if not and an R1 or R2 analysis is
selected.
* The save state dialog now only shows *.bz2 files to save as.
* The spin viewer now starts maximised on GNU/Linux and MS
Windows, and at a smaller size on Mac OS X.
* Polishing of the Question message dialog. The buttons are
now of fixed width and aligned to the right, and the relax-blue
version of the dialog-warning oxygen icon is being used.
* Created a relax blue version of the dialog-warning oxygen icon.
* Layout improvements in a number of user function and other
wizard pages, the description heights are now used (the variable had
been renamed), and the free file format GUI element containing user
function pages now use the space better and have been shortened.
* The free file format resetting now properly updates the GUI element.
* Polishing of the free file format GUI element. The internal
buttons are now placed to the right hand side rather than below to
save large amounts of space. A lot of unnecessary outside padding has
also been removed, and the divider position is now properly
calculated.
* Updates to the GUI fonts, and the addition of normal_italic.
* Improvements to the wildcards for the relax save state file
dialogs. There is now a separation between the compressed *.bz2 *.gz
files and the 'All files' entry for selecting an uncompressed version.
* The protected_exec() function now uses gui_raise() to handle errors.
* The gui_raise() function now prints the error message to
STDERR if the raise flag is not set.
* Redesign of all the file dialogs in the GUI. All file
dialogs are now instances of gui.filedialog.RelaxFileDialog. This
fixes many inconsistencies throughout the GUI, includes presenting an
wx.FD_OPEN style file dialog when a wx.FD_SAVE style should have been
shown.
* The PDB file selector of the structure.load_pdb GUI user
function now only shows *.pdb files.
* Removed combine_models from the structure.load_spins GUI
user function page as that argument no longer exists.
* Improvements to the free file format GUI elements (window
and element). This includes specifying fonts, button sizes, and a fix
for the button sizer in the GUI element.
* The GUI is now frozen while opening a relax state and then
finally thawed, removing visual artifacts on Mac OS X.
* Removed the 'Settings->Reset all settings' menu and added a
reset button to the free file format settings.
* The Question class can now have the parent specified to
allow for sub-windows to have the dialog focus.
* The missing data and question dialogs are now centred.
* Converted the question() dialog launching function into a
class derived from wx.Dialog. This implements a custom yes/no dialog
that is consistent between different operating systems.
* Layout improvements for the wizard pages on Mac OS X.
* Fix for the split/double help menu entry on Mac OS X, the
SetMenuBar() call happens after all the menus are created.
* Created a script for forcing relax's GUI mode (relax_gui_mode.py).
* Added a script for building application packages of relax.
This currently supports the building of a stand alone Mac OS X app
(i.e. no python needed).
* The exit relax dialog now has a title.
* The Mac OS X build and dist app directories have been added
to the scons clean_all target.
* Created a Mac OS X .icns version of the relax icon.
* Created a task bar icon for Mac OS X.
* The about windows now have titles (this makes the windows
identifiable).
* The relax icons are now used for all of relax's windows.
* Better icon support in the GUI. The ulysses.ico file is now
being used as it is an bundle of images, and the icon bundle is now
set for the main window.
* Created transparent background images of the diffusion
tensors for the model-free auto-analysis tab.
* Added a series of 4 buttons for calling value.set in the
model-free auto-analysis tab. This is to make it obvious that the
CSA, bond length, heteronucleus type, and proton type need to be set.
* A number of improvements to the value.set GUI user function.
The on_display() method has been renamed to update_parameters() so
the parameter list can be updated only when needed. The set_param()
method has been added to set a starting parameter and its default
value.
* The GUI user functions now show a busy cursor when loading
so that the user isn't confused, wondering why relax is not
responding.
* The value.set GUI user function now sets the value to the
default when parameters are selected.
* Expressions can now be used in the value.set GUI user
function for the number types.
* Modified the gui_raise() function to have the raise_flag
argument allowing the raising of the error to be skipped.
* Created the analysis tab base class variable
width_main_separator, this increases the space between the left hand
side graphic and the right hand side elements.
* relax is now started maximised in GUI mode.
* The value.set user function GUI page now properly converts
the value to the correct type.
* The relax controller is now colouring the status module lock
and observer print outs.
* Improvements and fixes for the debugging print outs from the
status module, and the text now goes to sys.stdout.
* The observer objects are now printing out execution
information when in debugging mode.
* All acquire() and release() calls for the spin_lock and
pipe_lock objects now are named, the name argument is now supplied to
these methods.
* The Relax_lock object now has much better debugging
facilities, and responds to the debug flag.
* Renamed the Relax_lock debug argument to fake_lock, again
this is used to fake the locking mechanism, whereas debugging could be
more fine grained.
* The Relax_lock object now has a 'name' argument which will
be used in debugging.
* The pipe_lock locking object is now the special Relax_lock,
this will allow for fine grained debugging.
* All pages of the Rx peak list wizard now cannot proceed on
an error, this will trigger the user function flushing.
* A copy of the GUI interpreter singleton is now initialised
in the wizard, this is used for the flushing of user functions prior
to proceeding.
* The GUI interpreter object has been converted into a singleton.
* Changed the missing spin parameter messages to indicated
that the value.set user function is needed.
* Converted the missing data dialog into its own wx.Dialog
derived class. The dialog is now completely constructed by relax and
will be constant across different operating systems.
* Added data checks for the dauvergne_protocol GUI
auto-analysis tab. This allows for a dialog telling the user what is
missing.
* Redesigned the dauvergne_protocol mode selection in the GUI.
A special GUI element has been added to the analysis tab with a
button that launches a new window for mode selection. Therefore
clicking on 'Execute relax' instantly starts the analysis.
* Redesigned how the auto-analyses are handled by the status
singleton. The init_auto_analysis() has been created, and each
analysis has its own status container within the status.auto_analysis
dictionary.
* Modified the dauvergne_protocol.py sample script to use the
new design of accepting a filled data pipe.
* Removed the 'exclude' file name from the model-free data
assembly in the GUI.
* Changing the model-free model selection in the
dauvergne_protocol of the GUI now sets a red flag on the button.
* The add_button_open() analysis base class method now returns
the button.
* Converted the relaxation data list GUI element to a
wx.ListCtrl to match the spectra list element.
* Converted the spectra list GUI element from a wx.Grid
element to a wx.ListCtrl element. This is visually more appealing,
and is easier to control.
* The question() dialog now only appears when the
status.show_gui flag is set.
* The SetValue() call for the model-free model list GUI
element now updates the element with the new values.
* A strong warning is now given to the user if they try to
modify the model-free model list.
* Implemented the model-free model selector window.
* Created the gui.misc.list_to_gui() function for converting
Python lists to GUI strings.
* Removed the GUI README file as it is very much out of date.
* Shifted all of the font definitions into the new fonts module.
* Shifted the model-free model selection GUI element into the
new Model_list class.
* Expanded the docs for the relax_data.read user function to
include the Varian and Bruker frequency parameters.
* The spectrum and relaxation data lists now post EVT_SIZE
events when modified. This forces the parent scrolled panel to
properly layout out its contents and refresh.
* Removed visual artifacts in the wx.grid.Grid elements used
in the spectrum and relax data lists. All cells are now set to the
background panel colour, and then individual cells are set back to
white. This removes the visual artifact of white outside of the wx
grids.
* Spacing improvements in all the auto-analysis GUI elements.
* The virtual width of the analysis GUI elements now matches
the real width. The horizontal scrollbar has also been disabled.
* Converted all of the GUI analysis objects into instances of
wx.lib.scrolledpanel.ScrolledPanel.
* The ds.relax_gui data structure is initialised if absent
when associating a pipe with a new tab.
* The popup menu is not shown if the status.show_gui flag is not set.
* The auto-analysis initialisation can now associate with a
pre-existing data pipe.
* The data pipe editor now has a new 'Associate with a new
auto-analysis' menu entry.
* Added a hybridise button to the data pipe editor.
* The data pipe editor is now registered with the gui_analysis
observer.
* The observer status.observers.gui_analysis is now notified
of all changes to the analysis tabs.
* Created an observer object (status.observers.gui_analysis)
for changes to the GUI analysis tabs.
* The execution of the callback functions in the observer
objects is now ordered based on the registration order.
* The data pipe editor can now be opened with Ctrl+D.
* Changed the pipe_switch observer object to pipe_alteration
and all pipe changes are now signalled.
* Implemented the data pipe editor window, this will be used
to manipulate data pipes including how they interact with the GUI.
* Converted the menu build_menu_item() method into a function
of gui.components.menu to allow it to be used more easily by other
parts of the GUI.
Bugfixes:
* Fix for the pymol.cone_pdb user function for frame order
models with no alpha average position angle. This is specifically for
the isotropic cone and free rotor model, although other models might
also be affected by this fix.
* Fixes for the add_molecule() structural API method.
* Fix for the internal structural object add_molecule() method
for when no models exist, now a model is created if none currently
exist.
* A lot of fixes for the internal structural object for
handling multiple models.
* The internal structural reader can now create PDB files if
atom numbers are missing, fixing the structure.write_pdb user function
in certain edge cases.
* Bug fix for the pymol.cone_pdb user function for when there
is no average domain position. This is necessary for the old 2-domain
N-state model analysis type.
* Bug fixes for the n_state_model.cone_pdb user function, the
code was old and not functional any more.
* Fix for the frame_order.cone_pdb user function, the
create_cone_pdb() function was referencing a non-existent variable.
* Fix for the set up of Monte Carlo data for fixed alignment
tensors in the N-state model. The _minimise_setup_fixed_tensors()
method has been fixed to return the actual tensor rather than
simulation for the fixed tensors, as there is no simulation tensor in
that case.
* Bug fix for the relax_io.read_spin_data() function for spin
IDs - spin IDs can now be handled if they are the first column in the
data file.
* Bug fix allowing relax to be run in profiling mode. This
has been broken since the merger of the multi-processor branch.
* Fix for the paramag.centre user function when a numpy array is used.
* Fixes for the N-state model optimisation setup if PCS or RDC
data is not loaded.
* Bug fix for the setup of the N-state model target function,
triggered by missing data.
* Fix for a divide by zero error in the PCS Q factor function.
* The RDC and PCS Q factor functions are now more robust when
data is missing.
* Bug fix for the grace.write user function for when the spin
ID is specified, the spin ID was previously unused.
* Bug fix for the Monte Carlo simulation data generation for
the N-state model. The create_mc_data() method was always skipping
RDC and PCS data due to an incorrect check for the presence of that
data.
* Bug fix for the logging and teeing command line options.
* Bug fix for missing RDC back-calculated data (rdc_bc). If a
sequence is read from a PDB file, but the N-H bond vector cannot be
extracted due to a missing proton, the alignment tensor fit to RDC
data (specifically the Monte Carlo simulations) would fail.
* Bug fix for a newly introduced dependency on the wxPython
module. This wx module is now optional, and only required for the GUI
mode. This allows relax to run without this module installed.
* Bug fix for IO capture in the test suite with Python 2.6 or
below. The RelaxTestRunner._makeResult() replacement method has been
reinstated. Replacing the class variable resultclass does not work
with earlier versions of the unittest site-package.
* Fix for bug #18790 (https://gna.org/bugs/?18790) - the
negative relaxation data errors.
* Fix for bug #18789 (https://gna.org/bugs/?18789) - the zero
errors in Grace files. The problem was that the errors were being
taken as the X-axis error values, which in the case of spin specific
data is zero. Now the Y-axis errors are taken rather than the unused
X-axis errors.
* The status.test_mode and status.show_gui flags are now
initialised only once in the singleton to prevent them from being
overwritten when a reset() call is made.
* Mac OS X bug fix for changing pipes in the spin viewer
window. The pipe selector element event GetString() method was
returning None as this is a read only ComboBox (in wxPython 2.9).
* Fixes for Mac OS X with wxPython 2.9 for the spin viewer
window activation/deactivation, this is now via wx.CallAfter() calls
to prevent memory leaks.
* Bug fix for Mac OS X when using wxPython 2.9.2.4 whereby
wx.SafeYield() is causing 'Bus errors'. The wx.SafeYield(None, True)
calls have been replaced by wx.GetApp().Yield(True) calls, which
should do the same thing but do not cause bus errors on this
developmental version of wxPython. This fix is important as the
future Mac OS X relax app will use this version of wxPython for 64-bit
and Cocoa support.
* Bug fix for the reporting of non-matching lines in the
spectrum.read_intensities user function. The file data printed did
not match the actual intensity data currently being processed, hence
the wrong data was being printed as non-matching.
* Fix for running the test suite in debugging mode. The
self.capt StringIO structure is always necessary for the final print
out.
* Fix for the results viewer window on MS Windows - it is no
longer hidden after switching pipes. For some reason MS Windows
always brings the main GUI window to the front when pipe switches
occur (probably the notebook switching).
* Bug fixes for racing in the results viewer window on MS
Windows, wx.CallAfter() calls are required for this to work.
* MS Windows bug fix for pipe switching in the data pipe
editor window, the pipe window would be hidden after the switch.
* MS Windows bug fix for the pipe editor window, the
wx.Yield() call has been removed from the update_grid() method as it
causes a wx._core.PyAssertionError on Windows.
* Bug fix for racing in the GUI on MS Windows when the relax
prompt window is open. This was caught in the test suite, and only
affects MS Windows. Now a wx.CallAfter() call is used to enable the
GUI element.
* Bug fix for the GUI interpreter thread flushing on MS
Windows. The Python Queue.empty() method is documented as being
unreliable - and that is indeed the case on MS Windows (not on
GNU/Linux or Mac OS X though). It sometimes returns false,
continually, when the queue is completely empty.
* A lot of bug fixes for MS Windows with the handling of the
busy cursor. All calls to wx.EndBusyCursor() are preceded by a check
via wx.IsBusy(). For some reason, in contrast to other operating
systems, MS Windows will sometimes turn off the busy cursor by itself.
A subsequence call to wx.EndBusyCursor() results in an error.
* Bug fix for the main window status bar on MS Windows, the
text is now being set with wx.CallAfter calls.
* Fixed a bug on MS Windows for the 'Close all analyses' menu
entry and toolbar button. The sequence of internal events is very
different on Windows compared to Mac OS X and GNU/Linux, and not
everything had been processed before everything was deleted resulting
in updates to dead GUI elements.
* Bug fix for the new analysis wizard cancelling on Mac OS X.
* Bug fix for the closure of the new analysis wizard window.
* Bug fix for MS Windows - the spin viewer window was being
hidden by the main window when switching pipes.
* Bug fix for racing in the spin viewer window when switching pipes.
* Fixes for the peak list wizards for the NOE and Rx
auto-analyses for Mac OS X.
* Bug fix for many unit tests on MS Windows. The os.tmpfile()
call has been replaced by tempfile.mkstemp() in the data types passed
into the unit tests of the prompt interface. The os.tmpfile() call on
Windows results in a "OSError: [Errno 13] Permission denied" error.
* Bug fix for the scons clean target on MS Windows. The build
and dist directories from the Mac OS X py2app program are now only
deleted by the clean_all target which checks for the paths.
* Bug fix for a race condition on MS Windows blocking the test
suite. The analyses update_spin_count() call sets the value of the
spin systems GUI element. This is now via a wx.CallAfter() call to
prevent the race in the GUI.
* Bug fix for MS Windows - the user function menus are now
fully deactivated during execution lock. The submenus were strangely
not all being deactivated, so now all submenu items are also
deactivated.
* Bug fix for the switching between analysis tabs on MS
Windows. The tab had not been changed when on_page_change() was being
called (in contrast to GNU/Linux and Mac OS X). Now
wx.EVT_NOTEBOOK_PAGE_CHANGED is being used to bind the page change
event rather than wx.EVT_NOTEBOOK_PAGE_CHANGING.
* Bug fix for the structure.vectors user function back end,
the check for already existing vector info now should work.
* Fix for the results viewer window on MS Windows, the user
functions now have the results viewer window set as the parent so that
the window is not hidden by the main GUI window coming to the front.
* Fix for the pipe editor window on MS Windows, the user
functions now have the pipe editor window set as the parent so that
the window is not hidden by the main GUI window coming to the front.
* Fixes for the residue.create and spin.create user function
GUI pages on MS Windows. The default values are now correctly set.
This affects the pop up menu in the tree part of the spin viewer
window.
* Fixes for the user functions launched from the tree part of
the spin viewer window on MS Windows. The spin viewer window is now
set as the parent, so that the main GUI window does not come to the
front.
* The user functions in the spin viewer window now have the
parent window correctly set. This is to help with an MS Windows
window ordering bug.
* Analysis tabs are now removed if the associated data pipe is
deleted, avoiding nasty GUI crashing.
* Fixes and improvements for the peak list wizards in the NOE
and Rx auto-analyses. The integration points page is now correctly
set up. And the spectrum ID is now only set if the field is blank,
preventing a reversion of the user selected value.
* The parent of the Question dialog in the pipe editor window
is set so the window doesn't disappear. Without this, the main GUI
window comes to the front after the dialog is shown.
* Fixes for the main GUI window moving in front of the spin
viewer window. The spin viewer window is now set as the parent for
the Question dialogs, so that this window remains at the front.
* Fixes for the residue user function GUI pages for when
default values are sent to the page. This fixes the user functions in
the spin viewer window.
* Fix for the new gui_to_str_or_list() function.
* Bug fix for the structure.read_pdb GUI user function, the
values from the GUI are now converted to the correct form.
* Fix for the Help->Licence menu entry for the new GUI user
function design, this additionally opens the relax controller window
so the user will see the text.
* Fixes for the pipe editor window to handle the new GUI user
function design.
* Fixes for the relaxation data reading GUI element for the
new GUI user function design.
* Fixes for some of the GUI user function calls from the tree
part of the spin viewer window.
* Fixes for the GUI user function launching in the model-free
auto-analysis tab.
* The spin viewer window now uses the full user function menu
of the Uf_menus class, this should now remove the MS Windows bug
whereby the spin viewer window would disappear to the back after
closing of the user function wizard dialogs.
* Fixes for the auto-analysis wizards for the new user
function GUI page design.
* Fixes for the GUI tests for the new design of the user
function GUI pages.
* Fix for the script user function GUI element for opening the
file dialog.
* Fixes for the relax controller, pipe editor and results
viewer windows under MS Windows. These windows were all dark grey,
the default frame colour under MS Windows. Now all elements are
packed into a wx.Panel which sits inside the wx.Frame.
* Added checks for a current data pipe to a number of GUI user
function pages, this prevents relax errors when trying to launch the
user functions but when no data pipes exist.
* Fix for the MS Windows BAT file so that relax can be
launched from the Windows PowerShell.
* Fix for the dauvergne_protocol model-free auto-analysis with
the deletion of data pipes. Now only the data pipes created by
dauvergne_protocol are deleted. This fixes the problem whereby data
pipes from other analyses are deleted by dauvergne_protocol, breaking
the GUI.
* Fix for the spin viewer window for MS Windows, the
get_info() method now catches if no item is selected in the tree
before trying to get the Python data from it. Asking for Python data
from a missing TreeCtrl item ID works on GNU/Linux and Mac OS X, but
not on MS Windows.
* Bug fix for MS Windows - the main relax window is now
maximized upon start up.
* Mac OS X fix for the relaxation data list element - the
height algorithm is now more robust. The ListCtrl.GetSize() method
appears not to work on Mac OS X. Therefore a different algorithm has
been designed to get around this Mac specific problem.
* Fix for the relax_fit.relax_time GUI user function. The
combobox GetValue() call has been replaced by GetStringSelection() for
the spectrum ID.
* Removed the wx.Yield() call from the spin viewer window
refresh() method, this is to prevent recursive wx.Yield calls on Mac
OS X from killing relax.
* Fix for the Rx peak list wizard for Mac OS X, the combobox
SetValue() call has been replaced with SetStringSelection().
* Fix for the NOE spectrum loading wizard - the comboboxes
need SetStringSelection rather than SetValue calls. SetValue and
GetValue on the read only combo boxes seems to fail on Mac OS X.
* Mac OS X bug fix - the busy cursor is only turned off in the
gui_raise window code if the busy cursor is on.
* Mac OS X bug fix for racing in the GUI interpreter thread.
The flush() method was not working properly on Mac OS X, so hopefully
now it is thread-safe.
* Bug fix for Mac OS X for the spectrum.replicated GUI user
function. A GetValue() call fails on Mac OS X for a read only
wx.ComboBox if no value is set.
* Fix for the Rx auto-analysis GUI test for the changes to the
spectrum.replicated user function GUI page.
* Another Mac OS X test suite fix - the spin viewer window
menu bar is now no longer set in the gui tests.
* Bug fix for the test suite under Mac OS X - the GUI's
SetMenuBar method is only called if status.show_gui is set. This
prevents the menu bar from starting when running the GUI tests.
* Bug fix for Mac OS X - the timer in the relax controller is
started with a wx.CallAfter() call. This is to ensure that it will
start from the main thread, which is essential.
* All wx calls to Show(), ShowModal() and PopupMenu() are now
suppressed if the status.show_gui flag is not set. This is to
eliminate problems of GUI elements starting up in the test-suite under
Mac OS X.
* Fixes for many user function GUI pages for when the apply
button is clicked. The combo box GUI elements were having data
appended each time on_display() is called (this happens with a click
on the apply button), but the previous values were not cleared out.
This results in very long repetitive lists.
* Removed a recursive call to wx.Yield in the spin viewer
window as this is fatal on Mac OS X.
* Fixes for the spectrum.replicated user function GUI page for
when the apply button is hit. The spectrum IDs were continually
appended to the ID boxes, so the lists could get quite long.
* Fix for the model-free model changing question dialog in the
dauvergne_protocol analysis. The dialog is now larger to see all
text, and the answer is no longer back to front.
* Bug fixes for all of the specific analyses for running Monte
Carlo simulations multiple times. Many of the specific analyses were
raising RelaxErrors if simulations had previously been run. Now this
no longer occurs, so that the analysis can be re-run which is
important in GUI mode.
* All of the major GUI and X freeze fixes have been ported to
the relax data list. The fixes for the spectrum list GUI element are
now present in the relaxation data list GUI element as well, as the
same problems occur in both code paths.
* Fix for the size_cols() method of the spectrum list GUI
element. With the asynchronous updating of the element, sometimes the
columns are not setup prior to a size_cols() call.
* Bug fix for the freezing of X windows! The spectrum list
GUI element is now updated with a CallAfter() call so that the element
is updated in a thread safe way. Without this, the entire X windows
system would sometimes freeze!
* Bug fix for the freezing of the GUI. The spectrum list GUI
element was trying to update itself during execution lock, causing
races if the spectrum data structures in the relax data store are
being modified as the GUI element update is occurring. This would
result in a hard lock of the GUI.
* Fix for the validate_sequence() function - the eval() calls
raise all sorts of errors.
* Fix for the reading of the sequence from generic formatted
files with None in some of the columns. This second problem is for
the non-integer columns as the text 'None' was being interpreted as
the name.
* Fix for the reading of the sequence from generic formatted
files with None in some of the columns. The
generic_fns.mol_res_spin.generate_spin_id_data_array() function now
checks for when the data list contains 'None'.
* Fix for the Rx peak height wizard, the user function flush
flag was incorrectly named.
* Fix for the wizard page _ok() method for the uf_flush flag.
* Fix for the results viewer window file opening.
* Fix for the results viewer window in testing mode - it is
now not shown.
* Fix for the pipe editor window - it is now updated when
initially created to show all loaded pipes.
* Fixes for all the calls to the GUI interpreter instance in
the spin viewer window. This is now a special thread object, and user
function calls are now queued.
* The auto-analysis GUI pages are now waiting for the data
pipe to be created, fixing race conditions.
* Some more fixes for the relax 'mode' class variable, these
problems were due to the multi-processor code merger.
* Fix for the GUI test mode - the mode variable should be a
class variable.
* Fix for the multi-processor code as the PrependOut class has
been renamed to IO_filter.
* Fixes for some of the file dialog wildcards.
* Fix for the opening of Grace files via the results viewer.
It was being launched in both Grace and a text editor!
* The spin viewer tree update() method now acquires both the
pipe and spin locks, preventing a major source of race conditions.
* The File menu entires for new or closing analyses or opening
a state are blocked with the execution lock. This is needed because
the accelerator keys are still active, even if the menu entry is
disabled (possibly a GTK bug).
* The pipe editor window is now acquiring the pipe lock prior
to updating its contents. This removes a lot of race conditions, as
the pipes can often change which the update occurs.
* The execution lock is properly locked or released before
notifying the observers. This will remove some race conditions where
the locked() method is called before the acquire() or release()
methods terminate.
* All wx object Append() calls now have their data passed
through str_to_gui() first as well, this prevents GUI failures due to
the wrong data type being encountered.
* All data passed into wxPython SetValue() calls now go
through gui.misc.*_to_gui() functions, this ensures that the correct
data type is sent into the GUI elements.
* Fix for the stereochemistry auto-analysis - the pipe_name
argument does not exist in this auto-analysis.
* Fix for the dauvergne_protocol - the maximum number of
optimisation iterations is now an int.
* The observers of pipe alterations should now all be thread
safe, pipe changes in relax were causing segfaults in the GUI.
* Fix for the dauvergne_protocol auto-analysis 'final' model.
The final stage of the dauvergne_protocol was broken. The data pipes
here need to be created rather than copied from the initial data pipe
as results are being read into these pipes.
* Fix for the dauvergne_protocol sample script - the mc_num
argument is now called mc_sim_num.
* Fix for the assemble_data() method of the NOE auto-analysis
- the number of spectra can be less than 3.
* Fix for the gui_to_float() for when an integer is given, it
is now converted to a float.
* Fix for the spectral list GUI element on Mac OS X, the
ListCtrl.DeleteColumn() method is faulty on Mac OS X. So instead all
columns are deleted in one go, and then the entire thing is created on
update.
* Fixes for the results viewer window updating on Mac OS X.
The EVT_SHOW event was not being triggered by the frame's Show()
method.
* Bug fix for the dauvergne_protocol - the pipe.copy() calls
are now followed by pipe.switch(). This is needed as previously the
pipe.create() user function call automatically switched pipes, but
pipe.copy() does not.
* The results viewer window no longer fails if relax is still
in the initial state.
* Bug fix for the value.set user function page - the parameter
rather than description is now used. The description rather than
parameter was being sent to the back-end.
* Fix for the spin data check in the dauvergne_protocol
auto-analysis - deselected spins are skipped.
* Fix for the relaxation data check in the dauvergne_protocol
auto-analysis.
* Fix for Mac OS X - the wizard buttons are now all of the
same size. SetMinSize() rather than SetSize() needs to be used with
wx.ADJUST_MINSIZE.
* The dialog Close() rather than Destroy() method is being
used to terminate the wizard, this is necessary for Mac OS X.
* Mac OS X bug fit - removed the Destroy() call after
ShowModal() in the wizard. The Destroy() method was actually being
called twice, the first time either by the _ok() or the _cancel()
methods, and the second time directly after the ShowModal(). This is
fatal on a Mac.
relax version 1.3.13.