This is the first relax version of the new 2.0 line. Due to
incredible number of changes to the core and large improvements
visible throughout prompt and graphical user interfaces (UIs), it was
decided that a brand new development line would be created. The 1.3
line will now be discontinued as it quite old - it came into existence
6 years ago (see
https://mail.gna.org/public/relax-devel/2006-10/msg00053.html).
The features of these release include a complete restructuring of the
user functions so that special 'definitions' are used to automatically
create the user function front ends in all UIs. This now means that
all user functions are now accessible from the GUI. The help system
in the prompt UI mode has been revamped and is now better formatted
(with better line wrapping for MS Windows). The core of the specific
analysis API has been redesigned to make it much easier for NMR
spectroscopists to add their own analysis types to relax. The GUI
test suite has been significantly expanded so that the GUI should now
be, and remain, robust. The XML formatted relax results and save
files have been redesigned and improved for both numerical accuracy
and readability. Data pipes can now be grouped together in special
data bundles, and analysis tabs in the GUI are now associated with a
specific bundle. BMRB export (as well as import) and support for
Bruker Dynamics Centre relaxation data files are now tightly
integrated into the GUI. Many other improvements can be found
throughout the GUI. The incredible number of changes that have gone
into this release can be seen below!
As this is the first release of a new line, a few minor bugs should be
expected. All feedback is appreciated. Bugs can be reported at the
official relax bug tracker through the link
https://gna.org/bugs/?func=additem&group=relax. Any error messages
that are not 'RelaxErrors', any strange behaviour in the GUI such as
windows disappearing out the back, elements not updating, etc., or
anything that does not behave exactly as you would expect should be
treated as a bug!
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:
* A complete restructuring of the user functions - all user
functions are automatically generated within all user interfaces (UIs)
including the prompt and script UI, and the graphical UI (GUI).
* The user functions now have special definitions in the
'user_functions' directory making it very simple to add or modify user
functions.
* Big improvements to the help system in the prompt UI mode.
This is now automatically generated when accessed by the user. Bold
font is now used for section titles and keyword arguments, the user
function class documentation has been expanded and is now related to
the functionality, the user function representation printout is
cleaner, and the text is now wrapped for better display on all
operating systems.
* Automatic creation of the "Alphabetical listing of user
functions" chapter of the relax manual from the user function
definitions.
* The analysis specific API of the specific_fns directory has
been redesigned to extensively use the parameter list objects. Many
API base methods will now automatically work with the parameter list
object, removing the need for a analysis specific implementation.
* The GUI test suite has been significantly expanded. The
system test relax scripts can now be used as GUI tests - the user
functions are executed through the self._execute_uf() method which
allows execution within all UIs, testing out the different code paths.
* The specific and GUI tests can now be executed by group.
For example all the model-free system tests can be run with '$ relax
-s Mf'. This is very useful for relax development.
* The XML formatted results and save files has been redesigned
(it has improved, is more accurate, is easier to read in Python
version 2.7.3 and above, and contains more metadata) and is now at
version 2.
* The printouts of spin specific data has improved with the
addition of an automatic column width algorithm.
* The addition of a new concept called data pipe bundles -
related data pipes can now be grouped together into bundles. For
example in the dauvergne_protocol model-free auto-analysis, all
internally generated data pipes are grouped together in the same
bundle.
* Each GUI analysis tab is now associated with a unique data
pipe bundle rather than a dedicated data pipe. This allows for better
data pipe handling.
* Improved BMRB support. The 'File->Export for BMRB
deposition' menu has been added to the GUI which opens a special BMRB
export window.
* More metadata is now read from the NMR-STAR files into the
relax data store.
* The bmrb.display user function is now operational.
* Big redesign of the Spectral_error_type_page wizard page
used in the auto NOE and Rx analyses - this now includes the full
description of the spectrum.error_analysis user function, so that the
user has easy access to a description of how peak intensity errors and
handled.
* Mac OS X font size and text layout improvements in the GUI.
* Improvements to the spacing at the top and bottom of the
list GUI elements - this includes a spacing before the bottom buttons.
* The relaxation data 'Add' button in the model-free GUI
analysis tab is now a multi-page wizard which allows all of the
relaxation data metadata to be input.
* The model-free GUI analysis tab now has a 'View metadata'
button for opening a window displaying all metadata associated with
the relaxation data.
* The model-free GUI analysis tab now has a button for loading
relaxation data from Bruker Dynamics Centre files.
Changes:
* Spun out the automatic column width formatting code from
relax_io.write_spin_data() to write_data().
* Used some colour for the relax GUI terminating print out
asking for citations.
* The completion of the test suite in the GUI mode now sets
the controller main gauge to 100%.
* Added checks to the BMRB export to make sure all necessary
data has been input. If not, then the Missing_data dialog will be
presented to the user to explain what is required.
* The Missing_data dialog can now have the parent wx element
specified. This is needed when launched from a child window such as
the BMRB export window.
* Improved the robustness of the bmrb.write user function for
missing data - this is in the
generic_fns.diffusion_tensor.bmrb_write() function, and is for missing
atomic information required for the Tensor_list saveframe.
* The bmrb.read user function is now reading in all of the
relaxation data metadata into the data store.
* Improved the robustness of the bmrb.write user function for
missing data - this is in the generic_fns.relax_data.bmrb_write()
function, and is for missing atomic information related to relaxation
data.
* The bmrb.read user function is now extracting the thiol
state of the molecule.
* BMRB improvements - the molecule type is now read from the
entity record and stored in relax.
* Added more display tests for the BMRB system test script.
* BMRB output improvements - deselected spins are no longer
skipped and the model-free BMRB output is also more robust to missing
data.
* More extensive testing of the bmrb user functions.
* Added a call to the bmrb.display user function in the
bmrb_rw.py test suite script.
* Shifted the GUI user function page _format_table() and
_table_line() methods into the misc module. These are now the
gui.misc.format_table() and gui.misc.table_line() functions, allowing
the code to be used in other parts of the GUI.
* Decreased the size of all the GUI auto-analysis wizards to
fit in a 1024x768 screen.
* Created a small molecule wizard graphic for the
structure.read_xyz user function.
* Refinement of all of the GUI user function wizard sizes.
* The default GUI user function description minimum height has
been increased to 300 px - removing a lot of scrolled descriptions
automatically.
* Increased the default size of the GUI user functions.
* Spacing and layout improvements for the GUI user function
descriptions.
* The dauvergne_protocol sample script initial pipe name has
been modified to include the pipe bundle.
* The GUI now sends the pipe bundle name into the relax_fit
and noe auto-analyses.
* The relax_fit and noe auto-analyses now centre around the
pipe bundle rather than data pipe name.
* The about dialog now used the gui.fonts module - this allows
the fonts to scale to a decent size on Mac OS X, so that the text is
readable.
* Added a set of roman fonts to the gui.fonts module - this
will be used by the about dialogs.
* Font size improvements for Mac OS X - the fonts are now
roughly the same size as on GNU/Linux and MS Windows. An operating
system specific font scaling is now used, with the Mac OS X fonts each
being increased by 2 pixels.
* The dauvergne_protocol auto-analysis now adds the pipe
bundle name to all created pipes as a suffix. This is to uniquely
identify the data pipes, and to allow more than one model-free
analysis to be executed per relax instance (useful for the GUI).
* The analysis wizard now suggests the starting data pipe to
be named 'origin - ' + pipe_bundle - this allows unique data pipe
names for each analysis.
* Temporarily disabled the Mac OS X task bar icon as it is
currently horribly broken in wxPython 2.8 and 2.9.
* Renamed the GUI toolbar() method to build_toolbar(), as the
toolbar object is also called 'toolbar'!
* Updated the relaxGUI splash screen copyright notice.
* Improved the button size and spacing in the list GUI elements.
* The bmrb.write user function now adds the file to the
cdp.result_files list and notifies observers.
* Converted all of the list GUI element 'stretch' args to
'proportion' - instead of a flag, this is now the direct window
proportion parameter used in the wx.Sizer.Add() methods. This has
been changed in the BMRB export window so that the central molecule
list GUI element is half the size of the others.
* Created the BMRB export window - this includes the following
elements: A title with description and BMRB icons; the data pipe
selection element; the relaxation data meta data GUI element; the
molecule list GUI element; the software list GUI element; the script
list GUI element; the citation list GUI element; buttons for
previewing, exporting, and cancelling.
* The action_export_bmrb() method now opens the BMRB export window.
* The base list objects are now updated when pipe changes occur.
* Created a 100x100 version of the BMRB logo - this will be
used for the export window.
* The spin viewer window now uses graphics.fetch_icon() and
shows the button text in the toolbar.
* Added the mimetypes/text-x-texinfo.png Oxygen icons. This
is for the relaxation data metadata button.
* Merged the spectrum list GUI element into the base list element.
* Merged the relaxation data list GUI element with the base
list element. The base list element now has a delete() method, though
I'm not sure if it is ever used. Now all list GUI elements are
derived from the Base_list class. This will simplify changing or
improving all of these elements.
* The base list element now has an Enable() method which
simply enables or disables all buttons (as is done in the relaxation
data list). The button size is now specified as a (x, y) tuple. And
the GUI object can now be passed into the elements, as this is needed
for the relaxation data metadata window.
* Large simplifications of the relaxation data metadata list
GUI element by using the Base_list class.
* Modified the molecule list GUI element to use the Base_list
base class. The base list GUI element has also been updated to
support popup menus and to change the StaticBox label upon updates.
The base is_complete() method has also been added to always return
True.
* Small updates to the base list GUI element.
* Created a GUI element for listing and setting the citations
relevant for the analysis - this will be used in the BMRB export
window.
* Created a GUI element for listing and setting the scripts
used in the analysis - this will be used in the BMRB export window.
* The GUI user functions now have a subtitle at the top
stating the name of the user function - this is to reinforce the user
function naming system to the user, and also to clearly identify which
window belongs to which user function.
* Split the software GUI element into the base_list base GUI
listing element - this base class will be useful for abstracting many
of the list GUI element methods.
* Created a GUI element for listing and setting the software
used in the analysis - this will be used in the BMRB export window.
* Created a GUI element for listing and setting molecule
attributes - this will be used in the BMRB export window.
* The lists in the GUI user function descriptions are no
longer separated by blank lines - this allows long lists to fit much
better into the wizard windows.
* More improvements for the bmrb user function definitions.
* The GUI user function objects can now be called with the
wx_wizard_sync and wx_wizard_modal args. This is used to force the
user function to operate synchronous or asynchronous mode, or to force
the user function wizard to be modal. This will allow a number of
hacks to be avoided throughout the GUI.
* Added a check to the bmrb.write user function to see if the
file name has been supplied. This results in a nicer message for the
GUI.
* The bmrb.display and bmrb.write user functions now have the
version defaulting to 3.1. The choices are now also restricted to
2.1, 3.0, and 3.1.
* The user function wizard pages now have an on_back() method
which unregisters the observer. This is needed as going back
previously did not unregister the observer the object, hence going
forwards after going back would fail.
* The wizard now has an on_back() method available to perform
actions when going back. The on_next() method has been fixed in that
it is called even when the page is skipped.
* Activated the apply and skip buttons in the relaxation data
GUI element data reading wizards.
* The relaxation data 'Add' and Bruker 'Add' buttons now
launch wizards whereby the first page is the original relax_data.read
or bruker.read user functions, but then this is followed by the
relax_data.peak_intensity_type, relax_data.temp_calibration and
relax_data.temp_control user functions. This allows the metadata to
be set up prior to the model-free calculations.
* The relax_data.delete user function now removes all of the
metadata associated with the ID.
* Changes to the relaxation data GUI element button layout.
The buttons are now all of the same width, and the metadata button is
now last.
* The relaxation data GUI element now has a button for opening
the relaxation data metadata element. This 'View metadata' button
will launch the new Metadata_window wx.Frame. This window contains
the relaxation data metadata GUI element stretched to fit the window.
* The relaxation data metadata list GUI element now can
stretch to fill the parent, if asked. This will be used when the list
is embedded within a window by itself.
* Created a GUI element for displaying and editing the
relaxation data metadata. This is very similar to the relaxation data
list GUI element, and it will be used in the BMRB export.
* Refinement of the relax_data.peak_intensity_type user
function definition.
* Big expansion and improvements of the
relax_data.temp_control user function definition. There are also a
few edits of the relax_data.temp_calibration definition.
* Created a 200x200 pixel version of the status.weather-clear
Oxygen icon. This is for the relax_data.temp_calibration and
relax_data.temp_control user function wizards.
* Big expansion and improvements of the
relax_data.temp_calibration user function definition.
* Improvements for the Force_true object for the 'force flag'
user function argument types. This invisible GUI element can now have
its value set. The SetValue() method will internally store the value,
and GetValue() will then return this value. The initial value is
True. This allows the BMRB GUI tests to pass again.
* The spin.name and spin.element user functions in the BMRB
system and GUI tests now use the force flag set to False. This is to
try to replicate the old behaviour of the test and to allow it to pass
again.
* The BMRB icons now also have transparent backgrounds.
* Made the background of the BMRB wizard graphic transparent -
this just looks better.
* Created a menu entry called 'File->Export for BMRB deposition'.
* The spectrum and relaxation data list GUI elements now use
graphics.fetch_icon for all icons.
* Renamed some of the methods in the relaxation data list GUI element.
* The spectrum and relaxation data list GUI elements now use
the user function definitions for icons.
* Changed the relax_fit.relax_time icon to the
actions.chronometer Oxygen icon.
* Added the chronometer.png Oxygen icon.
* Large expansion of the pop up menu for the spectral list GUI
element. This now includes most of the spectrum and relax_fit user
functions.
* Added accelerator keys for all of the spin viewer window
tree pop up menus.
* Large expansion of the pop up menu for the relaxation data
list GUI element. This now includes most of the relax_data user
functions.
* Implemented the relax_data.frq and relax_data.type user
function definitions and backends.
* Created the Relax_data.test_reset() system test for testing
relax_data.frq and relax_data.type.
* Big reworking of the spin viewer window tree element. Many
new pop up menu entries have been added covering almost all of the
molecule, residue, and spin user functions. The methods bound to the
pop up menu entries have all been renamed to 'action_'+type+'_'+user
function name. And the residue and spin changes checking has been
fixed to include checks for the naming and numbering.
* Set the force flag args for a few spin and residue user
functions to the 'force flag' arg type.
* The molecule.name and molecule.type user function force args
are now of the 'force flag' arg type. This hides the arg in the GUI.
* Added support for the user function arg type 'force flag' to
the GUI user functions. This arg type will, in the GUI, always return
True. This is because a user clicking on 'Ok' or 'Apply' is
essentially saying that this operation should be performed. The
special Force_true class was created for these arguments which simply
ignores SetValue() calls and always returns True from GetValue()
calls.
* Formatting fixes for the molecule.create user function definition.
* The relax save and results XML files now include subversion
details in the <relax> tag. This indicates the repository version and
the URL, allowing for better debugging.
* The 'relax --version' print out now includes the full
subversion info, if it is a checked out copy.
* Improvement for the model-free auto-analysis in the GUI.
After execution, the main data pipe of the analysis tab is now set to
the 'final' data pipe generated by the dauvergne_protocol. This means
that when switching between analysis tabs, that going back to the
model-free tab will make the 'final' data pipe the current one, rather
than the data pipe used to initialise the analysis.
* Better handling of the GUI wizard termination. The
_handler_close() method is now handling the close events and together
with the _ok() method,both now execute the current page's on_next()
method. This means that on_next() is called for all avenues for
exiting the wizard. This allows the user function pages to unregister
themselves with the observer objects.
* The wizard window _cancel() method now calls the current
page's on_next() method. This allows the page to clean itself up.
* The GUI analysis pipe_deletion() method now works with pipe
bundles instead of pipe themselves. This is because the analysis tabs
are now associated with the bundles rather than pipes.
* The 'bundle' arg is now functional in the model_selection
user function back end.
* Added the 'bundle_to' arg to the pipe.copy user function
back end. This arg is now functional.
* The dauverge_protocol auto-analysis now uses the new
'bundle' user function args. This is used in the pipe copying to
place the newly created pipe and in the model selection, both so that
all pipes created during the analysis are located within the pipe
bundle reserved for that analysis.
* The GUI user function window titles are now set to the
'title_short' value. This is because the long title can be far too
long for a GUI window title!
* The long title or synopsis is now added to the GUI user
function description text as italic text.
* Added the 'bundle' arg to the model_selection user function
specification.
* Improvements to the 'bundle' arg specification of the
pipe.create user function.
* Added the new 'bundle_to' arg to the pipe.copy user
function. This will be used to associated a newly copied data pipe
with a pipe bundle.
* Added some backwards compatibility code for old GUI state
files missing pipe bundles.
* Created a GUI test for loading an old relax 1.3 save state
containing GUI analyses.
* Updated the dauvergne_protocol auto-analysis to spawn all
pipes into the named bundle.
* The generic_fns.pipes.pipe_names() function now can restrict
the list of names to a specific bundle.
* The pipe editor window now handles the pipe bundling
concept. There is a new button for the pipe.bundle user function, a
new column showing the pipe bundles, and the pop up menu allows pipes
to be associated with bundles if not already bundled.
* The pipe.bundle user function back end now notifies all the
pipe_alteration observers of the change. This is required for proper
GUI interaction.
* Refinements to the pipe.create user function definitions.
* The GUI analysis tabs now work with data pipe bundles rather
than the original data pipe. The analysis wizard now uses the unique
name for the new data pipe bundle field, and the starting data pipe
defaults to 'origin'. The analysis pages show the bundle name rather
than associated data pipe.
* The pipe.delete user function is now cleaning up the data
pipe bundles as needed. The deleted data pipe name is removed from
any bundle it is in, and empty bundles are eliminated.
* Implemented the generic_fns.pipes.has_bundle() function for
determining if a bundle exists.
* Modified the pipe.display user function backend to show the
pipe bundles. This required the addition of the
generic_fns.pipes.get_bundle() function.
* Implemented the pipe.bundle user function, including the
full description and the back end.
* The data store is_empty() method works again - the
pipe_bundles structure is now blacklisted.
* Shifted the pipe bundle graphic and created a wizard PNG
file for the GUI user function.
* Created icons for the pipe bundle concept.
* Implemented the generic_fns.pipes.bundle_names() function
for returning a list of all pipe bundles.
* The pipe.create user function now creates pipe bundles in
the back end. The new ds.pipe_bundles dictionary is used to hold
lists of pipes associated with the pipe bundle name as the dictionary
keys. The 'bundle' arg is passed into the ds.add() method for
storage.
* Added the 'bundle' keyword arg to the pipe.create user
function definition.
* Preparation for the implementation of pipe bundle concept -
addition of system and GUI tests. This new pipe bundling concept is
simply a way of grouping data pipes together. This will be useful
for: grouping and categorisation of data pipes when multiple analyses
are performed, the model-free dauvergne_protocol auto-analysis will
place all the data pipes it creates into one bundle, for the GUI mode
analyses will be linked to pipe bundles rather than data pipes. This
will allow switching data pipes to activate the correct analysis.
* The 'verbatim' user function description elements are now
properly formatted in the GUI. These elements now use the
font.modern_small formatting to have fixed-width characters.
* Table formatting improvements for the GUI user function
descriptions.
* Improved the whitespace formatting of the spin data write
out of relax_io.write_spin_data(). Now the column sizes are
dynamically changed to match the data being written out. This is to
fix the ugly write outs for when the name of the molecule is very
long.
* Replaced all mention of 'arguments' from the user function
docstrings with human readable text.
* The state.load user function will now recreate the GUI tabs.
For this, the new state_load observer object has been created. The
GUI analysis load_from_store() is registered with this object. And to
prevent fatal racing in the GUI, the state.load user function
operation is now synchronous. The state.load and state.save file arg
defaults are now also set to 'state.bz2'.
* Removed a printout in the API documentation compilation.
* All of the user_function.object.Table instances in the
specific code descriptions are now private. This hides them from the
specific API, and allows the unit tests to pass.
* Removed the vertical lines in the tables of the prompt UI
help strings. The tables now look much more professional.
* The GUI user functions now use the new Desc_container and
Table user function classes. The descriptions for the user function
wizard pages are now being taken from the new
user_functions.objects.Desc_container objects, lists of which are the
user function definition 'desc' objects. The tables via the
user_functions.objects.Table object is being formatted as in the
prompt user function help text, though without vertical lines. The
lists and itemised lists are currently formatted the same as in the
prompt UI.
* The Desc_container.element_loop() method can now yield the
title too, if asked.
* Better spacing in the list of tables section of the PDF user manual.
* Complete rewrite of the docs.latex.fetch_docstrings module.
This is a significant simplification for the creating of the user
function documentation within the user manual. Some of the long list
of changes include: The file docs/latex/fetch_docstrings.py is no
longer an executable script and now operates solely as a Python
module; all of the original docstring section parsing code has been
eliminated; the searching for user functions in the prompt UI
namespace has been replaced; the new user function definitions are
directly used and the documentation for each user function section
generated via the self.build_*() methods; the complicated ascii table
parsing and rebuilding into a LaTeX table has been eliminated; the
self.write_*() methods have been created for building the various
sections of the user function documentation (paragraphs, verbatim
text, prompt examples, lists, itemised lists, and tables); tables are
no longer duplicated, triplicated, etc. and instead a reference to the
first instance of the table is inserted - this is a significant space
saver as one of the copies of the multi-page X11 colour table is
removed.
* Renamed the Uf_tables.add_table() 'title' arg to 'caption',
and added the new 'caption_short' arg. The name change is fairly
logical, as this is a caption. The 'caption_short' arg will be used
for the list of tables in the LaTeX user manual.
* The Molmol colour table is no longer a LaTeX longtable in
the user manual.
* The prompt UI table creation is now using the Table.spacing
variable for adding empty lines between rows.
* The Monte Carlo description now uses an itemised list for
the listing of the steps involved.
* The prompt UI help string construction code is now handling
the new Uf_tables singleton.
* Added a check to Uf_tables.get_table() to make sure that the
table corresponding to the label exists.
* Added a check to Desc_container.add_table() to make sure the
label is a string.
* All of the user function documentation tables now use the
new Uf_tables singleton structure. The special properties for the
colour module tables (longtables and now spacing) have been added as
well.
* Created a new way of defining and inputting tables into the
user function descriptions. This introduces the
user_functions.objects.Table for holding all the table data and
metadata, and the user_functions.data.Uf_tables singleton object for
holding all the tables. This design will allow more metadata (for
example using longtables in the LaTeX user manual) to be specified.
The singleton collection of tables with unique labels will also allow
the elimination of duplicated tables in the PDF and HTML user manuals.
The new table title metadata will also be used for the table headings
in the user manuals.
* Converted a number of add_verbatim() calls to
add_item_list_element() with items of None. This allows for proper
formatting and indentation of equations. In the future, a possible
add_equation() method might be added to provide text and LaTeX
representations of equations in the user function documentation.
* Itemised lists without items are now supported in the prompt
help strings. This is to mimic the LaTeX behaviour to allow lists
with no 'bullets'.
* Shifted the prompt examples to the end of the description
for the value.display user function.
* Converted all of the user functions to use the
Desc_container class design. All of the user function descriptions,
prompt examples, and additional documentation scattered around the
relax sources have been merged into the Uf_info.desc list of
Desc_container objects.
* The 'prompt_examples' and 'additional' user function
structures are no longer passed into the prompt objects.
* Removed the 'prompt_examples' and 'additional' variables
from the Uf_info containers. These have been superseded by the
Desc_container objects.
* Prompt examples are now followed by 2 newlines in the prompt
help strings. This restores much of the original formatting for these
examples.
* Added support for no spacing in tables for the prompt help
strings. The Desc_container.add_table_titles() method now accepts and
stores the 'spacing' arg. This is passed all the way into the prompt
help system to format the tables with.
* Added a check in the prompt help _build_doc() method for the
user function description. This should, together with the
_build_doc() unit tests, help to uncover all unconverted user function
'desc' variables.
* Created an algorithm for wrapping table columns to fit
within status.text_width. This is for the prompt user function
docstring tables. The columns are now dynamically wrapped so that the
table will not be wider than the given width. For example the
value.set user function description table would normally have a total
width of 238 characters, but this now fits within one screen of text
under all operating systems.
* Created two unit tests for the _build_doc() methods of the
prompt user function objects. This is for the prompt user function
class objects and the user function objects themselves. The
_build_doc() methods are used to generate the prompt help strings.
* Converted all of the OpenDX user functions to the new
Desc_container design. This tests out the use of 'additional' outside
documentation.
* Improved the user function class prompt help string. The
user function list now uses bold text, and the user function title is
also now given.
* The prompt help string for user function classes now
includes info about the member user functions.
* The Uf_info.uf_loop() method can now restrict the looping
over a given user function class.
* Large improvements to the prompt help strings for the user
function classes. These are now formatted with section using bold
text.
* The user function default args prompt help string text is now
wrapped.
* Removed the starting newline from the user function prompt
help string.
* Converted the calc, grid_search and minimise user function
descriptions to use Desc_container.
* Tables in the user function descriptions are now formatted
for the prompt help strings. This is for the Desc_container objects.
The list of lists are now converted to the text format originally used
for the user function docstrings.
* Converted all of the alignment tensor user functions to the
new Desc_container design.
* Itemised lists and verbatim text are now formatted properly
for the prompt help strings.
* Converted align_tensor.init to the Desc_container object
design to test itemised lists.
* The Desc_container object now supports itemised lists.
* Lists are now formatted for the prompt user function help
strings from the Desc_container objects.
* Converted the align_tensor.display user function to the new
Desc_container design. This is to test out the list generation.
* The Desc_container.add_list_element() method now groups list
elements together.
* Converted the prompt user function objects to use the new
Desc_container objects for the help strings.
* Started to redesign the user function definition
descriptions. The desc object has been converted into a list which
will contain instances of the new Desc_container class. This class
will hold the description information as blocks of text, including
unformatted paragraphs, verbatim text, lists, tables, and relax prompt
examples. The object has a number of methods used for inputting all
of the information, as well as extracting it. The information in the
Desc_container object is not formatted, for example tables will be
stored as lists of lists. This will remove the need for parsing list,
tables, verbatim text, etc. by the docs.latex.fetch_docstrings module.
But these will need to be recreated for the prompt help strings, for
the GUI user function descriptions, and for the user manual.
* Converted the align_tensor.copy user function description to
the new design. This is a test for the implementation of the
description abstraction through the Desc_container objects. The
'desc', 'additional', and 'prompt examples' will all be merged into
one 'desc'structure.
* Converted a few user functions to use the special "spin ID" arg
type.
* Converted the structure.vectors spin_id arg to the special
"spin ID" type. This is to improve vector loading in the GUI.
* Increased the size of the unit vector loading wizard in the
model-free analysis. This now matches the structure.read_pdb user
function size and allows it to fit.
* The min length is now handled much better in the Combo_list
GUI input element.
* The GUI user function object create_wizard() method now
returns True upon success. This is needed for calls to these objects.
* The GUI user functions now called by the results viewer
window now have the parent set to this window.
* The GUI user function page update_args() method now has a
docstring and returns True when successful.
* Rearranged the spin.name args and converted the spin ID to
the special spin ID type.
* Prevention of multiple RelaxErrors from the user functions.
The update_args() method returns False if an error occurred on
updating the list of choices for an arg. This is now caught by all
parts of the code where it is called, preventing further execution.
* Improvements to the structure.load_spins user function
definition. The spin_id arg now uses the special 'spin ID' arg type
for the spin ID GUI input element.
* A number of improvements for the spin ID GUI input element.
This includes: the use of SetValue() for strings not in the list of
choices; defaulting the choices to ['@N', '@C', '@H', '@O', '@P'] if
not supplied; a tooltip white space fix; and removal of the None
element in the list of choices, as this is not a read only box.
* Increased the size of the spin loading wizard to match that
of structure.read_pdb.
* The Value GUI input element UpdateChoices() method now
handles non-selection strings in the ComboBox. The
SetStringSelection() method is now only used when the combo default is
one of the choices, and SetValue() when not in the list of choices.
* Decreased the amount of waiting time in the GUI interpreter
flush() method. This will allow speed ups in certain parts of relax
(for example some GUI tests).
* The GUI test _execute_uf() base method now allows the wizard
run() method to be executed. This gives a better work out of the user
functions and matches more closely to what a user will experience.
* Deleted a ton of now unused and useless code from
gui.analyses.results_analysis.
* Print statement conversions to function calls for Python
3.x. All non-debugging print statements are now function calls. The
debugging printouts have been deleted.
* Complete redesign and creation of the 2nd version of the
relax XML format for save and results files. This is a BIG set of
changes! It includes the following: the XML files now have the new
'file_version' attribute within the 'relax' XML element, this is now
set to '2', and if unset it is assumed that the file version should be
1; the file_version integer value is now propagated through all of the
from_xml() methods so it can be passed into the
data.relax_xml.xml_to_object() function - this prevents a mixture of
v1 and v2being assumed for different parts of the XML; an XML
namespace fix - the xmlns="http://www.nmr-relax.com"; attribute is now
finally visible; the data.relax_xml.object_to_xml() function has been
added for creating the new relax XML syntax - this will handle and
convert many more basic Python object types into IEEE-754 byte arrays,
for example lists and dictionaries of floats, or numpy vectors and
matrices, and this function is now used throughout the code base for
converting Python objects to XML; the data.relax_xml.xml_to_object()
function has been expanded to match the functionality of
data.relax_xml.object_to_xml(); the Python object XML elements now
have the 'type' attribute indicating the Python object type - this is
important for the processing of the file, especially for handling all
types of numpy structures; the Python object value is now stored in a
sub XML element called '<value>' - if it is a float, or is a simple
type which contains floats, then the sub XML element
<ieee_754_byte_array> is created for storing a full precision version
of the floats; the v1 and v2 of the format together with the pre- and
post-Python 2.7.3 XML toprettyxml() changes are now represented as
test_suite/shared_data/model_free/OMP/final_results_trunc_1.3*.bz2
files, and a 5th file is added to test the IEEE-754 conversions by
corrupting many of the floats.
* The arg_check.is_float_matrix() function can now handle empty lists.
* Deleted the NOE data_names() specific analysis method. This
should operate through the base methods now.
* Spelling fix - converted the noun 'print out' to 'printout'.
* Added minimisation parameters to the N-state model specific
analysis parameter list.
* Updated the OMP model-free results file in the test suite
shared data directories for recent changes. The ordering of
model-free parameters is slightly different now.
* The 'select' global param can have a corresponding MC
simulation structure.
* The specific API data_names() method now accepts the 'scope'
argument. This is used to differentiate global verses spin
parameters.
* Lots of improvements for the specification of the model-free
global and spin parameters.
* The specific API param list base_loop() and loop() methods
now match against the parameter scope. This allows for the
differentiation of global from spin parameters.
* Improvements and fixes for the minimisation parameters in
the specific API param list object.
* The specific API param list get_desc() method now skips the
error and sim structures.
* Removed a number of specific API methods from the model-free
analysis. These are now provided by the base class.
* Large reworking of the specific analysis API. Many specific
methods relating to parameters have been shifted into the API base
class. These include: data_names(), data_type(), default_value(),
return_conversion_factor(), return_data_desc(), return_data_name(),
return_grace_string(), return_units(). These are now essentially
provided by the parameter list object. All of the global and spin
parameter lists have now also been merged into the single
'self.PARAMS' structure.
* The py_type is now set for the minimisation parameters.
* Renamed 'param_set' to 'set' in the specific API param list object.
* Split the specific API parameter object loop() method into
two. The new base_loop() method loops over the parameter names
according to set, whereas the loop() method now supports and returns
the error and simulation parameter names as well, if set.
* The specific API param list object now sets up a number of
spin params and min params. The spin 'select' and 'fixed' parameters
are set up in the __init__() method, whereas the add_min_data() method
will be used to add minimisation parameters.
* Added the 'scope' arg to the specific API param list add()
method. This will be used to merge the GLOBAL_PARAMS and SPIN_PARAMS
lists into one.
* Created the specific API param list loop() method for
looping over parameter names.
* All the get_*() methods of the specific API parameter list
objects now call self.check_param(). This new check_param() method
raises a RelaxError if the parameter is unknown.
* The parameter set 'params' or 'generic' can now be specified
in the specific API parameter lists.
* The GUI tests _execute_uf() base method now simulates a
click on the 'ok' button. This gives the user function wizards a much
deeper work out.
* Renamed the Python type arg from 'type' to 'py_type'.
* Added the 'min_stats' flag to the specific API parameter
list objects. This indicates if the minimisation statistics are part
of the parameter set. This is a flag to the __init__() method, as it
applies to the entire parameter list.
* Expanded the specific API parameter list object to include
the Python type and error and sim flags. This includes the addition
of the get_err(), get_sim(), and get_type() methods.
* Created the Dead_uf_pages.test_mol_create() GUI test
demonstrating a failure in the user functions. This mimics a click on
the 'ok' buttons, showing a problem with running a GUI user function
twice.
* The relax GUI state_load() method now checks if the data
store is empty. Previously a warning was only giving is analysis tabs
are loaded. Now the warning occurs whenever there is data in the
relax data store.
* Eliminated all of the wizard GUI input methods. These are
now all covered by the gui.input_elements package, so are no longer
needed. The analysis wizard had to be converted to using the package,
but the methods are now no longer used.
* Converted the spin_id_element() wizard method into the
gui.input_elements.spin_id.Spin_id GUI element.
* The gui.string_conv.list_to_gui() function can now handle
numpy arrays.
* The structure.rotate R arg now defaults to the identity
matrix. This is simply for the GUI.
* The frame order system tests are now being run as GUI tests as well.
* Converted all of the frame order system test scripts to be
executable as GUI tests.
* GUI test scripts are now executed via
prompt.interpreter.exec_script(). This allows the preservation of
imports within the scripts. The old execfile() method was causing the
'globals' to be overwritten, hence imports in the scripts are not
visible inside methods or classes.
* The GUI auto-generated user function SetValue() method now
skips function and function arg arguments. These are not supported in
the GUI.
* Loosened the checking conditions for the test_set_value()
J(w) mapping system (and GUI) test. Just like the consistency
testing, the GUI string conversions to and from floats introduces a
slight truncation.
* The consistency testing test_set_value() system (and GUI)
test has been made less strict. The conversion of the bond length and
CSA values to GUI strings and back to floats causes a slight numerical
truncation.
* The specific analysis API base return_data_desc() now has a
basic implementation. This will search through the global and then
spin parameters objects, returning whatever is found.
* The specific analysis API base method calls to
RelaxImplementError now send in the function name. This allows for
better identification of what needs to be implemented.
* The specific analysis base API default_value() method is now
functional. Rather than raising a RelaxImplementError, this method
now searches in the global parameters then the spin parameters for a
default value.
* Shifted out the interpreter components of the J(w) mapping
tests into scripts. This allows the tests to work in the GUI test
framework.
* Converted the consistency tests script to the new
_execute_uf() design. This allows it to work with the GUI for the GUI
tests.
* The jw_mapping system tests are now run as GUI tests.
* The user function intro string echoing has been turned back
on for the GUI. The removal of the need for the prompt UI interface
for the GUI user functions removed the intro print outs. These have
been reimplemented within the GUI code now.
* Renamed the status.prompt_intro flag to status.uf_intro.
This is because the flag will be used in all UIs.
* The sequence.write user function back end now defaults to
True for all sequence columns.
* The grid_search user function inc argument cannot be None.
* Converted all of the prompt unit tests to the new
auto-generated user function design.
* Updated the model-free auto-analysis GUI test to pass.
Changes include opening and closing the about dialog, loading the
sequence via the spin viewer window - testing this GUI element for the
first time and the use of the methods behind the specific value.set
buttons.
* The model-free GUI auto-analysis 'About' dialog is now
stored as a class instance variable. This allows it to be manipulated
remotely, for example by the GUI tests.
* The GUI user functions are now going straight to the back
end rather than through the prompt. The GUI user functions were
previously passing through the prompt UI user functions for argument
checking, which then passed on to the back end. Now the prompt is
bypassed, and the back end is being directly called. This should
speed up the user functions, and specifically the GUI tests.
* The prompt UI versions of the auto-generated user functions
are now stored in self._uf_dict. This is a dictionary whereby the
keys are the full user function names as text. This is designed for
speed, so that the user function object can be retrieved much faster.
* All the wizard method 'event' arguments have been converted
to keyword arguments. This is for better remote control, for example
by the GUI tests.
* All the model-free GUI auto-analysis method 'event'
arguments have been converted to keyword arguments. This is for
better remote control, for example by the GUI tests.
* Converted many GUI functions expecting a wx.Event to have
the event as an optional argument. These are now keyword arguments
defaulting to None. This allows remote control of GUI elements, which
is needed for the GUI tests.
* Removed the reinitialisation of the relax data store GUI
object in the GUI test tearDown() method. This is not needed as it is
done by the data store reset anyway.
* Removed a time.sleep() call which slows down the GUI tests
by a significant amount. This adds 0.5 seconds per user function
which display info. For example this is 8 seconds for just the Bmrb
GUI tests! This delay is not necessary, so has been eliminated.
* The user function docstrings are now created when the help
system is invoked. This prevents all user function docstrings from
being built at the start, or any time the interpreter class is
instantiated. Instead the docstrings are created on demand.
Therefore for most relax usage, the docstrings for most user functions
will be rarely built. This decreases start times of ~6 seconds down
to ~0.06 seconds!
* The GUI tests are now recycling the GUI user function
wizards and pages as well. This required a number of modifications;
the user function object wizard creation has been shifted into the
create_wizard() method; the status.gui_uf_force_sync flag has been
introduced to force synchronous operation of the GUI user functions;
the wx_wizard_run keyword arg has been added to the user function
object to prevent the automatic running of the wizard; the GUI test
tearDown() base method no longer destroys the GUI or wizards, as they
are needed in subsequent tests.
* Removed the useless GUI interpreter flush() call in the GUI
tests base _execute_uf() call. This is not needed as the GUI user
function calls are synchronous. This cuts the GUI test running time
down by about 1/4!
* The wizards for the individual user function pages are now
recycled. This should speed up the GUI (and the GUI tests massively).
Closing the wizard calls the Close() rather than Destroy() method, so
the wizards are still in memory. A new call to an old GUI user
function object will simply call SetValue() for all keyword arg GUI
elements, hence reset the element. The Wizard GUI object has been
modified to only add the buttons if they do not currently exist.
Without this, a new set of buttons is added each time the user
function wizard appears.
* The GUI base class now has access to math.pi. This is
necessary as the system test scripts are run in this namespace rather
than the interpreter namespace in which pi is defined.
* The Combo_list GUI input element can now handle values typed
out by the user. This affects both the GetValue() and SetValue()
methods.
* The value.set user function 'param' argument can now be
manually set by the user rather than selected. A number of N-state
model parameters require this.
* Better handling of empty data in the Sequence.GetValue() method.
* The non-supplied user function arguments in the GUI tests
are now set to the default. This is for the _execute_uf() base
method, and is essential for the free file format where the column
arguments must, in many cases, be set to None.
* Updates to the N-state model specific code. The
default_value() and return_data_desc() methods are now defined, and
the data_names() method returns a few parameter names.
* The Sequence.GetValue() method now properly handles the
Combo_list and single values.
* The Combo_list.GetValue() method now returns a proper list
of values rather than the string representation.
* The Value GUI input element UpdateChoices() method now
restores the current selection. This matches the Combo_list GUI
element changes.
* Renamed all of the ResetChoices() GUI methods to
UpdateChoices(). This is because they are for updating a list while
retaining the current selection.
* The Combo_list GUI input element ResetChoices() method now
remembers the current selection. This allows the selection to be
restored when the element is updated, rather than resetting to the
default value.
* The GUI test _execute_uf() base method now handles
non-keyword arguments, by converting them to keyword arguments.
* All system test scripts are now executed through the base
script_exec() method. This allows them to be run in the GUI tests as
well.
* The execute_uf() method is now private.
* Added all of the N-state model system tests as GUI tests.
* Modified the GUI tests so that they can operate in the same
way as the system tests. Now entire test suite classes can be
executed in isolation by typing, for example: "$ relax --gui-test
N_state_model".
* Converted all of the N-state model scripts to use the new
self._execute_uf() interface.
* Added some error checking for the system test class
execution. This is for better user feedback for when the user
supplied class does not exist.
* Entire classes of system tests can now executed. Rather
than running the entire system test suite or individual tests, the
system tests can now be run by class. For example to execute all of
the N-state model system tests, just type: "$ relax -s N_state_model".
* Eliminated the self._test_dir test class variable. The
system and GUI tests will now use the same script path.
* Modified and renamed the self._execute_uf() method so that
it will work with the system test scripts. The file and directory
arguments are now merged, as required by the GUI user function pages.
* Converted the bmrb_rw.py system test script to use the new
prompt self._execute_uf() method. The GUI test framework will need
slight modification to use this script directly still.
* Created a special private method for the prompt/script UIs
for executing user functions. This self._execute_uf() method will be
used for the sharing of scripts in the system and GUI tests.
* Re-factored the system and GUI tests for code sharing. The
GUI tests now can inherit tests from the system tests. This is done
for the BMRB system tests,both of which now run as GUI tests. For
this, a test class specific script_exec() method has been added. For
the system tests, it passes the system tests script into the
interpreter. For the GUI tests, it executes the script using the
function locals so that the GUI test execute_uf() method is
accessible.
* Created a pair of Python object to GUI string and reverse
conversion functions.
* Spun out the GUI sting conversion functions from the
gui.misc module into the new string_conv module. This set of
functions is now large and diverse enough to justify a separate
module, as the remaining three functions of gui.misc have nothing to
do with GUI strings.
* The Sequence GUI element now better handles single values in
the GetValue() method.
* The specific_fns get_specific_fn() function now determines
the data pipe type, if not supplied.
* Improved the value.set user function definitions.
* The model-free GUI auto-analysis now sets the default value
for the parameter buttons. The CSA, bond length, proton and
heteronucleus type buttons now launch the GUI user function with the
default value set.
* The Sequence GUI input element can now handle single values
passed into SetValue().
* The user function page is now updated prior to setting any
argument values. This is necessary for when a value from a
pre-defined list is to be selected. Without the update,the list will
be blank and the selection will not work.
* The user function GUI objects can now be called with their
argument values. This allows the argument to be set upon page
creation.
* The auto-generated file and dir selection dialogs now have
wildcards and styles. This is provided through the new
'wiz_filesel_wildcard', 'wiz_filesel_style' and 'wiz_dirsel_style'
user function argument arguments which are then passed on to the file
and dir selection GUI elements. All user functions dealing with files
and directories have been updated.
* Updated the model-free auto-analysis GUI test for the new
user function design.
* The Value GUI element as a ComboBox can now handle input
values which are not in the list. This allows user functions with the
'wiz_combo_choices' argument argument set and the 'wiz_read_only' arg
arg of False to function. This is for the user to select from a list
of pre-defined defaults, or input their own value.
* The GUI tests base execute_uf() method now runs all user
functions in synchronous mode. In combination with the previous
gui_raise() change, this allows the GUI tests to actually fail when a
RelaxError occurs.
* The gui_raise() function now simply re-raises the RelaxError
when in test mode. This allows the GUI test to properly fail.
* Removed all of the dir user function arguments in the BMRB
GUI test. These need to be part of the file argument, as the file and
dir arguments are merged into one GUI file selection element.
* The Combo_list GUI input element SetValue() method now
handles single values and lists. This is required for the GUI tests.
* The ComboBox data values are now set to the choices in the
__init__() method if not given. This is required by the GUI tests, as
the ResetChoices() method which does the same thing has not been
called.
* Shifted the combo_list GUI element into the
gui.input_elements package.
* The NOE auto-analysis GUI test has been converted to the new
auto-generated user function design.
* The NOE auto-analysis peak loading wizard has been converted
to the new auto-generated user function design.
* The prompt-based interpreter no longer sets the
status.prompt_intro flag in the __init__() method. This flag is now
set by the instantiation of the singleton status object. This
prevents multiple calls to the Interpreter.__init__() method
overwriting this flag. This fixes problems in the GUI tests.
* The GUI tests base class execute_uf() method will now try to
set all keyword arguments. This allows the user functions with free
file format keyword arguments to be operational.
* The Combo_list GUI element now handles the
wiz_combo_list_min user function argument argument. If not enough
elements are set, Combo_list.GetValue() will return None. This is
caught by the auto-generated GUI user functions on_execute() method,
preventing the execution of the user function.
* The spectrum.replicated user function back end now checks
for lists of None or of 1 element.
* Renamed the user function argument argument
wiz_combo_list_size to wiz_combo_list_min. This will be used by the
Combo_list object to ensure a minimum length.
* The Rx auto-analysis peak loading wizard has been converted
to the new auto-generated user function design.
* Individual elements of the Sequence and Combo_list GUI
element can now be set via the SetValue() method. The
Sequence.SetValue() method now accepts the index arg, and this is
passed onto the Combo_list.SetValue() method. The individual elements
of the Sequence element still cannot be set via the index.
* The free file format object can now be remotely controlled
in the auto-generated user functions. This allows the test suite to
set these values. For this, a special
Free_file_format.SetValue()method was created, and the user function
SetValue() method will call this when needed.
* Removed the desc_short arguments to the Sequence* GUI input
element classes. These do not exist.
* The GUI test base execute_uf() method now only sets an
argument if the argument has a corresponding GUI element.
* Missing import causing all GUI tests to fail.
* Edited all the module docstrings in the user_functions package.
* Split up the gui.wizard_elements into a number of modules in
the new gui.input_elements package.
* The user function GUI page arguments are now updated after
execution of the user function. This allows ComboBox lists to be
dynamically updated, and is useful for when the user clicks on
'Apply'.
* Created the Free_file_format.GetValue() method for returning
a dictionary of arguments. This abstracts the GUI element's input
fields.
* Redesigned the set up of the user function arguments in the
GUI pages. The wizard element_*() methods have been removed as these
were pointless wrappers. The Uf_page add_contents() method now builds
the argument GUI elements and stores them in the self.uf_args
dictionary. The wizard methods Clear(), GetValue(), ResetChoices()
and SetValue() have been shifted into the Uf_page class as these are
only for the auto-generated user functions.
* More independence for the wizard_elements - the height of
the element must now be passed in as an argument.
* Started to make the wizard_elements module classes
independent of the wizard. The references to parent._div_left have
been eliminated, this is now expected to be passed in by the parent
which has that variable as the divider argument.
* Converted the Interpreter.script() method into a proper user
function. This pseudo user function was no longer functional after
the auto-generation changes.
* Redesigned the prompt help system for the auto-generated
user functions. The documentation is closer to the style in the relax
manual, including 'Synopsis' and 'Default' sections (i.e. see
http://www.nmr-relax.com/manual/value_set.html).
* The _build_doc() method now returns the documentation.
* Eliminated the build_doc() function as this is no longer
used. The new auto-generated user functions use a variant of this
function as the _build_doc() method.
* The uf_docstring functions are no longer private.
* Renamed the 'base_class' module to 'uf_docstring'. This
module now only contains functions relating to the auto-generated user
function docstrings.
* Shifted the prompt.base_class._strip_lead() function to
relax_string.strip_lead().
* Renamed the 'doc_builder' module to 'relax_string'. This
will be used to hold more string related functions used throughout
relax.
* The status.text_width variable is now used to wrap the user
function docstrings. This is for the prompt help system.
* Shifted the prompt ps1, ps2 and ps3 variables into the
'interpreter' module. This is the only place they are used, so they
are better there.
* Eliminated the defunct User_fn_class base class.
* The Sequence GUI elements now default to not being read-only.
* The frq user function class submenu mnemonic is now 'f',
conforming to the other user function classes.
* Improved the keyboard mnemonics for the user function
sub-menus. There are no longer any clashing letters.
* The user function menu has been split in half as it was far too
long.
* The spin viewer window is now using the new build_uf_menu()
function for its menus.
* Shifted the user function menu creation into
gui.uf_objects.build_uf_menus(). This will allow the code to be
reused by the spin viewer window.
* The GUI user function storage object now populated itself.
This singleton object is no longer populated from the main GUI object,
shifting the auto_generate()method code into the singleton
instantiation. The user function __call__() method not extracts the
main window GUI object for use as the parent of the wizards, if a
parent is not supplied.
* Removed the dependence on the old GUI user function system.
Now the GUI user function storage object is used throughout.
* The user function GUI objects can now be called with the
'parent' keyword argument. This allows a window other than the main
relax window to be the parent, preventing the main window from always
coming to the front.
* Converted all of the GUI code to use the auto-generated user
function design and storage object.
* The Uf_page.create_page() method now accepts the 'sync'
argument for deciding user function operation.
* Shifted the user function page creation into the
Uf_object.create_page() method. This will be useful for the creation
of the special wizards which are composed of many user function pages
strung together. In this case, the __call__() method which creates
and packs the page into a Wiz_window instance can be bypassed.
* The Spectral_error_type_page class now inherits from
Wiz_page as UF_page has been eliminated.
* Eliminated the gui.uf_pages package. This removes a lot of
code and many modules! This has all been rendered useless by the
auto-generated user functions.
* Eliminated the old user function menu system. The
auto-generated menu system is now complete, so the old system is now
of no use.
* Improved the argument description by making it more readable.
* Renamed the 'user_functions' module to 'uf_objects'. This
is due to a name clash with the 'user_functions' package.
* Renamed the auto-generation user function module from
'objects' to 'user_functions'.
* Clean up of the prompt.interpreter module. This includes
the merging of the _auto_generate() method into _setup() and the
clean up of the imports.
* Created RelaxValListValError and RelaxNoneValListValError
for the arg_check.is_val_or_list() function.
* The prompt UI can now handle the user function argument type
of 'val_or_list'.
* Eliminated the try logic in the arg_check is_*() functions
as the raise_error flag can now be used instead.
* Created the arg_check.is_val_or_list() function for the
value.set user function. The value argument of this user function is
now classified as a 'val_or_list' object, hence this is_val_or_list()
replaces the use of is_str_or_num_or_str_num_list().
* Clean up of the prompt package __init__ module.
* Converted the vmd user functions to the auto-generation design.
* Eliminated the view user function as this is ancient dead
code. This user function has essentially remained the same as when it
was introduced at r788 back in the 0.3 relax line in October 2003! It
has never actually performed any function and has somehow managed to
survive in the source tree unnoticed.
* Converted the value user functions to the auto-generation design.
* The auto-generated GUI user functions can now handle the
'val_list' argument type. This is needed for the value.set user
function whereby the 'value' argument can be almost anything,either as
a single float, int, str, None, etc or as a list.
* Converted the temperature user function to the auto-generation
design.
* Converted the sys_info user function to the auto-generation design.
* Converted the structure user functions to the auto-generation
design.
* Float and int numpy arrays and matrices are now supported
for GUI user function arguments.
* Converted the spin user functions to the auto-generation design.
* The can_be_none value is now propagated into the Combo_list
GUI element.
* The can_be_none argument is now propagated and stored in the
Sequence and Sequence_2D GUI elements. Some debugging print outs have
also been removed.
* Converted the spectrum user functions to the auto-generation design.
* Added the spectrum.integration_points user function back end
so that the auto-generated class can work. This raises a
RelaxImplementError as this is not implemented, but allows the front
end to be accessible.
* Renamed the results.read and results.write user function
'directory' argument to 'dir'. This in both the front and back ends.
* Shifted the free_file_format GUI element into its own class.
The wizard page free_file_format() method for generating the GUI
element has been shifted into the
components.free_file_format.Free_file_format class.
* Redesigned the free file format window. The settings module
has been renamed to components.free_file_format, as it simply contains
the free file format window. This renaming is in preparation for
shifting all of the free file format code into this module to create a
special GUI element object for it, rather than being part of the
wizard page code base. The Base_window code has been merged into the
Free_file_format_window code, as no other windows use it any more.
* Eliminated the ancient unused load_sequence() GUI element.
This was part of the settings menu in the original version of the GUI,
but now has no purpose.
* Converted the sequence user functions to the auto-generation design.
* The model_selection user function now defaults to AIC.
* Converted the results user functions to the auto-generation design.
* The reset user function is now called in synchronous mode in the
GUI.
* The user function 'gui_sync' attribute is now passed all the
way into the GUI user function objects.
* The Uf_container now has the 'gui_sync' variable for
switching between asynchronous and synchronous operation.
* Converted the reset user function to the auto-generation
design. A fast and dirty wizard graphic was also added for the user
function.
* Converted the residue user functions to the auto-generation design.
* Created an icon for the relax_fit user function class.
* Converted the relax_fit user functions to the auto-generation
design.
* Converted the rdc user functions to the auto-generation design.
* Removed the old __docformat__ module variable.
* Converted the pcs user functions to the auto-generation design.
* Read only arguments as combo boxes can now be set to None,
if allowed, in the GUI user functions. The empty string and None are
prepended to the combo box choices and data respectively.
* Improved the titles of the Sequence and Sequence_2D GUI
element for the user functions. The 'desc_short' user function
argument property is now used to create the title rather than the
'name' value.
* The Sequence and Sequence_2D GUI elements can now handle
fixed sized sequences. When the 'dim' Uf_container.add_keyarg()
argument is set, then the 'Add' and 'Delete all' buttons are turned
off, the ListCtrl sizes are pre-made, and their SetValue() methods no
longer append to the list. This will allow for better user editing of
points, vectors, and matrices.
* Converted the 'size' user function argument argument to
'dim'. The name 'dim' better reflects what this is.
* Absorbed the user function argument argument 'dim' into
'size'. This is only used by one user function, structure.rotate,
which has not been converted to the auto-generation design yet. The
size argument is perfectly suitable for specifying the matrix
dimensions.
* The Sequence and Sequence_2D wizard page GUI element buttons
now have a tooltip.
* The paramag user functions are now using the align_tensor
icons and wizard graphics.
* Converted the paramag.centre user function to the
auto-generation design.
* The n_state_model user function menus now use icons.
* Created a set of basic icons for the N-state model user functions.
* Improved the PyMOL ray-traced n_state_model wizard graphic
by ray-tracing to 1000x1400 and shrinking.
* Created a wizard graphic for the n_state_model user functions.
* Converted the n_state_model user functions to the
auto-generation design. Some of the documentation was updated as it
was incorrect.
* The integer user function GUI elements which can be None now
are simply set to a wx.TextCtrl. The wx.SpinCtrl used previously was
incorrect, as a wx.SpinCtrl only handles integers, always defaulting
to the minimum of the control. Therefore the can_be_none user
function argument argument is now propagated into the wizard page
Value, Sequence and Sequence_2D elements (though they are not
functional in the Sequence* classes yet).
* The wx.SpinCtrl used in the Value wizard page element is now
fail-safe. The code now catches min and max values of None, and does
not set the initial value so that a default value of None does not
break the wx element.
* The min and max arguments now default to 0 and 1000 for the
Uf_container.add_keyarg() method.
* Improved the frame_order relax icons.
* Increased the content of icons in the auto-generated user
function menus.
* Improved the relax noe icons by modifying the wizard SVG file.
* Converted the noe user functions to the auto-generation
design. The noe wizard graphic has been converted into icons for the
menus.
* Created the generic_fns.spectrum.get_ids() function for
returning all current spectrum IDs. This will be used by the
noe.read_intensities user function.
* Increased the icon content in the auto-generated user function menu.
* Added the archive-extract Oxygen icon.
* Added the document-edit Oxygen icons.
* Added all sizes of the dialog-ok and dialog-ok-apply Oxygen icons.
* The user function arguments can now have minimum and maximum
values for integers specified. The min and max arguments can now be
given,and these are then propagated all the way to the GUI elements.
For the Sequence and Sequence_2D elements this has no effect yet as
they do not implement wx.SpinCtrl elements.
* Eliminated the 'prune' argument to the
monte_carlo.error_analysis user function. This will never be used
again, and might tempt some users into changing the value and damaging
their analysis!
* Created a wizard graphic for the monte_carlo user functions
from the oxygen 'actions/roll' icon.
* Converted the monte_carlo user functions to the
auto-generation design.
* Added the 'roll' Oxygen icon and a blue coloured version for
use in the monte_carlo menus.
* Created an icon representing frequency. This is being used
by a number of user functions and classes.
* Created an icons for the jw_mapping user function class.
* The model-free user function class now has a menu icon.
* Converted the molecule user functions to the auto-generation design.
* Created a basic icon set for the model-free theory.
* The failure of the user function page on_display() method
now prevents the wizard from being displayed.
* The Uf_page.on_display() method now gracefully handles
RelaxErrors from the user function argument iterators. This now
catches the error and uses gui_raise to report to the user.
* The Uf_container object can now have the 'desc' variable set
multiple times. This allows for molecule user functions where the
generic_fns.mol_res_spin.ALLOWED_MOL_TYPES list values are appended to
the description.
* Big improvements for the Combo_list GUI element. The client
data is now set and returned instead of the string values, allowing
for more descriptive choices. The SetValue() method has been
implemented. And floats and ints are now supported as data types.
* Converted the model_free user functions to the auto-generation
design.
* The consistency_tests.set_frq and jw_mapping.set_frq have
been synchronised. These perform exactly the same purpose, and have
been made almost identical.
* Improved the jw_mapping.set_frq wizard page size.
* Refinement of the jw_mapping.set_frq user function. The
wizard page now shows a read only ComboBox of the allowed spectrometer
frequencies, so that the user does not need to input the exact value.
The descriptions have also been improved.
* Created the generic_fns.frq.get_values() function for
returning a list of unique spectrometer frqs.
* Improved the relax_data.read user function docs to stress
the importance of frequency.
* Converted the jw_mapping user functions to the auto-generation
design.
* Improvements for the consistency_tests.set_frq user function
descriptions.
* The select.spin and deselect.spin user function arguments
spin_id can be None.
* Removed the leading whitespace from the colour module
documentation variables.
* All leading whitespace is stripped from the docs before
creating the auto-generated user function description. The detection
of the end of the table has also been simplified, as stripping the
whitespace broke the logic.
* The simple Value wizard page element default for an integer
is now a wx.SpinCtrl. If the element_type argument is set to
'default' and the data type is integer, then a wx.SpinCtrl will be
used.
* The align_tensor.init param_types argument is now a ComboBox
with the choices in the GUI.
* The generic_fns.grace.get_data_types() function is even more
fail proof. The return_data_desc() call was sometimes raising a
RelaxError when not implemented for certain analyses.
* Converted the grace user functions to the auto-generation
design. This required created the generic_fns.grace.get_data_types()
function for returning the data type descriptions and values for the
current data pipe. This is to replace the code in the old grace user
function update_parameters() method so that the data type fields are
updated according to the analysis.
* The Value.SetValue() method can handle default values when
the list is empty.
* For the Value wizard page element, the default can be the
string or data for a ComboBox now. If the default is a data value,
then this is translated to the string. This allows the default in the
user function data objects to be either the string or data value,
removing a source of coding errors.
* Converted the frq user functions to the auto-generation design.
* Created icons and wizard graphics for the frame_order user
functions.
* Converted the frame_order user functions to the
auto-generation design.
* Added error checking to the Uf_container to eliminate typo
coding mistakes. This checks that a variable is not set twice (copy
and paste error).
* Converted the fix user function to the auto-generation
design. The object-locked and object-unlocked Oxygen icons have been
combined to create a wizard graphic for this user function.
* Created wizard graphics for the eliminate user function.
* Converted the eliminate user function to the auto-generation design.
* Function arguments are now ignored as well in the
auto-generated GUI user functions.
* Created icons and wizard graphics for the auto-generated dx
user functions.
* Converted the dx user functions to the auto-generation
design. Some of the checks at the prompt level had to be shifted into
the back end, where they belong.
* The Value wizard page GUI element can now be set to a
wx.SpinCtrl. This is only allowed for integers.
* The default file name is now passed all the way into the
RelaxFileDialog. This is for the auto-generated GUI user functions.
* Improvements to the Selector_dir wizard page GUI element.
The icon is now for a directory open and not file open, the tooltip is
also fixed, and the default value is now passed all the way through.
* The auto-generated user functions and classes are now always
alphabetically sorted. The Uf_object.add_class() and
Uf_object.add_uf() method now sort the lists at the end. The data
objects are stored in dictionaries to avoid sorting issues.
* Created wizard graphics for the select and deselect user
function classes. The spin and spin_grey icons are used for the
menus.
* Converted the select and deselect user functions to the
auto-generation design. The boolean_doc variable has been shifted
from the deleted prompt.select module into the generic_fns.selection
module, where it belongs.
* The new icon fetching system is now being used for the relax
icons in the menus.
* The relax Ulysses butterfly icons are now in the icon
directory and in all sizes. The 16x16 icon has also been improved.
* Shifted all the gui/images graphics into the graphics/misc
directory. This finally brings in all of the graphics into one place.
* Set the state user function class menu icon to the relax icon.
* Converted the molmol user function to the auto-generation
design. For this process, the molmol.macro_apply and
molmol.macro_write user function colour_start and colour_end arguments
had to be split, just as in the pymol user functions. They previously
accepted both a Molmol or X11 colour name or an RGB colour array but
are now separate arguments.
* Converted the pymol_control user function to the
auto-generation design. For this process, the pymol.macro_apply and
pymol.macro_write user function colour_start and colour_end arguments
had to be split. They previously accepted both a Molmol or X11 colour
name or an RGB colour array. Now there are separate arguments for the
colour name and RGB colour array.
* The Sequence based wizard page GUI elements now return None
if the field is empty. This was previously returning [] or () to the
auto-generated user functions when they were expecting None.
* The auto-generated user function menu is now correctly sorted.
* Converted the model_selection user function to the
auto-generation design.
* Added graphics for the model_selection user function.
* Created icons and wizard graphics for the calc and minimise
user functions.
* Created icons for the grid_search user function.
* Eliminated the wiz_combo_default and combo_default arguments
from the GUI auto-generated user functions. These are now provided by
the 'default' argument.
* Eliminated the 'wiz_combo_default' user function argument
argument. This argument is duplicative of the 'default' argument.
* The default value of the user function arguments is now set
in the wizard page elements. This is for the auto-generated user
functions.
* Converted the calc, grid_search and minimise user functions
to the auto-generation design. The minimise user function required a
lot of work, as the minimise(*args, *kargs) construct is incompatible
with the auto-generation design. As this is hardly used in the field,
everything has been converted to specific keyword arguments. This
will have a side benefit of being easier to understand for a user.
The back end was modified accordingly.
* The 'additional' sections are now shown before the
'examples' section in the prompt help system.
* The user functions without a base class are now supported in
the prompt, script, and GUI modes. This is for the auto-generated
user functions not stored in a user function class object.
* The 'num_or_num_list' and 'num_or_num_tuple' argument types
are now supported in the GUI. These are for the auto-generated GUI
user functions. The 'num_or_num_tuple' argument type is used for the
diffusion_tensor.init user function, for example.
* Improvements for the diffusion_tensor.init user function data setup.
* Converted the diffusion_tensor user functions to the
auto-generation design. The icons and wizard graphics for these user
functions has also been created.
* Created icons and wizard graphics for the palmer user functions.
* Converted the palmer user functions to the auto-generation design.
* The auto-generated user function additional documentation is
now used by the prompt UI. The data was not being passed into the
prompt user function objects.
* The additional documentation for the auto-generated user
functions is now properly processed in the GUI.
* Converted the dasha user functions to the auto-generation design.
* Added support for the directory selection wizard page
element for the auto-generated user functions. This uses the new
Selector_dir GUI element.
* Converted the consistency_tests user functions to the
auto-generation design.
* Converted the angles user functions to the auto-generation design.
* Converted the bruker user functions to the auto-generation design.
* Converted all of the state user functions to the
auto-generation design.
* List of lists types are now properly handed by the
auto-generated user function in prompt/scripts.
* Significantly increased the number of icons used in the
auto-generated user function menus.
* Added icons and wizard graphics for the align_tensor user functions.
* Converted all of the relax_data user functions to the
auto-generation design.
* The buttons of the Selector_file wizard page element now
have better tooltips. The open button now has a tooltip related to
opening. The preview button has the "Preview" tooltip rather than the
element_file_sel tooltip, so that the user knows what the button does.
* The wizard description height is now functional in the
auto-generated user functions. The height_desc argument was being
overwritten by the base class Wiz_page.__init__() method.
* Added support for the free format file settings GUI element
to the auto-generated user functions. The normal argument elements
are suppressed if the arg_type arg is set to 'free format', and the
free format element will then be added to the end. The 'data_col'
argument is searched for to see if the data elements should be
activated.
* Created the generic_fns.relax_data.get_ids() function for
returning all relaxation data IDs. This is needed for the
auto-generated user functions in the GUI.
* The user function argument type of 'num' is now handled as a
float in the auto-generated GUI elements.
* The wizard height_desc variable can now be set in the
auto-generated user functions. This is via the wizard_height_desc
variable.
* The user function data object add_class() and add_uf()
methods now check for uniqueness. This is to catch coding errors
whereby the user function class or name has been duplicated.
* Removed the now useless 'user_functions.functions' module.
* The Bmrb.test_bmrb_rw GUI test is now complete and fully
uses the new auto-generated user functions. This test will only pass
once all the relevant user functions are converted to the
auto-generation design.
* The 2D sequence arguments of the auto-generated GUI user
functions now matches the normal sequence elements. The
String_list_of_lists_window has been converted to Sequence_window_2D
which inherits from Sequence_window. All Python types and sequences
supported by the Sequence GUI element are now supported by the
Sequence_2D element (which is the old String_list_of_lists).
* Converted all of the align_tensor user functions to the
auto-generation design.
* Merged all of the sequence wizard page GUI elements into
one. This is to significantly simplify the code.
* Added GUI conversion functions for tuples.
* Better checking of the contents of the GUI element by
Value.GetValue().
* Merged the Base_value, Float, Integer, and String wizard
elements together into the single Value class. This simplifies the
code, as the differences between them was very minor.
* Floats and tuples of numbers are now supported by the user
function GUI argument elements.
* The align_tensor.display user function backend argument is
now a keyword argument. This is for supporting the auto-generated
user functions.
* Created the align_tensor.get_ids() method for use in the GUI
wizards. This will be required for the auto-generated user function
GUI front ends.
* The pipe.copy pipe_from wizard element is now read only.
* The user function intro is now printed out before the
argument checking. This is for better user feedback.
* The pipe editor window now uses the auto-generated pipe user
function GUI objects.
* The user function backend and title values are now enforced.
If these are not set, a RelaxError is thrown. This should avoid
fatal coding accidents.
* Converted all of the brmb user functions to the new user
function design.
* All of the exp_info user functions now check for the
presence of the cdp. This allows for better user feedback.
* The default list element now defaults to read only, whereas
the Combo_list object defaults to not read only.
* The List objects can now handle bad user input.
* The wiz_read_only flag now defaults to None, to allow the
GUI elements to decide the best option.
* The read_only flag now is fully functional in the
String_list wizard page element.
* The wiz_read_only user function flag is now propagated into
the String_list GUI elements.
* The Combo_list GUI element can now handle an initial size of
None, converting this to 1.
* The list wizard GUI elements no longer show empty lists.
* The Base_value class can now accept the element_type
argument value of 'default'. This will then use the TextCtrl.
* The add_keyarg() wiz_element_type argument default is now
'default' to be able to handle all element types. The previous
default of 'text' for a TextCtrl was causing failures with certain
wizard GUI elements.
* The relax controller is now shown for the auto-generated GUI
user functions if 'display' is set. This is the 'display' variable in
the user function data store. This allows all the user functions
which print to STDOUT to pop up the controller in front of the user,
so they see the result.
* The user function data structure now accepts the 'display'
boolean variable. This is used to indicate that a user function would
like to display some output to STDOUT.
* All of the user function argument arguments are now handled
by the add_keyarg() method.
* All of the argument checking types are now supported for the
auto-generated user functions. This covers every type of
arg_check.is_*() function used in relax.
* Boolean argument types are now supported by the
auto-generated GUI user functions. The Selector_bool object and
element_bool() wizard page method have been written for this.
* The can_be_none user function argument argument is now used.
This is needed for proper argument checking in the auto-generated
user functions.
* The wizard page GetValue() method now returns None if the
corresponding key is missing. This is needed for the directory
arguments as these are not shown in the GUI.
* Improvements to the element_file_sel() wizard page method.
* Created the special Selector_file wizard element object.
This is modelled on the file_selector() wizard page method.
* Created the element_dir_sel() and element_file_sel() wizard
page methods. This will require the selector objects to be written.
* The auto-generated GUI user functions objects now support
the special UI types. This includes the file and dir selection
dialogs, and skipping the dir arguments.
* The arg_type argument for the auto-generated user functions
is now accepted. This will be used to allow special UI elements to be
used for the argument, for example a file selection dialog.
* Integers and string list of lists are now accepted by the
auto-generated GUI user functions.
* Expanded the wizard page element_int() method to accept all
the arguments of element_string(). All these arguments will be
handled properly by the Integer class as this derives from Base_value.
* The list_titles argument is now accepted for the
auto-generated user functions. This is for a list of lists, and are
the titles for the lists.
* The auto-generated Uf_page.add_contents() method now raises
a RelaxError if the Python type is unknown.
* The menu_text variable now defaults to '' so that the GUI
does not die if this is not set.
* Removed the wiz_desc arguments from the pipe user functions.
* Eliminated the wiz_desc argument in the auto-generated user
functions. Now the desc_short argument will be used instead for the
GUI user function elements.
* The desc_short rather than wiz_desc argument is now used for
the GUI elements. This is for the auto-generated user functions.
* The wiz_desc argument is no longer compulsory for the
auto-generated user functions. This will eventually be merged with
the desc_short argument anyway.
* The GUI test execute_uf() base method now operates with the
auto-generated user functions.
* Advancements for the auto-generated GUI user functions.
String list GUI elements are now supported. The wizard element are
now updated on display, allowing for example the current set of data
pipes to be displayed in the ComboBoxes of the pipe user functions.
* The List and Combo_list class now have ResetChoices()
methods. This allows these elements to fit with the auto-generated
GUI user functions.
* Big set of changes enabling the auto-generation of the GUI
user function front ends. This will create user function objects
which are bound to the menu items, and the user function page objects
automatically from the user_function data object. The pipe user
functions have been updated to supply the needed data, and additional
arguments have been added to the Uf_container.add_keyarg() method.
The Uf_container object can now accept additional wizard related
variables.
* The graphics package image variables are now imported into
the paths module. This is for backwards compatibility with the old
user function pages.
* Shifted a number of the image path variables from the
gui.paths module to the graphics package.
* The user function GUI menu item is now being auto-generated.
This will require future work to support user functions not within a
user function class.
* The graphics.fetch_icon() function now returns None if no
icon is specified.
* Created the graphics.fetch_icon() function for a better API
for the icon paths. This will eventually replace the gui.paths
module.
* The graphics directory has been converted into a Python
package. This will be used to store special functions related to
graphics manipulation, retrieval, etc.
* Renamed the gui.user_functions package to gui.uf_pages to
avoid import clashes. This package was clashing with the base
user_functions package, breaking imports everywhere.
* Started to write the auto-generated user function GUI menu.
* Created methods for returning user function and class data
objects from the user function data object. These are called
get_class() and get_uf().
* The auto-generated prompt user function front end objects
are now executable. The uf.backend variable is now the executable
Python object. The pipe user function class has been updated for the
uf.backend change.
* Implemented the missing back end of the pipe.current user function!
* Expanded and fixed the argument checking for the prompt
auto-generated user function front ends.
* The auto-generated prompt user function front ends now
convert arguments to keyword arguments. This is important as a
keyword argument can be supplied without the keyword in Python.
* Removed the last reference to the eliminated Exec_info prompt
object.
* Clean up of the prompt intro strings for the auto-generated
user functions.
* The prompt intro strings are now created for the
auto-generated user functions.
* Absorbed the Exec_info prompt object into the relax status
singleton and eliminated it. The prompt strings are now
prompt.base_class module variables, and the current ones are stored in
the status object. The user function intro flag is now stored in
status.prompt_intro. The prompt_colour_on() and prompt_colour_off()
methods are now methods of the interpreter class. Now that the
Exec_info class no longer exists, the Basic_class class has also no
purpose and has been eliminated.
* The prompt help system now uses bold text for the title line
and all subtitles. The subtitle underlines are now not used, but the
ability to underline is retained.
* The relax prompt help system is now being passed through
pydoc.pager to page the text. This system will be used by the
auto-generated user functions.
* The documentation for the auto-generated user functions is
now being created. This is stored in the __relax_help__ string, and
mimics the old system, reusing many of the base functions. All the
user function data required for the prompt interface is now being
passed in to the object.
* Renamed the private _args variable to the non-private kargs.
* The user function object now has a __repr__ method to give
better feedback to the user.
* Primitive auto-generation of the user functions. This
simply creates an object for the user function, but it is not callable
yet or uses any of the user function data.
* Modified the pipe user function class description.
* The __description__ attribute from the old help system is
now supported in the auto-generated classes.
* The new auto-generated user function classes now fit into
the prompt help system.
* Documented the prompt-based help system _Helper.__call__() method.
* The auto-generated user class object now accepts the desc
argument and stores it for use in the help system.
* Added a __repr__ method to the user function class objects
for presenting a better message to users.
* Added the prompt.objects module which contains the user
function auto-generation objects.
* The interpreter now auto-generates the user function classes.
* Modified the Class_container class to be more like the
Uf_container class.
* Added two iterator methods for looping over the user
functions and classes. These are class_loop() and uf_loop().
* The user function container arguments variable is now
private and modifiable. It needs to be modifiable so the __init__
method can initialise it.
* Clean up of the pipe module (removal of useless imports and
syntax fixes).
* The pipe module is now imported in the __init__ module to
set up the data structures.
* The user function data object is now imported into the interpreter.
* Added the desc_short argument to the add_keyarg() user
function container method. This argument is used in RelaxErrors for
when incorrect parameter are supplied.
* Converted the entire of the 'pipe' module to populate the
user function data structure.
* Big improvements to the user function data container. The
changes are: More attributes are now accepted; now only allowed
attributes can be modified, to prevent programming errors; docstring
improvements; and more keyword argument data can be input.
* Shifted a check from the pipe.create front end to the back
end. Tests do not belong in the front end! And this is not
compatible with the new user function design.
* Removed the pipe user function class import and
instantiation from the interpreter object. This will be re-introduced
later with a new auto-generation architecture, taking the info from
the user_function data object.
* Shifted the pipe module from the prompt to user_functions
package. This is in preparation for the full conversion of this user
function class into the new auto-generation design.
* Added a unit test for the contents of the user_function package.
* The unit test _user_functions package is now actually a package.
* Created a unit test package for the user_function package.
* Shifted the Uf_info singleton into the new
user_functions.data module. This will avoid a lot of circular
imports.
* Created a module for setting up all of the user function
data. This is just a test, so probably will not be permanent.
* Created the Uf_info singleton class for holding all of user
function data.
* Created a number of special objects for the user function
data storage.
* Created the user_functions package.
* Added checks for the proton frq for the relax_data.read and
relax_data.back_calc user functions - if the frequency is not exact or
is less than 1 MHz, warnings are now given to the user.
* Made the bond vector extraction print out from
structure.vectors more informative.
* Created a sample script for BMRB data deposition.
* The relax data store is_empty() method now only prints to
STDERR if the verbosity flag is set.
* Changed the behaviour of the generate_spin_id() and
generate_spin_id_data_array() functions. This is a large change
affecting many parts of the code base. The problem that this solves
is the incorrect usage of the '&' character in spin IDs, tripping up
on the powerful Selection object of Chris MacRaild. For example, the
spin ID ':2&:Glu' cannot be correctly handled. This actually matches
all residues with the number 2, and all residues with the name 'Glu'.
* The scons 'clean' target now removes *.pyo files as well.
Bugfixes:
* Fixes for the bmrb.write backend - the generic_fns.exp_info
module should be used rather than the cdp. The abstraction via the
generic_fns.exp_info module is needed to make sure all the relevant
current data pipe structures are set up.
* Fix for the bmrb.display user function - this user function
never worked as pystarlib expects a file path as a string, but a
modification of pystarlib fixes this.
* Fix for the model-free about dialog - the fonts for the
different titles can now be set. The new font.roman_font_18 has been
added, and the about dialog draw_title() method now takes the alt_font
arg for specifying an alternative font.
* Bug fix for the model-free specific analysis
duplicate_data() method - the cdp.exp_info should be skipped. This
was not picked up before as this structure is normally non-existent
during the analysis.
* Fix for the Bruker system tests - the NMR proton frequency
is in Hz, not MHz.
* Fix for the GUI for when a script is launched from the
command line - the analysis tabs are now updated at the end of the
__init__() method, and the ds.relax_gui data store object is no longer
overwritten if it already exists.
* Bug fix for running a script when launching the GUI. This
was completely failing but now the script is executed prior to the
launching of the GUI.
* Bug fix for the generic_fns.spectrum.replicated_ids()
function for when no replicates exist. This will now return an empty
list instead of an error being raised.
* Fix for the spectrum.read user function - a RelaxError is
now raised if the file name is not given. This is important for the
GUI to prevent unintelligible errors to be presented to the user.
* Fix for the experimental information in the relax data store
- the information can now be reset.
* Bug fix - the 'relax --version' print out now works from any
directory. This was only working if relax was being run from the
installation directory!
* Fix for the prompt and script UI user function intro
printouts. This text is no longer passed through the format_text()
function which has problems with newline characters.
* Fixes for the GUI tests tearDown() method. All wx events
are now flushed before the deletion of GUI elements.
* The pipe.delete user function now operates synchronously in
the GUI to avoid the GUI blowing up!
* The user function pages are now registered and unregistered
with the 'gui_uf' observer object. This allows the ComboBox args to
be properly updated with asynchronous user function calls. The old
update method suffered from racing and hence often updated before the
user function had executed. Now the on_display() method registers the
GUI user function page update_args() method, and the on_next() method
unregisters it, allowing the observer to update the page only when it
is visible to the user.
* Fix for the GUI tests - the ds.tmpfile string is now being
created by the base setUp() method. This is needed to stop files from
being created within the relax directory tree.
* Bug fix for the model-free specific analysis - the Dr
diffusion tensor parameter is now defined.
* Fix for the arg_check.is_float_matrix() function for rank-1
arrays. The function failed on lists of Python values, for example a
list of bools. An additional check has been added to make sure that
the list elements are also lists.
* The delete all analysis method now does what it warns and
resets relax at the end.
* Fix for the model-free GUI auto-analysis test under certain
conditions. The spin viewer window was loading the spins
asynchronously, but the subsequent relaxation data loading was
synchronous. If a previous GUI test failed this would often trigger a
racing condition.
* Mac OS X bug fix for the non-read only ComboBox GUI input
elements. This is for the Value and Combo_list GUI input elements.
The problem was two-fold. First the convert_to_gui() call was
required to convert the value to a unicode string, as a normal string
will be not be set via the ComboBox.SetValue() method. Secondly old
selections need to be turned off. On other operating systems, the
SetValue() call will reset this - but not on Macs.
* Mac OS X bug fixes for the GUI ComboBox input elements. The
ComboBox.GetClientData() method on Mac OS X fails if the
ComboBox.GetSelection() method returns -1 (or wx.NOT_FOUND).
* Bug fix for all of the specific analysis code. The
SPIN_PARAM and GLOBAL_PARAM structures are now initialised within the
__init__() methods rather than being class variables. This bug was
only uncovered by the auto-generated user functions. The problem with
them being class variables of the base class is that the objects are
then the same for all specific analyses.
* Fixed the N-state model description so that it is no longer
about domain motions. This stands out in the GUI when creating data
pipes!
* The GUI user function on_execute() method no longer shows
the controller in test suite mode. The controller Raise() method was
being called at the end of the method, without checking
status.show_gui.
* Fix for the pipe editor - this window is now the parent for
the user functions it calls. Therefore the pipe editor no longer
disappears behind the main relax window.
* Fix for two of the arg_check.is_*() fns - the individual
elements were incorrectly checked.
* Bug fix for the Combo_list.GetValue() method - it can now
handle no user input cleanly.
* Fix for the Analysis_controller.on_page_changed() method for
reset events. The relax data store now always has a ds.relax_gui
object!
* Fix for the post_reset() method of the Analysis_controller
object. This unregisters all the analyses from the observer objects,
and calls the set_init_state() method only once all analysis pages are
deleted. This in combination with the synchronous reset user function
calling prevents the GUI from blowing up!
* Fix for the gui.misc.gui_to_tuple() function. This was
failing in many cases, especially where the value is not a tuple to
start with.
* Bug fix for the bruker.read user function for reading Bruker
Dynamics Centre files - the spectrometer frequency needs to be
converted from MHz to Hz.
* Bug fix for the loading of the molecule name and type from
relax state or results files. The str() builtin function is now used
to convert the string from unicode to a normal string. This is needed
as u'My mol' != 'My mol', breaking a number of tests.
* The relax_data.delete user function is now finally properly
implemented (bug #19785, https://gna.org/bugs/?19785).
* The model-free minimisation is now checking for multiple
vectors per spin, and raises a RelaxError.
* Fix for the relax controller SplitIO() setup for logging and
teeing modes. The SplitIO() usage is now disabled for the test suite.
This prevents a doubling of the print outs in the GUI tests. The
problem was introduced at r15843 with the accommodation for the
logging and teeing modes with the GUI.
* Created a system test Mol_res_spin.test_residue_delete()
demonstrating a failure of the user function - deleting the first
residue removes the entire sequence.
* Fixes for most of the structure user functions - the pipe
check is now performed at the start.
relax version 2.0.0