This is the first release of the new relax 3 series. This release
marks a major shift of relax towards becoming a scientific computing
environment specialised for the study of molecular dynamics using
experimental biophysical data. It is designed to be a replacement for
numerical computational environments such as GNU Octave, MATLAB,
Mathematica, Maple, etc. From the perspective of a user, however, not
much has changed. There are only a few modifications to the prompt,
script, or graphical user interfaces. Most changes are for the power
user as they are rather in the backend. The infrastructure changes
are comprehensive and include the reorganisation of most of the relax
code base, a large expansion of the relax library, and general
improvements and fixes to the user manual, the GUI, and the whole code
base. The huge number of changes can be seen below.
The new relax versions can be downloaded from
http://www.nmr-relax.com/download.html. If binary distributions are
not yet available for your platform and you manage to compile the
binary modules, please consider contributing these to the relax
project (described in section 3.6 of the relax manual,
http://www.nmr-relax.com/manual/relax_distribution_archives.html).
The full list of changes is:
Features:
* Huge amounts of code throughout the relax codebase has been
shifted into independent functions in the relax library.
* Many new functions added to the relax library.
* Complete rearrangement of the relax package and module layout.
* Clean up and improvements to the relaxation curve-fitting C
module including the removal of a severe memory leak eating up all the
RAM when lots of spins are analysed simultaneously.
* Complete redesign of the 2D graphing code for improved data
visualisation and to allow expansion to software other than Grace.
* Polishing of the GUI - many bug fixes and improvements
throughout the GUI.
* Addition of the --time command line option for the relax test suite.
* Large speed ups of the relax test suite.
* Merger of the dipole_pair and interatomic user function
classes into the new interatom user function class.
* Added support for J couplings.
* Import cleanups throughout relax, avoiding potential future
bugs and making the code much cleaner.
* Addition of many new scripts for use by the relax developers.
* Support for the NMRPipe SeriesTab format in the
spectrum.read_intensities user function.
* Improvements for all code examples in the relax user manual
including much better fonts, formatting, line wrapping, line
numbering, and colouring using the lstlisting LaTeX enviroment.
* Created the relax language definition for the lstlisting
LaTeX environment for better colouring of relax scripts in the user
manual.
* Converted the Citations chapter of the relax user manual
into a preface chapter.
* Overhaul of the indexing in the relax user manual.
* Higher level structuring of the user manual into parts.
* Creation of the optimisation chapter of the relax user manual.
* General improvements throughout the user manual.
Changes:
* Some small clarifications and reordering of the release
checklist document.
* Shifted the pipe_control.structure.superimpose module to
lib.structure.superimpose.
* Shifted the pipe_control.structure.statistics module to
lib.structure.statistics.
* Created the unit test infrastructure for the lib.structure package.
* Shifted the pipe_control.structure.pdb_read and
pipe_control.structure.pdb_write modules to lib.structure.
* Shifted the pipe_control.structure.cones module to
lib.structure.cones.
* Split the pipe_control.structure.mass module into two with
the CoM code going to lib.structure.mass.
* Removed the data pipe checks from the internal structural
object. This decoupling from the relax data store is in preparation
for moving into the lib.structure package.
* More decoupling of the internal structural object from the
relax data store. Removed the ability of the internal structural
object to determine if two atoms are connected by consulting the relax
data store.
* Created the empty lib.structure.internal package for holding
the internal structural object.
* Shifted part of the internal structural object into the
lib.structure.internal.models module. This contains the two classes
ModelList and ModelContainer from the pipe_control.structure.api_base
module.
* Shifted part of the internal structural object into the
lib.structure.internal.molecules module. This contains the class
MolList from the pipe_control.structure.api_base module.
* Shifted the MolContainer class from
pipe_control.structure.internal into lib.structure.internal.molecules.
This is in preparation for shifting the internal structural object to
lib.structure.internal and for the elimination of the unused and no
longer useful ScientificPython structural object.
* Created the empty lib.structure.represent package. This
will be used to hold modules which generate 3D structures as geometric
representations of abstract ideas such as tensors, cones, frames, etc.
* Shifted the lib.structure.rotor module to
lib.structure.represent.rotor.
* Total elimination of the ScientificPython PDB object.
Maintaining this reader was too much effort and the internal
structural object has now surpassed the capabilities of the
ScientificPython PDB object (for example the internal object is not
PDB specific). And ScientificPython is very much a dead project,
largely replaced by the more successful scipy.
* Merged the structural API base module api_base into
pipe_control.structure.internal. The API base class is no longer
needed as the ScientificPython PDB reader has been eliminated.
* Deleted the unit tests of the structural API base class.
* Moved the residual pipe_control.structure.api_base module to
lib.structure.internal.displacements. This is because the base module
still contained the Displacements class.
* Docstring consistency in the internal structural object.
* Shifted the pipe_control.structure.internal module to
lib.structure.internal.object. This is the new location of the
internal structural object.
* Shifted the selection object out of
pipe_control.mol_res_spin and into the new lib.selection module. The
dependence on the MoleculeContainer, ResidueContainer and
SpinContainer objects have been removed, as this is part of the relax
data store. Therefore all of the private methods (__contains__,
__contains_mol_res_spin_containers, and __contains_spin_id) have been
deleted. The contains_*() will need to be used instead.
* The pipe_control.mol_res_spin functions no longer use the
selection object __contains__() method. All functions now use the
contains_*() methods of the lib.selection.Selection object.
* Shifted parse_token() and tokenise() from
pipe_control.mol_res_spin to lib.selection.
* The lib.selection.parse_token() function is using the new
Python way of splitting strings. This is via the string's split()
method.
* Removed the no longer used parser argument for reading PDB
files from some unit tests.
* Removed the unit test of the parser argument of the
structure.read_pdb user function. The argument no longer exists.
* Shifted the cone geometric object representation functions
to lib.structure.represent.cone. The structure.create_cone_pdb user
function first calls pipe_control.structure.main.create_cone_pdb()
which then calls lib.structure.represent.cone.cone(). This allows the
pipe_control function to write out the file and add it to the data
pipe's results file list.
* Fixed some name classes in the namespace of
pipe_control.structure.mass.
* Shifted the diffusion tensor structural object code to
lib.structure.represent.diffusion_tensor. The user function routes to
pipe_control.structure.main.create_diff_tensor_pdb(), which pulls the
tensor info out of the data store, and then calls the
diffusion_tensor() function of
lib.structure.represent.diffusion_tensor to create the representation,
writes out a PDB file, and finally adds the file to the data pipe's
results file list.
* More removals of the now dead parser argument for the
structure.read_pdb user function.
* Removed the parser argument from structure.read_pdb in the
stereochemistry auto-analysis.
* Restored the selection object __contains_spin_id() method as
contains_spin_id(). This will allow for faster checks for matches to
spin ID strings.
* Speed ups for the interatom_loop() by restoring some of the
code previously deleted. This spin ID lookup table is being used
again, as this is much faster than the string parsing of spin IDs.
* The frame order analysis is now using the correct centre of
mass function.
* Shifted calc_chi_tensor() and kappa() from
pipe_control.align_tensor to lib.alignment.alignment_tensor.
* Shifted some of the pipe_control.diffusion_tensor functions
to lib.diffusion.main.
* Created the empty lib.software package. This will be for
functions which create input, read output, or control external
programs.
* Shifted and decoupled some of the grace code into
lib.software.grace. This includes most of the write_xy_header() and
write_xy_data() functions. The data store specific part of
write_xy_header() has been shifted into
pipe_control.grace.axis_setup().
* Missing import fix for the lib.alignment.alignment_tensor module.
* Shifted the lib.opendx package to lib.software.opendx.
* Shifted the lib.xplor module into the lib.software package.
* Shifted the Bruker Dynamics Centre parsing code into the new
lib.software.bruker_dc module.
* Deleted the completely unused
pipe_control.spectrum.Bruker_import class. This was added by Michael
Bieri in Oct 2011, but the code has never been used. Other, simpler
code has replaced its functionality.
* Created the Ct.test_bug_20674_ct_analysis_failure system
test for catching bug #20674. This was reported by Mengjun Xue
<mengjun dott xue att mailbox dott tu-berlin dot de> at
https://gna.org/bugs/?20674.
* Decreased the number of Monte Carlo simulations in the
Ct.test_bug_20674_ct_analysis_failure system test.
* Created the Jw.bug_20674_jw_mapping system test. This is a
modification of the Ct.test_bug_20674_ct_analysis_failure system test
for catching bug #20674 (https://gna.org/bugs/?20674). The test
script was duplicated and the small modifications made to convert it
into the J(w) mapping analysis. This now reveals the same bug but for
the J(w) mapping analysis.
* System test speed ups - decreased the number of Monte Carlo
simulations in many tests. Running 500 simulation optimisations in a
system test is a total waste of time!
* Converted the bug_20674_jw_mapping.py system test script to
use the self._execute_uf() interface. This allows the script to be
used in the GUI.
* Created the Mf.test_bug_20683_bdc_inf_values system test.
This is for catching bug #20683 (https://gna.org/bugs/?20683) reported
by Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>.
The problem is due to infinite and NaN values in the Bruker Dynamics
Centre file.
* Ported the changes of r19302 to the consistency testing and
J(w) mapping analyses. This is the code for checking for infinite
relaxation rates imported from Bruker Dynamics Centre files.
* Missing imports of the lib.float.isInf() function.
* Modified the bug_20674_ct_analysis_failure.py system test
script to use self._execute_uf(). This allows the test to operate as
a GUI test, which was failing.
* Created the specific API common method _data_init_spin().
This will be used as a general method for aliasing to data_init() for
initialising spin parameters.
* Added printouts for the select.read and deselect.read user
functions to identify the spins affected.
* Created the new lib.list module with the function
count_unique_elements(). This function will be used to determine the
unique number of elements in a list.
* Shifted the Sparky peak intensity reading code to
lib.software.sparky.read_list_intensity(). This new function comes
from the old pipe_control.spectrum.intensity_sparky() function, but
with the spin ID code removed.
* Shifted the XEasy peak intensity reading code to
lib.software.xeasy.read_list_intensity(). This new function comes
from the old pipe_control.spectrum.intensity_xeasy() function, but
with the spin ID code removed.
* Docstring fix for the
lib.software.xeasy.read_list_intensity() function.
* Shifted the NMRView peak intensity reading code to
lib.software.nmrview.read_list_intensity(). This new function comes
from the old pipe_control.spectrum.intensity_nmrview() function, but
with the spin ID code removed.
* Created the lib.software.sparky.write_list() function and
associated unit test. This will be used to create simple Sparky .list
files.
* The relaxation curve-fitting analysis parameters are now all
lowercase. This is to match the other analysis types so that the
parameter names are identical to the corresponding variable name.
This is assumed by some of the specific analysis API methods.
* Removal of junk code in the _assemble_scaling_matrix()
relaxation curve-fitting method.
* Parameter scaling is now functional in the
target_function.relax_fit.c code. Previously the scaling was not
being used and the Python to C conversion was broken.
* The scaling matrix is now converted into a usable list of
diagonal elements for the relax_fit C module.
* Simplified the code of the relax_fit C module.
* The common spin methods of the specific analysis API now
ignore parameters not in the model. This affects the
_data_init_spin(), _sim_init_values_spin(), and
_sim_return_param_spin() methods. The result is that the spin
containers no longer hold parameter variables set to None for
non-model parameters.
* Created the pipe_control.plotting module. This will be used
as a base for the plotting of all types of data. This includes the
current OpenDX and Grace modules, as well as future modules. The
determine_functions() function has been added and is used to simplify
the pipe_control.grace.get_data() function.
* The grace.write user function data type argument sequence
values have changed. Instead of 'spin', this can now be 'res_num' or
'spin_num' to specify that either the residue number or spin number
should be plotted on the desired axis. The x_data_type now defaults
to 'res_num'.
* Created the
pipe_control.mol_res_spin.count_max_spins_per_residue() function.
This will be used by the plotting module to determine if more than one
spin per residue exists.
* Fixes for the change of the grace.write user function data
type 'spin' to 'res_num'.
* Updated the pipe_control.plotting.determine_functions() function.
* Added the skip_desel flag to the important
pipe_control.mol_res_spin.spin_loop() generator function. This is
used to skip deselected spins within the loop. As must of the code in
relax using the spin_loop() does this anyway, this can be used to
simplify many of the spin looping elements in relax.
* Expanded the relax_fit system test script to produce all
types of currently supported Grace graphs. This is to more
extensively test the grace.write user function.
* Large redesign of the 2D graphing code in relax. This
currently affects only the grace.write user function, but the new
infrastructure will make it much easier to expand the graphing
abilities and to support other 2D graphing software. The plotting
code has also been significantly simplified. The
pipe_control.grace.get_data() function has been shifted into the
pipe_control.plotting module. It has been split up into the base
assemble_data() function with the data assembly shifted to
assemble_data_scatter(), assemble_data_seq_value() and
assemble_data_series_series(). This split massively simplifies the
code by not packing all different graph and set combinations into one.
In addition the auxiliary functions classify_graph_2D(),
fetch_1D_data(), get_functions(), and get_data_type() have been
created to maximise code sharing between the different assemble_*()
functions.
* Modified the relax_fit system test script to generate a new
type of graph. This is the residue number sequence verses the peak
intensity series data (and vice versa) via the grace.write user
function. This is to help in the implementation of this graph type.
* Created the pipe_control.plotting.assemble_data_seq_series()
function. This is to allow the residue or spin numbering to be
plotted against any series type data (lists or dictionaries), or vice
versa.
* Added a link to the PDF user manual from the HTML user
manual. This will affect all pages at
http://www.nmr-relax.com/manual/ by adding an icon to the navigation
bar pointing to the PDF manual at
http://download.gna.org/relax/manual/relax.pdf.
* The plotting of residue or spin numbers verses values now
handles multiple spin types properly. This is in the
pipe_control.plotting.assemble_data_seq_value() function. The spin
name is being used to identify different spin types for the graph
sets.
* The pipe_control.mol_res_spin.count_max_spins_per_residue()
function now accepts a spin ID argument. This can be used to restrict
the spins to count.
* The spin ID string is now being used by the plotting
functions. The spin ID was not being passed into the
assemble_data_*() functions.
* Changed how pipe_control.plotting.assemble_data_seq_value()
determines the number of graph sets. Instead of counting the maximum
number of spins per residue, different spin names are now checked
across the sequence. This is needed as a single residue could have a
different type of spin. This was caught by the
Mf.test_dauvergne_protocol system test.
* Modified pipe_control.plotting.assemble_data_series_series()
to handle dictionaries with keys as values. This will be useful in,
for example, relaxation dispersion for plotting the dispersion curves.
In this case, the R2eff values are in a dictionary where the keys are
the values to plot against. This is different from the current case
where the X and Y data dictionaries are required to have the same
keys. These changes expand the capabilities of the grace.write user
function.
* Formatting change for the auto_analyses __all__ package list.
* Removed the import of the auto-analysis modules into the
auto_analyses package __init__ module. This import is not needed.
* The N-state model system test module now imports the
auto-analysis to fix an import order error.
* Added a warning for the spectrum.read user function if a
peak intensity of zero is encountered. This value can cause singular
matrix failures in certain optimisation algorithms.
* The spectrum.error_analysis user function can now be
performed on a subset of all spectra. The subset argument has been
added to allow the error analysis to be restricted to a subset of all
loaded spectral data.
* Created the lib.list.unique_elements() function for
returning a list with duplicates removed.
* Shifted the standard deviation code from the Monte Carlo
error_analysis() function to the lib package. The new function
lib.stats.std() is now used to simplify the error_analysis() function
and allow the code to be reused. This will be useful for expanding
the pipe_control.monte_carlo.error_analysis() function to handle
parameters which are dictionaries, for example as in the relax_disp
branch.
* The Monte Carlo error_analysis() function now handles
dictionary type parameters.
* Renamed the new lib.stats module to lib.statistics.
* Spun out the model list GUI element from the model-free
auto-analysis into its own module. This GUI element is now the
gui.analyses.model_list.Model_list class. This code has been spun out
as the GUI element will be used by the relaxation dispersion branch.
* The gui.analyses.model_list.Model_list GUI element now can
have tooltips via the tooltip class variable.
* Rearrangements of the gui.analyses package. The new
gui.analyses.elements package has been created and the model list and
text and spin GUI elements have all been shifted into the package.
* Spun out the Spin_ctrl analysis GUI element into its own
module in gui.analyses.elements.
* The relaxation time part of the spectra list GUI element can
now be turned on or off.
* The execution of the user function GUI pages can now be
delayed. The create_page() execute flag has been added to disable
execution. This can be later forced with the new on_execute()
force_execute flag.
* Modified the GUI new analysis wizard to return a list of
user function on_execute methods. This will be used in the relax_disp
branch and in the future for when a special user function page is
added to the new analysis wizard. This allows the use of user
function pages with execution delayed until the analysis __init__()
method is being run.
* Standardisation of the text of the GUI elements of the
analysis frames and expansion of the tooltips. All the text parts of
the Spin_ctrl and Text_ctrl elements now end in a colon. Tooltips are
now present on all elements and have been expanded and improved.
* The Text_ctrl analysis frame GUI elements now have separate
tooltips for the buttons. This is to give a hint to the user as to
what the button does.
* The model selection GUI analysis element can now have a
different tooltip for the button.
* Added tooltips to the model-free model list GUI elements in
the model-free analysis frame.
* Created the gui.wizards package for holding all of the relax
wizards. The gui.wizard module is now called gui.wizards.wiz_objects.
* Shifted and merged the NOE and Rx peak intensity wizards
into a new module. The wizards were separate and a part of the
analysis frame class objects. The two wizards have been merged into
the gui.wizards.peak_intensity.Peak_intensity_wizard class as most of
the code is shared. This one wizard class will be useful for reusing
in the relaxation dispersion branch.
* The peak intensity wizard class now inherits from
Wiz_window. This allows the class to be a wizard window instead of
launching a wizard window from within the class.
* Small rearrangements in the gui.wizards.peak_intensity module.
* Alphabetical ordering of the methods in the
gui.wizards.peak_intensity module.
* Simplified all of the peak analysis wizard wizard_update_*()
methods. They now all defer to the wizard_update_ids() method which
updates the spectrum ID fields.
* Simplified the wizard_update_noe_spectrum_type() method as
in the previous commit.
* Fixes for the frq.set user function in the GUI. The ID list
is now set to the spectrum IDs, and the frequency units are no longer
all fused into one string.
* Unicode is now used for the tau symbol in the model-free
model parameter lists in the GUI. This is only when modifying the
models to optimise, which shouldn't be changed anyway.
* Removed the 'string' from 'Spectrum ID string' in the
spectrum list GUI element. This is a GUI - the word string is
meaningless here!
* The delay times column string now specifies seconds in the
spectrum list GUI element.
* Formatting improvements for the relaxation data list GUI
element. The data type column entries are now descriptive and use
subscript.
* More unicode strings are used for the GUI for subscripts and
Greek letters.
* Fixes for the R1 and R2 GUI analyses for the recently
introduced unicode subscript characters. There is now self.label for
a pure string version and self.gui_label for the fancier unicode
version.
* The frq.set user function 'id' argument is no longer read
only - this was causing test suite failures.
* Removed a nasty kludge for releasing the execution lock on
failure. This kludge, after the bug fix for
https://gna.org/bugs/?20756, was causing failures in the test suite.
* Changed the 'Execute relax' button in all analyses in the
GUI to 'Execute analysis'. It makes no sense to execute relax as
relax has been executing during the analysis initialisation and the
user setting up all the data for the analysis. This is a remnant of
ancient design of Michael Bieri's GUI being a separate program to
relax, which would execute relax with the click of this button.
* Restored the Py_INCREF() function call in the relaxation
curve-fitting C module. This was deleted at r12632 along with
Py_XDECREF() and Py_DECREF() calls. The absence of a Py_INCREF()
function call causes the module to crash the Python interpreter under
certain conditions. The problem was found in the relax_disp branch.
* Clean up of unused headers and declarations in the
exponential curve C module.
* The relax_fit C module setup() function now uses the
Py_RETURN_NONE macro to terminate. This macro does exactly what the
old code does anyway.
* Removed an unused declaration in the relax_fit C module
setup() function.
* Increased the maximum number of relaxation times for the
relax_fit C module to 50.
* Shifted the C array creation to the relax_fit C module
header. The params, values, sd, relax_times, and scaling_matrix C
arrays are now declared and allocated in the header file rather than
using malloc() calls in the setup() function. This is to attempt to
remove a memory leak. The arrays are now of fixed length and reused
for each setup() call. These, as well as the other variables declared
in the header, are no longer declared in the functions.
* Improved the Python and C documentation of the functions of
the relax_fit C module.
* Converted the Py_BuildValue() calls to PyFloat_FromDouble()
in the relax_fit C module. This doesn't change much.
* Documentation improvements for the back_calc_I() function of
the relax_fit C module.
* The exponential C file now uses the exp() function from
math.h rather than Python.h. This file is independent from Python.
* The numpy include is no longer used for the compilation of
the C modules. Numpy is not used at all in the C modules, so this
just adds an annoying dependency for those who need to compile the
module themselves.
* Removed some bad calls to status.exec_lock.release(). This
commit may have to be reverted in the future. The problem is that the
execution lock is not being held when these calls are made. The calls
were added as a kludge to handle certain situations where the
execution lock was not released. There may be cases were this
behaviour is still needed.
* Added a developer script for testing of memory leaks in the
relax_fit C modules.
* Removed the numpy dependence from the manual C module
compilation script.
* Created the lib.mathematics relax library module. This
currently contains two functions, order_of_magnitude() and
round_to_next_order().
* Added unit tests for the lib.mathematics module.
* The relax_fit analysis now uses
lib.mathematics.round_to_next_order() for the scaling matrix. This
allows the optimised I0 value to be better understandable in the
printouts.
* Created the new Value system test class with the first test
Value.test_value_copy. This test demonstrates some pretty large bugs
in the value.copy user function.
* Modified the Value.test_value_copy system test to check the
copying of errors as well.
* Added the error flag argument to all of the specific
analysis API set_param_values() methods. This will allow parameter
errors as well as values to be set.
* The Value.test_value_copy system test now checks all of the
values and errors.
* Added the error flag argument to the value.set user
function. This will allow for parameter errors to be set by the user.
* The specific analysis API _return_value_general() method now
returns errors even when values are missing.
* The internal structural object PDF file creation now writes
out http://www.nmr-relax.com. Previously the link
http://nmr-relax.com was written out.
* Diffusion tensor PDB file fixes for the internal structural
object changes. This is because the relax website link is now written
into the PDB file as http://www.nmr-relax.com rather than
http://nmr-relax.com. This fixes the diffusion tensor system tests.
* Converted all of the specific analysis modules into
packages. The model-free and steady-state NOE analyses were already
packages, and this now brings all other analyses in line with the
package design of specific_analyses. The only change is that the
files specific_analyses/x.py have been shifted to
specific_analyses/x/__init__.py and the __all__ package variable
added.
* Epydoc docstring fixes for the compat module.
* The peak intensity wizard can now function remotely when the
spins are not named. This will be needed for the GUI tests to allow
the Question() call to be bypassed and still adding the spin.name user
function as the first page of the wizard. The key for spin.name page
has also been fixed so that the page can be accessed.
* The timing of individual tests in the relax test suite can
now be printed out. The new command line argument --time has been
added which, when supplied with one of the test suite arguments, will
cause the time required to complete each individual test to be
displayed. Instead of just printing the characters '.', 'F', and 'E'
for each test, now these characters are postfixed with the time in
seconds, the name of the test and ending in a newline character.
* Big speed up of the test suite by skipping a large number of
redundant Frame Order system tests. These are tests of using only PCS
or only RDC data. These tests are still active for the pseudo-ellipse
just to make sure that a whole missing data type can be handled.
* Suppressed the reporting of skipped tests in the test suite
if the module is set to None.
* The preview button in the file selection elements of the
user function windows can now be disabled. This is via the new
wiz_filesel_preview argument being set to False.
* Merged the frq.set and temperature user functions into the
new spectrometer user function class. The frq.set user function is
now called spectrometer.frequency and temperature is now
spectrometer.temperature. To match these changes, the cdp.frq
variable is now called cdp.spectrometer_frq.
* Modified the spectrometer.frequency user function so that a
frequency list and count is stored. These are the new
cdp.spectrometer_frq_list and cdp.spectrometer_frq_count variables.
This will allow various parts of relax which assemble frequency
information to be simplified and made more consistent.
* Created basic SVG and PNG graphics for the spectrometer user
function class. The spectrometer is black so as not to offend Bruker,
Varian, or Jeol users by avoiding a colour from one of these
companies.
* The pipe_control.spectrometer.get_frequencies() function can
now return MHz or Tesla units.
* Renamed the functions of the pipe_control.spectrometer
module. The frequency() and temperature() functions are now called
set_frequency() and set_temperature().
* Added backwards compatibility support for the spectrometer
frequency list and count. This is needed for old relax state files.
* A whitelist is now being used to limit the number of frame
order GUI tests to 1.
* Shifted all frequency data handling associated with
relaxation data to pipe_control.spectrometer. This includes the
deletion of the relax_data.frq user function as this replicates the
behaviour of spectrometer.frequency. A number of functions from the
pipe_control.relax_data module have changed: frq() has been deleted
as it is replaced by pipe_control.spectrometer.set_frequencies();
frq_checks() has been shifted to
pipe_control.spectrometer.frequency_checks(); frq_loop() has been
shifted to pipe_control.spectrometer.loop_frequencies(); num_frq() has
been deleted as the new variable cdp.spectrometer_frq_count contains
this info. Two new functions in the pipe_control.spectrometer module
have been added to remove the functionality from
pipe_control.relax_data. These are copy_frequencies() and
delete_frequencies().
* The molmol.macro_run user function file argument now has a
description.
* Huge speed up of the system tests for the loading and
creation of model-free saved states. The OMP files used for the
system test have been truncated from 134 to 7 spins, changing the
timing of 6 system tests from 11-13 seconds to less than 0.5 seconds
each.
* All of the binary file arguments for the user functions now
are file selection GUI elements. The GUI user function wizard pages
now have file selection buttons for selecting the executable to run.
These all have the preview button disabled. The results.read and
state.load GUI elements also have the preview button disabled.
* The user function 'prompt' description elements as now
displayed in the GUI wizard page.
* The monte_carlo.error_analysis user function can now handle
parameters which are lists.
* Added the ability for specific analyses to override the
optimisation constraint algorithm. The default is still the 'Method
of Multipliers', but if the constraint_algorithm() method returns a
different string, then that will be used to select the algorithm.
This allows the 'Log Barrier' method in minfx to be used.
* The value.display and value.write user functions can now
handle list and dictionary type parameters.
* Added two methods to the specific analysis common API class.
These are the _model_type_global() and _model_type_local() methods
for always specifying that the model type is global (i.e. at the level
of the data pipe) or local (i.e. there can be multiple clusters of
models).
* Added some more functions to the lib.statistics module.
These include the bucket() function for creating a discrete
distribution from a list of floating point numbers, and the gaussian()
function for calculating the probability of a point on a Gaussian
distribution.
* Added a directory and files for testing the white noise in
relaxation data. This includes scripts and graphs.
* The initial parameters are now the real parameter rather
than the optimised ones. This is for the script for testing white
noise in relaxation data.
* The spectrum.peak_intensities is now more robust when
reading in a generic formatted file. Firstly there is a check that
the intensity column number has been supplied. And then there is a
checks that all relevant data could be extracted from each row of the
file. This replaces traceback errors with RelaxErrors explaining the
problem if the user inputs bad data or forgets the intensity column
argument.
* Changed the "Execute analysis" button text back to the
original "Execute" text of the old relax GUI.
* Added the 'test.seq' file from bug report #20873
(http://gna.org/bugs/?20873). This is from Troels E. Linnet
(http://gna.org/users/tlinnet). The bug report and link to
http://thread.gmane.org/gmane.science.nmr.relax.user/1452 explains the
contents. The file will be used to construct a system test to catch
the bug.
* Created the Peak_lists.test_bug_20873_peak_lists system test
to catch bug #20873. This was reported by Troels E. Linnet
(http://gna.org/users/tlinnet) at https://gna.org/bugs/?20873. The
test has been created by copying the user function calls from the
original bug report and slightly modifying them to suite a 'relax_fit'
analysis type.
* Fix for the Peak_lists.test_bug_20873_peak_lists system
test. The spectrum IDs are now strings.
* Added checks of the peak intensities to the
Peak_lists.test_bug_20873_peak_lists system test.
* The spectrum.integration_points page in the peak analysis
GUI wizard has been fixed. It is only shown when volume integration
is selected with no replicated spectra.
* Removed a debugging printout which is killing the relax unit
tests in Python 3.
* Added an EPS version of the 128x128 pixel spectrometer icon.
This is for use in the relax manual.
* Added a README file for the relax 128x128 icons describing
how the EPS files should be created.
* Updated the spectrometer 128x128 icon to be of the correct
size and colour.
* Added a README file to the graphic/analyses directory
describing how to create the EPS files.
* Merger of the dipole_pair and interatomic user function
classes. The functionality of these two classes overlaps
significantly. And the dipole_pair user functions are not related to
magnetic dipole-dipole interactions. Therefore all the user functions
from both classes were shifted into the new interatom user function
class. This change will affect almost all relax scripts but, as this
will form part of the relax 3 release, script breakage should be
expected anyway.
* Removed the pipe_control.dipole_pair module as its contents
is now in pipe_control.interatomic.
* Removed the dipole_pair module from the pipe_control package
__all__ list.
* Merged the interatom.create user function into
interatom.define. These user functions had overlapping functionality
which would be confusing for a user.
* Added polish to all of the interatom user function docstrings.
* Improved the functionality of the interatom.read_dist user
function. The file data is now stripped using lib.io.strip to remove
comments and blank lines. And now if the iteratomic data container
cannot be found, it is created instead of raising a RelaxError.
* Improvements to the RelaxZeroVectorWarning - the warning
message was terribly out of date.
* Polish for the rdc.read user function. Comment lines and
blank lines are now removed to suppress useless warning messages about
these lines containing no valid data.
* Added some basic initial relax icons for J couplings.
* Created some basic initial GUI wizard graphics for J couplings.
* Modified the titles of all the auto-analysis GUI elements.
The text 'Setup for' has been removed as it is meaningless.
* Added more emphasis on the titles of the auto-analysis GUI
elements. There is now more space below the title, and a different
font (16pt roman italic) is being used.
* Removed some now irrelevant information from the rdc.read
user function docstring.
* Removed a false prompt example from the rdc.read user
function docstring.
* Created an entire new user function class for handling J
couplings in the relax data store. This derives from the RDC user
function modules. The following functions have been created:
j_coupling.copy, j_coupling.delete, j_coupling.display,
j_coupling.read, and j_coupling.write.
* Added a check for the RDC data type to the rdc.read user function.
* The rdc.read user function can now handle T = J+D type data.
Support for this in the specific analyses is yet to be added.
* Fixed for the rdc.read, j_coupling.read and
interatomic.read_dist user functions. Comment lines are no longer
removed, as it is impossible to tell a comment line from a spin ID
string.
* Split up the specific_analyses.n_state_model package into
modules. The new data and parameter modules have been created by
shifting out method from the __init__ module and converting them into
functions of the two new modules. This is to simplify the package.
* Shifted another method from the N_state_model class to the
specific_analyses.n_state_model.data module.
* Added support for the T = J+D RDC data type to the N-state
model target function. The J couplings are sent into the target
function class when the 'T' RDC data type is encountered. These
measured values are then added to the back-calculated RDC values to
produced T(theta) which is then compared to T via the chi-squared
function.
* Fix for the new
specific_analyses.n_state_model.data.opt_uses_j_couplings() function.
The cdp.rdc_data_types appears not to have all alignments IDs within
it.
* Removed the check for Numeric Python in the dep_check
module. This Python module not been used within relax for the better
part of a decade. This check is not needed.
* Added the j_coupling module to the pipe_control __all__ list.
* Fix for the pipe_control.rdc.q_factors() for T = J+D type
data. The Q factor normalisation was incorrect, as the J coupling
should be subtracted from T first.
* Unit test fixes for the N-state model. This is needed due
to the recent package rearrangements.
* Removed the absolute argument for all of the
lib.alignment.rdc functions. This should be performed at the level of
the target function, as mathematical operations may be required prior
to taking the absolute value.
* Fixes for the N-state model target functions for the
lib.alignment.rdc changes. The absolute value is now calculated
within the target function rather than when back calculating the RDCs.
* Errors are now handled correctly for the N-state model when
T = J+D values are used for the RDCs. The error is the square root of
the average variance of the RDC error and J coupling error.
* The RDC back-calculation function now supports T = J+D values.
* Created the N_state_model.test_absolute_T system test. This
is for checking the optimisation of absolute T=J+D values to find
alignment tensors.
* Epydoc docstring fix for the RelaxTestResult.write_time() method.
* Created a script to look through the entire relax source
tree for unused imports.
* Removed a large amount of unused imports throughout the
relax code base. These were identified by the new
./devel_scripts/find_unused_imports.py script together with pylint.
* Fixes for the pipe_control.rdc module for when the structure
cdp.rdc_data_types is missing.
* Improvements to the devel_scripts/find_unused_imports.py script.
* More cleanups of unused imports throughout relax.
* Fixes for how the devel_scripts/find_unused_imports.py
script runs pylint.
* More cleanups of unused imports throughout relax.
* Fixes and expansion of the test_suite.unit_tests._lib
package __all__ list.
* Fixes and improvements to Gary Thompson's
unit_test_runner.py script. The printouts have been improved and the
script can now handle more than 3 levels of directories for a package.
* The unit_test_runner.py script now defaults to verbose mode.
* More cleanups of the unit_test_runner.py script.
* Added a printout to the unit_test_runner.py if the TestCase
class cannot be found. This normally continued the test loading
silently without warning that the TestCase class name is missing or
incorrect.
* Missing import in the unit test module for the
lib.frame_order.matrix_ops module.
* Shifted the spin_id_to_data_list() function from
pipe_control.selection to lib.selection. This is because the
selection object requires this function, and the function has nothing
to do with the relax data store.
* Lots of import cleanups including removal of '*' imports,
missing imports, and unused imports.
* Small change to the find_unused_imports.py printouts.
* Large removal of unused imports throughout relax found using
the devel_scripts/find_unused_imports.py script.
* Clean up of all the imports in the relax code base. This is
mainly alphabetical reordering of the imports required due to the huge
layout changes in the trunk.
* Shifted the user function initalisation. This is from the
import of the user_functions package to the package initialise()
function. This is for saner importing dependencies in the relax
sources.
* The lib.io.open_write_file() function now catches file names
of None and raises a RelaxError. This is useful for the GUI if the
user forgets to select a file name.
* The rdc.corr_plot user function can now handled T=J+D type data.
* The N-state model analysis can now handle RDC data of mixed
D and T=J+D.
* Added support for mixed RDC data types per alignment. This
is to allow, for example, one bond RDC values of the 'D' data type and
two bond RDC values of the T = J+D data type to be loaded for the same
alignment ID. This is now handled in the N-state or ensemble analysis
by handling a different RDC data type per RDC value.
* The Peak_lists.test_bug_20873_peak_lists system test is now
skipped if the C modules are not compiled. This test requires the
presence of the C modules.
* Added a completely empty PNG image to use in the new
analysis GUI wizard for blank buttons. This will be used in the
relax_disp branch to eliminate a Mac OS X only bug.
* Added the scripts for backing up the relax SVN repository
and mailing lists to the repository. This is to make it easier for
others to set up the backups on their systems.
* Added comments to the backup scripts to make it easier to use them.
* Added the listings package to the relax user manual LaTeX
file. This will be used to improve the formatting and look of relax
scripts in the manual.
* Started to convert the relax user manual to use the
lstlisting environment for scripts. This is to prettify the scripts
in the manual.
* Improvements to the script UI section of the NOE chapter of
the user manual. The lstlisting environments now have the correct
numbering to match the script at the start,comments have been copied
into the split up script elements, and a few comments improved.
* The NMRPipe script in the relaxation curve-fitting chapter
of the manual now uses lstlisting. The language has been explicitly
set to csh to override the global default of Python.
* Converted all of the relaxation curve-fitting chapter of the
user manual to the lstlisting environment. This is for all parts of
the script UI section of the chapter.
* Converted all of the model-free chapter of the user manual
to the lstlisting environment. This is for all parts of the script UI
section of the chapter.
* Converted all of the J(w) mapping chapter of the user manual
to the lstlisting environment. This is for all parts of the script UI
section of the chapter.
* Converted all of the Consistency testing chapter of the user
manual to the lstlisting environment. This is for all parts of the
script UI section of the chapter.
* Created a new listings language definition for relax for the
user manual. This is for better highlighting of relax scripts and
code in the relax manual.
* Added an EPS version of the 128x128 J coupling icon for use
in the relax user manual.
* Removed some junk text from the relax script text in section
6.3.8 of the user manual.
* The relax language definition is now auto-generated by the
fetch_docstrings.py script. This is for use in the relax user manual
using the listings package. The fetch_docstrings.py script now
creates the docs/latex/script_definition.tex file. This is used by
the relax.tex file via an \include{} statement. This setup allows all
of the relax user functions to be dynamically set as keywords for the
relax language definition.
* Converted all of the Development chapter of the user manual
to use the listing package. This is for all of the code examples,
which are now much more colourful.
* Small typo fix for the relaxation curve-fitting chapter of
the user manual.
* Fixed some out of date script code for the relaxation
curve-fitting chapter of the user manual.
* Added a section label to the relaxation curve-fitting
chapter of the user manual.
* Adding a test data file in NMRPipe SeriesTab format.
Progress sr #3043: (https://gna.org/support/index.php?3043) - Support
for NMRPipe seriesTab format *.ser. A file in NMRPipe SeriesTab
format is added to the test-suite for further development.
* Test function for NMRPipe SeriesTab format implemented.
Progress sr #3043: (https://gna.org/support/index.php?3043) - Support
for NMRPipe seriesTab format *.ser. An assertEqual test is
implemented for the reading of NMRPipe SeriesTab format. The
standalone call is: relax -s
Peak_lists.test_read_peak_list_NMRPipe_seriesTab
* Adding a NMRPipe function file in the folder
lib\software\nmrpipe.py. Progress sr #3043:
(https://gna.org/support/index.php?3043) - Support for NMRPipe
seriesTab format *.ser. Initial file for: lib\software\nmrpipe.py.
This file will hold the function calls handling NMRPipe SeriesTab
format.
* Fix for commit
(http://article.gmane.org/gmane.science.nmr.relax.scm/18004). The
spin naming was wrong. Progress sr #3043:
(https://gna.org/support/index.php?3043) - Support for NMRPipe
seriesTab format *.ser. 'spin_id' keywords should be supplied
different. Ex: spin.name(name='NE1', spin_id=':62').
* Autodetect format implemented for NMRPipe SeriesTab format
implemented. Progress sr #3043:
(https://gna.org/support/index.php?3043) - Support for NMRPipe
seriesTab format *.ser. The file is determined a NMRPipe SeriesTab if
the first two words of the first line is: REMARK SeriesTab.
* Update of the rotation matrix example in the intro chapter
of the user manual. The function is now in
lib.geometry.rotations.euler_to_R_zyz(). The example has also been
converted to the lstlisting environment for better formatting.
* The relax prompt strings and help system are now keywords
for the relax listings package definition. The prompt strings
"relax>" and "relax|" are now recognised as keywords and are coloured
blue. The help system has been added as a normal Python keyword for
highlighting.
* Converted all relax prompt examples in the intro chapter of
the manual to the lstlisting environment. This is simply for a more
colourful representation.
* The prompt examples in the user function chapter of the
manual now use the listing environment. This is via the
fetch_docstrings.py script and results in much better formatting of
these subsections.
* Added function destination for auto-detected NMRPipe
SeriesTab format. Progress sr #3043:
(https://gna.org/support/index.php?3043) - Support for NMRPipe
seriesTab format *.ser. Auto-detected NMRPipe SeriesTab format make
function calls to the file: lib\software\nmrpipe.py in function
nmrpipe.read_list_intensity_seriestab().
* Imported the missing lib.software.nmrpipe module into
pipe_control.spectrum. Progress sr #3043:
(https://gna.org/support/index.php?3043) - Support for NMRPipe
seriesTab format *.ser. Expected modules for use in
lib\software\nmrpipe.py is imported.
* Release checklist minfx and bmrblib version update to the
newest versions.
* Spacing fix in an import statement (found using the 2to3
conversion program).
* Added the relax wiki backup script for dumping the MySQL
database contents locally. This is from
http://article.gmane.org/gmane.science.nmr.relax.devel/4163.
* Added the script from Troels Linnet for backing up the relax
wiki via FTP. This is from the post
http://article.gmane.org/gmane.science.nmr.relax.devel/4168.
* Added a link to Troels' post to the relax-devel mailing list
to the relax wiki FTP backup script. The link is
http://article.gmane.org/gmane.science.nmr.relax.devel/4168
* The relax info printout now works in the absence of the
bmrblib module.
* Added some Oxygen icons for a boolean GUI input element.
The media-record-relax-green.png files are the media-record.png files
with the hue set to 117.
* Created a boolean input element for the auto-analyses of the
GUI. This simply turns on and off.
* The boolean GUI auto-analysis input element now has a
SetValue() method.
* Completed NMRPipe SeriesTab reader. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser. Completed NMRPipe SeriesTab reader for
assignment according to SPARKY format. Changes implemented according
to: http://article.gmane.org/gmane.science.nmr.relax.devel/4120.
* Extraction of NMRPipe SeriesTab changed. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser. The Extraction of NMRPipe SeriesTab data is
changed in pipe_control/spectrum.py in the read() function.
* Added flag for single or multiple extraction of spectrum.
Progress sr #3043: (https://gna.org/support/index.php?3043) - support
for NMRPipe seriesTab format *.ser.
* Flag change added to reading of NMRPipe SeriesTab. Progress
sr #3043: (https://gna.org/support/index.php?3043) - support for
NMRPipe seriesTab format *.ser.
* Some small edits to the intro chapter of the relax user manual.
* Many improvements to the indexing in the relax user manual.
* Removed the flag for single_spectrum. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Fixed wrong reference to Sparky format. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Modfied the intensity list to handle intensities for all
spectra per spin. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Fixed the extraction of NMRPipe seriestab data in
pipe_control.spectrum.read(). Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Fix for handling reading spin of type heteronuc='NE1' and
proton='HE1'. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Adding NMR seriesTab data file for a multiple column /
multiple spectrum formatted file. This file is from
https://gna.org/support/download.php?file_id=18618 attached to the
support request https://gna.org/support/?3043 by Troels Linnet. This
is if the command "seriesTab -in ../../peaks.dat -out
seriesTab_multi.ser -list nmrfiles.list -sum -dx 1 -dy 1" where
nmrfiles.list contains file reference to 10 .ft2 files.
* Fix for unit test of nmrpipe. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Replacing a pointer-reference structure to an empty creation
of list of lists. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* The ID of spins in seriesTab_multi.ser was not formatted
correctly to SPARKY format. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Added system test for reading of a multi column formatted
NMRPipe seriesTab file. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser. Generated the reference data in Excel, for
the system test. The spectrum ID's are auto generated by supplying
the keyword spectrum_id='auto'. The first few tests was matched
against integers rather than floats. Adding '.0' to the end of each
number. Spaces added after the commas in the self.assertAlmostEqual()
calls. The 2to3 conversion program (for Python 2 to Python 3
conversion) highlights this issue.
* Added check for number of supplied spectra ID's and the
number of returned intensity columns. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Made it possible to autogenerate spectrum ID's, if
spectrum_id='auto'. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Remove from datalist where empty list starts. These are
created where spins are skipped for ID = '?-?'. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Moved checks for matching length of spectrum IDs and
intensities columns. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Moved the adding function of adding the spectrum id (and
ncproc) to the relax data store. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser. Shifting it to later will prevent the
cdp.spectrum_ids list to be populated after the user calls the user
function incorrectly.
* Added epydoc documentation in pipe_controlspectrum.read()
when supplying keyword 'auto'. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Added GUI description for when supplying 'auto' to the
spectrum_id. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Added a stub GUI describtion in the File formats, for
NMRPipe seriesTab. Progress sr #3043:
(https://gna.org/support/index.php?3043) - support for NMRPipe
seriesTab format *.ser.
* Fix for two spaces are used after a period in documentation.
Progress sr #3043: (https://gna.org/support/index.php?3043) - support
for NMRPipe seriesTab format *.ser. relax uses the double space for
easier for the eyes to pick up the sentence structure.
* The relax user manual is now broken into parts. The higher
level LaTeX part command is now used to group related chapters. This
should make it easier for users to navigate this huge thing.
* Creation of the optimisation chapter of the relax user
manual. The main text of this chapter originates as part of the
model-free chapter. As this most of this text was not model-free
specific, it has been spun out as its own chapter. Text has also been
taken from the "Optimisation of relaxation data – values, gradients,
and Hessians" chapter. The indexing for the optimisation topics has
also been improved.
* Changed the chapter layout of the relax user manual. The
development chapter has been moved forwards.
* Fix for the spectrum.read_intensities user function
docstring. Grammatically, the text "spectrum ID's" should be
"spectrum IDs". The problem though was that this text was strangely
causing the user manual compilation to fail.
* Added subsubindexing for the optimisation algorithm index entries.
* Added extensive cross-referencing to the index of the relax
user manual.
* Added some hyphenation rules for better formatting in the
user manual. For this, the external hyphenation.tex has been created.
* Better indexing in the relax user manual. The imakeidx
LaTeX package is now used instead of makeidx, and the hyphenation has
been improved.
* Lots of spelling fixes for the relax user manual.
* Updated the minimum Python version from 2.3 to 2.5 in the user
manual.
* Epydoc docstring fix for the pipe_control.spectrum.read()
function. The text "Z_A{i}" causes problems when compiling the API
documentation, so it has been changed to "Z_Ai".
* Python 3 fix for the new test_suite.clean_up module. The
exceptions Python module does not exist in Python 3, so instead the
relax compat.builtins object is being used to store the WindowsError
variable of None.
* Added a paragraph to the installation chapter of the manual
about not supporting the EPD.
Bugfixes:
* Fix for bug #20674 (https://gna.org/bugs/?20674) - the
failure of the consistency testing analysis. This was reported by
Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The
problem was that the first residue did not have a single proton 'H' in
the PDB file, and therefore the dipolar relaxation interaction was not
set up. The overfit_deselect() method of the consistency testing
specific API was not checking for this. The method is now much more
like that of the model-free specific analysis.
* Fix for the model-free analysis specific overfit_deselect()
method. The tests for the presence of dipolar relaxation was not
correct and was non-functional.
* Fix for the J(w) mapping analysis matching that for the
consistency testing. The overfit_deselect() method is now identical
to that of the consistency testing analysis.
* Fix for bug #20683 (https://gna.org/bugs/?20683) - the
infinite and NaN data in Bruker DC files. This was reported by
Mengjun Xue <mengjun dott xue att mailbox dott tu-berlin dot de>. The
model-free specific overfit_deselect() method now checks for infinite
relaxation data and deselects the spin if such data is encountered.
* Fix for the analysis specific API common method
_data_init_spin(). The data types are now correctly checked - they
are not strings but types.
* Fix for the relaxation curve-fitting
_assemble_scaling_matrix() method. The intensity scaling was never
activated before due to a lower vs. uppercase parameter name mismatch.
This scaling is now correctly set up as the previous code assumed
cdp.relax_times was a list whereas it has been a dictionary since the
early 1.3 releases.
* The grid search bounds for the relaxation curve-fitting are
no longer affected by scaling. The parameter scaling recently
activated revealed a bug in the lower and upper data structures for
the grid search in that these were continuously scaled down.
* Fix for the target_functions.relax_fit C module - the
scaling was incorrectly performed.
* Fix for the relaxation curve-fitting _back_calc() method for
the changes to the C module. The setup() method requires that the
scaling matrix is converted to a list of the diagonal elements.
* Fix for the analysis specific API common
_return_value_general() method. The value of None is now handled
properly when a simulation value is asked for.
* Restored the default behaviour of the spin_loop(). The
skip_desel flag is now functional and defaults to False.
* Fix for the relax_times and intensities parameter
definitions for specific_analyses.relax_fit. These are dictionaries,
not lists.
* Fix for the spectrum.error_analysis user function for
replicated spectra and subsets. A second call to
spectrum.error_analysis was removing the results from the first call.
This is now avoided.
* Bug fix for the right click popup menu in the spectra list
GUI element. This affects the NOE, R1, and R2 analyses. The actions
of the menu items were all mixed up.
* Fix for the nasty bug #20756 (https://gna.org/bugs/?20756).
The problem was that the global execution lock was not always released
by a relax script when certain errors are raised during the script
execution. This does not occur for all types of error though. Now
the release of the lock has been shifted into the 'finally' statement
to absolutely force lock release.
* Big bug fix for a memory leak in the relaxation
curve-fitting C module. Proper reference counting is used for the
temporary 'element' Python objects used in the conversion between
Python and C objects. The use of the Py_CLEAR() macro removes the
memory leak. However the number of references as seen by
sys.gettotalrefcount() in a debugging Python version keeps rising and
might be a problem in the future.
* Big bug fix for the value.copy user function - it is now
functional again.
* Bug fix for the value.copy user function. The user function
can now handle parameter errors, and the values are set in the correct
data pipe.
* Bug fix for an incorrect print statement in the
N_state_model.test_paramag_centre_fit system test. This is in the
script, and was uncovered using WinPython by Troels E. Linnet
(http://gna.org/users/tlinnet) via the relax system tests at
http://thread.gmane.org/gmane.science.nmr.relax.devel/3863. The
Python bug was detailed at
http://thread.gmane.org/gmane.science.nmr.relax.devel/3863/focus=3867.
* Fix for the package checking as part of the unit tests.
This was identified from the bug report #20820
(https://gna.org/bugs/?20820) submitted by Troels E. Linnet
(https://gna.org/users/tlinnet). The problem was that on some
systems, the full path is required for checking the presence of the
directories which are the sub-packages of the main package being
checked. The result was that checking for the package in the __all__
list was skipped. Note that this change does not fix the bug
reported.
* Fixes for the Jw.test_calc system test - the spectral
density value comparison is now significant.
* Bug fix for the pipe_control.spectrometer.get_frequencies()
function. The units argument was incorrectly referenced.
* Fix for bug #20820 (https://gna.org/bugs/?20820). Solution
found - 'software' was not mentioned in __init__.py, and failed at
import.
* Partial fix for bug #20873 (https://gna.org/bugs/?20873).
The spectrum_id argument for the spectrum.read_intensities user
function can now be both a string and a list of strings.
* Fix for bug #20873 (http://gna.org/bugs/?20873). This was
reported by Troels E. Linnet (http://gna.org/users/tlinnet). The
ability to load multiple peak intensities from a single generic
formatted file has been correctly implemented. This involves added
checks to make sure that the user supplies reasonable arguments and to
then loop over the intensity column argument.
* Python 3 fixes via the 2to3 program.
* Bug fix for the value.write user function for list or
dictionary type data. This is for the case where the variable of one
spin is set to None rather than a list or dictionary type.
* Bug fix for the Sequence GUI input element. This complete
the removal of bug #20873 (https://gna.org/bugs/?20873). The problem
was that the gui_to_str() function was not failing to convert the
string into a string list, so the list was deemed as a single string.
Now the first character of '[' or '(' for lists or tuples are now
searched for instead of relying on the conversion to trigger an error.
* Fixes for the value.write user function for simple parameter
values of None. This is a recently introduced bug which causes a
complete failure of the user function is the parameter for any spin is
None.
* Fix for bug #20888 (https://gna.org/bugs/?20888), the
autoscaling of Grace graphs. This solution was mentioned in the post
at http://thread.gmane.org/gmane.science.nmr.relax.devel/3920/focus=3930.
Instead of using minimum and maximum values for the axes in the Grace
graphs produced by the lib.software.grace module, which was the old
solution for having the graphs scaled to reasonable values, instead
the '@autoscale' command is appended to the end of all graphs. This
is performed by the write_xy_data() function.
* Bug fix for the running of the test suite in the relax GUI.
The fix of r19727 was extended to apply to the GUI as well. Too many
arguments were being sent into TextTestRunner Python class on certain
Python versions (3.1 and <= 2.6).
* Big bug fix - the relax execution lock now truly supports
nesting. This fixes bug #20891 (https://gna.org/bugs/?20891) reported
by Troels Linnet (https://gna.org/users/tlinnet). Scripts can now be
executed from the GUI. Note that this is a very dangerous fix.
* Completed the fix for bug #20889
(https://gna.org/bugs/?20889). The problem was that the
spectrum.read_intensities user function was incorrectly updating the
cdp.spectrum_ids list when the spectrum_id argument is set to a list.
The list of IDs was being set as a single element of cdp.spectrum_ids,
causing problems with the GUI when updating the ComboBox choices and
then subsequent setting of the spectrum IDs. This bug and fix is
independent of the relax_disp branch, despite being uncovered there
and being caught by the Relax_disp.test_bug_20889_multi_col_peak_list
GUI test in that branch.
* Bug fix for the GUI element for the interatom.define user
function. The special spin ID GUI elements can not be set to the
get_spin_ids() function as then SetValue can no longer work for IDs
not in the list.
* Fixes for the TestCase class names for a number of lib
package modules. As the test class name was incorrect, previously the
test suite was skipping these silently. This was dangerous.
* Fixes for the unit tests of the lib.selection module. The
contains_*() methods now should be used. And the
test_Selection_ful_spin_id() unit test has been completely deleted as
this way of checking the selection object is no longer valid.
* Fix for bug #20910 (https://gna.org/bugs/?20910) - the
broken grace.write GUI interface. The problem was that the Value GUI
input element was not detecting list-type data returned by the
wiz_combo_iter method.
* Fix for bug #20915, (https://gna.org/bugs/?20915) - Failure
of Grace opening in MS Windows Troels E. Linnet provided this patch,
and was discovered during work on a Windows 7 system: telinnet aaattt
bio_dot_ku_dot_dk. This is a small fix for a wrong call to "raise
RelaxMissingBinaryError(binary)", when issuing an external call to
xmgrace. The "path_sep" would be equal = [\/], and the RE search
would not find(True) the full path specified for the xmgrace file.
This is now shifted to python: os.path.isfile
http://docs.python.org/2/library/os.path.html. Another fix, is that
as a standard the command "xmgrace" is provided. This will work fine
through windows cmd, but the true name for program in windows is
"xmgrace.exe", and so an additional search for +".exe" is also
performed.
* Fix for the N_state_model.test_absolute_T system test for
Mac OS X. The precision of the check needed to be decreased.
* Fix for bug #20918 (https://gna.org/bugs/?20918), the
hanging of the data pipe editor. This was reported by Troels Linnet
(https://gna.org/users/tlinnet) and is an MS Windows only problem.
The problem is in the wxMSW part of wxPython, and it may be fixed in
newer wxPython versions. The issue is nevertheless now avoided by
calling the GUI user function store objects with the arguments
wx_wizard_sync=True and wx_wizard_modal=True. This appears to solve
the problem.
* Decreased the precision of the check in the
Frame_order.test_rigid_data_to_rigid_model system test. This is to
allow the test to pass on a MS Windows 7 test machine.
* More MS Windows fixes, this time a nasty kludge, for the
relax system tests. This is strangely needed for the relax_disp
branch and not the trunk for a 64-bit MS Windows 7 test system. The
reason why this WindowsError is triggered by the base tearDown()
method in the relax_disp branch and not trunk is a total mystery.
Actually why Windows refuses to complete the file close() operations
of the results.write and state.save user functions before calling the
tearDown() method is the greater mystery.
* Bug fix for the batch file permissions for executing Art
Palmer's Modelfree4 program. This was identified in the post
http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.
The file was set to be executable, but on Unix systems it would end
up with the permissions "---x------".
* Small comment fix in the sample_scripts/consistency_tests.py script.
* Fix for the scons fetch_docstrings target. The user
functions need to be explicitly initialised in the fetch_docstrings
script as this is not running through relax.
* Fix for bug #20921 (https://gna.org/bugs/?20921), the GUI
tests freezing in MS Windows. The problem was that the dipolar
interaction wizard in the model-free auto-analysis GUI element was
calling its user functions asynchronously. This can lead to racing
conditions. The commit r80084
(http://article.gmane.org/gmane.science.nmr.relax.scm/17840) somehow
randomly triggers this racing on MS Windows systems only together with
the Mf.test_mf_auto_analysis GUI test. Now all user functions are
called synchronously.
* Fix for the relax GUI splash screen. On certain systems,
the GUI was failing due to the splash screen. It is now shown after
the main wxPython window has been created.
* Fix for the new analysis wizard when running the GUI tests.
If the create_button() method is called without a function argument,
the wizard is still created. This is triggered in the relax_disp
branch on certain systems.
* Bug fix for the spin parameter array always being converted
to lowercase. The is in the
data_store.mol_res_spin.SpinContainer._back_compat_hook() method. It
always calls the _back_compat_hook_mf_data() method which converts the
spin 'params' list all to lowercase. Now the _back_compat_hook()
method first checks that the data pipe is that of a model-free
analysis.
* Proper bug fix for the spin parameter array always being
converted to lowercase. The previous fix was causing failures in
certain cases. One system test and one GUI test were failing. Now
the spin container is checked for the presence 'equation' variable to
determine if this is a model free data pipe.
* Fix for the relax version file for the relax user manual
construction. This was causing 'scons user_manual_pdf' and related
targets to fail when a local git repository is used (via git-svn).
* Bug fix for the page numbers in the index - these were often
out by a few pages. The makeindex command was being run too early in
the repetitive LaTeX compilation chain, causing the page numbers to be
incorrect. It is now run twice to fix the problem.
* Fix for the spectrum.read_intensities user function in the
GUI. The menu string was truncated to spectrum.read.
* Python 3 fix for the
lib.software.nmrpipe.read_list_intensity_seriestab() function. The
inbuilt Python filter() function does not return a list in Python 3,
as previously, but rather a filter object. Therefore a call to list()
is required to properly convert the data.
* An attempt at better handling MS Windows not releasing the
file handle on time in the test suite. The system and unit tests
tearDown() method should now be resilient to the strange MS Windows
behaviour of not releasing the relax state files. The tearDown()
method should now complete even when this error occurs. A delay of 3
seconds has been added when the WindowsError occurs to give the OS
some time before attempting to delete the file again. If this fails,
then the file deletion operation is skipped.
* Better handling of temporary file and directory removal in
the relax test suite. The new test_suite.clean_up.deletion() function
has been created from the recent method of the same name. This is
used by the tearDown() method of the system, unit, and GUI tests. It
should prevent rare MS Windows errors from appearing due to the OS not
releasing a temporary file after a close() call.
relax version 3.0.0.