Author: bugman
Date: Tue Nov 25 20:13:17 2014
New Revision: 26723
URL: http://svn.gna.org/viewcvs/relax?rev=26723&view=rev
Log:
Merged revisions 26708,26710 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26708 | bugman | 2014-11-24 13:37:15 +0100 (Mon, 24 Nov 2014) | 6 lines
Backported the relax 3.3.3 CHANGES file changes to trunk.
The command used was:
svn merge -r26703:r26704 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/3.3.3 .
........
r26710 | bugman | 2014-11-25 10:27:00 +0100 (Tue, 25 Nov 2014) | 3 lines
Small updates for the wiki section of the release checklist document.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/docs/CHANGES
branches/frame_order_cleanup/docs/devel/Release_Checklist
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Nov 25 20:13:17 2014
@@ -1 +1 @@
-/trunk:1-26681
+/trunk:1-26722
Modified: branches/frame_order_cleanup/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/CHANGES?rev=26723&r1=26722&r2=26723&view=diff
==============================================================================
--- branches/frame_order_cleanup/docs/CHANGES (original)
+++ branches/frame_order_cleanup/docs/CHANGES Tue Nov 25 20:13:17 2014
@@ -1,3 +1,80 @@
+Version 3.3.3
+(24 November 2014, from /trunk)
+http://svn.gna.org/svn/relax/tags/3.3.3
+
+ Features:
+ * Implemented the lib.geometry.vectors.vector_angle_atan2() relax
library function. This is for calculating the inter-vector angle using the
more numerically stable atan2() formula.
+ * Implemented the lib.geometry.vectors.vector_angle_acos() relax
library function. This is used to calculate the inter-vector angle using the
arccos of the dot product formula. The function has been introduced into the
relax library as the calculation is repeated throughout relax.
+ * Expanded the basis sets for the align_tensor.matrix_angles user
function to allow the correct inter-tensor angles to be calculated. This
includes the standard inter-matrix angles via the arccos of the Euclidean
inner product of the alignment matrices in rank-2, 3D form divided by the
Frobenius norm of the matrices, irreducible spherical tensor 5D basis set
{A-2, A-1, A0, A1, A2}, and the unitary 9D basis set {Sxx, Sxy, Sxz, Syx,
Syy, Syz, Szx, Szy, Szz} (all of which produce the same result).
+ * Expanded the basis sets for the align_tensor.svd user function to
allow the correct singular values and condition number to be calculated.
This includes the irreducible spherical tensor 5D basis set {A-2, A-1, A0,
A1, A2} and the unitary 9D basis set {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy,
Szz} (both of which produce the same result).
+ * Added the angle_units and precision arguments to the
align_tensor.matrix_angles user function to allow either degrees or radians
to be output and the number of decimal points to be specified.
+ * Added the precision argument to the align_tensor.svd user function
to allow the number of decimal points for the singular values and condition
number to be specified.
+ * Updated the align_tensor.display user function to output the
irreducible spherical harmonic weights. This is the alignment tensor in the
{A-2, A-1, A0, A1, A2} notation.
+
+
+ Changes:
+ * Basic Epydoc fix for the data_store.exp_info module.
+ * Epydoc fix for the name_pipe() method of the relaxation dispersion
auto-analysis for repeated data.
+ * Fixes for the HTML user manual compilation. The index.html file
was not being created as the main page has changed from
'relax_user_manual.html' to 'The_relax_user_manual.html'.
+ * Added a line to the release checklist document about updating the
wiki release links. These are for the combined release notes pages at
http://wiki.nmr-relax.com/Relax_releases,
http://wiki.nmr-relax.com/Relax_release_descriptions,
http://wiki.nmr-relax.com/Relax_release_metadata,
http://wiki.nmr-relax.com/Relax_release_features,
http://wiki.nmr-relax.com/Relax_release_changes,
http://wiki.nmr-relax.com/Relax_release_bugfixes,
http://wiki.nmr-relax.com/Relax_release_links.
+ * Updates for the release announcement section of the release
checklist document.
+ * Created a system test to catch a rare relaxation data loading
problem.
+ * Created the Mf.test_dauvergne_protocol_sphere system test. This
catches bug #22963 (https://gna.org/bugs/?22963): Using '@N*' to define the
interatomic interactions for a model-free analysis fails when using
non-backbone 15N spins.
+ * Set more reasonable default values for the lib.structure.pdb_write
functions atom() and hetatm(). The occupancy now defaults to 1.0 instead of
'', and the temperature factor to 0.0 instead of ''. This avoid painful
errors when using these functions, as these arguments must be floating point
numbers at all times, hence the default value of '' causes a TypeError.
+ * Updated the PDB file in the
test_suite/shared_data/model_free/sphere/ directory. The relax library is
now being used to create the PDB file. Additional TER and CONECT records are
now being created so the result is a more correct PDB file.
+ * Converted all ATOM records to HETATM in the sphere.pdb file.
+ * Renamed vector_angle() to vector_angle_normal() in the
lib.geometry.vectors module. This is to standardise the naming as there are
now the standard vector angle formula implemented as the vector_angle_acos()
and vector_angle_atan2() functions.
+ * Added 6 unit tests for the
lib.geometry.vectors.vector_angle_acos() function. These are similar to
those of the vector_angle_normal() function but unsigned angles are checked
for.
+ * Created 6 unit tests for the
lib.geometry.vectors.vector_angle_atan2() function.
+ * Created a script and log file to demonstrate differences between
alignment tensor basis sets. This shows that the inter-tensor angles and
condition numbers are dependent on the basis set used.
+ * Improved the printouts from the align_tensor.svd user function by
including the basis set text.
+ * Updated the log file for comparing different alignment tensor
basis sets for align_tensor.svd changes.
+ * Implemented a new default basis set for the
align_tensor.matrix_angles user function. This is uses standard definition
of the inter-matrix angle using the Euclidean inner product of the two
matrices divided by the product of the Frobenius norm of each matrix. As
this is a linear map, it should produce the correct definition of
inter-tensor angles.
+ * Improvements to the description of the align_tensor.matrix_angles
user function.
+ * Updated the test_matrix_angles_identity() unit test for
pipe_control.align_tensor.matrix_angles(). This is the test in the
_prompt.test_align_tensor.Test_align_tensor module. The basis set has been
set back to the now non-default value of 0, and the value checks have been
converted from assertEqual() to assertAlmostEqual() to allow for small
truncation errors.
+ * Conversion of the basis_set argument for the
align_tensor.matrix_angles user function. The argument is now a string that
accepts the values of 'matrix', 'unitary 5D', and 'geometric 5D' to select
between the different matrix angles techniques. This has been updated in the
test suite as well.
+ * Added a check for the values of the basis_set argument. This is
to the align_tensor.matrix_angles user function backend.
+ * Printout improvements clarifying the align_tensor.matrix_angles
user function.
+ * Conversion of the basis_set argument for the align_tensor.svd user
function. The argument is now a string that accepts the values of 'unitary
9D', 'unitary 5D', and 'geometric 5D' to select between the different SVD
matrices. This has been updated in the test suite as well.
+ * Expanded the N_state_model.test_5_state_xz system test. This now
covers the new 'unitary 9D' basis set for the align_tensor.svd user function
and the new 'matrix' basis set for the align_tensor.matrix_angles user
function.
+ * Expansion of the align_tensor.matrix_angles user function. The
new basis set 'unitary 9D' has been introduced. This creates vectors as
{Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz} and computes the inter-vector
angles. These match the 'matrix' basis set whereby the Euclidean inner
product divided by the Frobenius norms is used to calculate the inter-tensor
angles. In addition, the user function documentation and printouts have been
improved. And the backend code has been simplified.
+ * Updated the script and log file for demonstrating differences
between alignment tensor basis sets. This now handles the changes to the
basis_set arguments used in the align_tensor.matrix_angles and
align_tensor.svd user functions, and includes the new basis sets.
+ * Added the irreducible tensor notation of {A-2, A-1, A0, A1, A2} to
the alignment tensor object. This follows from the definition of Sass et al,
J. Am. Chem. Soc. 1999, 121, 2047-2055, http://dx.doi.org/10.1021/ja983887w.
The equations of (2) were converted using Gaussian elimination to obtain a
reduced row echelon form, so that the equations in terms of {A-2, A-1, A0,
A1, A2} were derived. These have been coded into the alignment tensor object
calc_Am2, calc_Am1, calc_A0, calc_A1 and calc_A2 methods respectively, and
the values can be obtained by accessing the Am2, Am1, A0, A1, and A2 objects.
To check that the implementation is correct, a unit test has been created to
compare the calculated values with those determined using Pales.
+ * Expanded the unit test of the alignment tensor {A-2, A-1, A0, A1,
A2} parameters to cover all values.
+ * Created functions in the relax library for calculating the
inter-vector angle for complex vectors. This is in the lib.geometry.vectors
module. The function vector_angle_complex_conjugate() has been created to
calculate the angle between two complex vectors. This uses the new auxiliary
function complex_inner_product() to calculate <v1|v2>.
+ * Added the 'irreducible 5D' basis set option to the
align_tensor.matrix_angles user function. This is for the inter-tensor
vector angle for the irreducible 5D basis set {S-2, S-1, S0, S1, S2}. Its
results match that of the standard tensor angle as well as the 'unitary 9D'
basis sets.
+ * Added the 'irreducible 5D' basis set option to the
align_tensor.svd user function. This is for the inter-tensor vector angle
for the irreducible 5D basis set {A-2, A-1, A0, A1, A2}. Its results match
that of the 'unitary 9D' basis set.
+ * Editing of the description for the 'irreducible 5D' alignment
tensor basis set. This is for the align_tensor.matrix_angles and
align_tensor.svd user functions. All Sm element have been converted to Am.
+ * Editing of the description for the align_tensor.matrix_angles user
function.
+ * Editing of the align_tensor.svd user function description.
+ * Updated the script and log file for demonstrating differences
between alignment tensor basis sets. The 'irreducible 5D' basis set in now
used for both the align_tensor.matrix_angles and align_tensor.svd user
functions.
+ * Fix for a spelling mistake in the align_tensor.matrix_angles user
function printouts.
+ * Small fix for the align_tensor.matrix_angles user function
documentation.
+ * Expanded the N_state_model.test_5_state_xz system test for more
alignment tensor basis sets. The align_tensor.matrix_angles and
align_tensor.svd user functions are now being called with the additional
'irreducible 5D', and 'unitary 9D' basis sets, to make sure these work
correctly.
+ * Created the Align_tensor.test_align_tensor_matrix_angles system
test. This is to check the angles calculated by the
align_tensor.matrix_angles user function. As there are no external
references, this essentially fixes the angles to the currently calculated
values to catch any accidental changes in the future.
+ * Created the Align_tensor.test_align_tensor_svd system test. This
is to check the angles calculated by the align_tensor.svd user function. As
there are no external references, this essentially fixes the singular values
and condition numbers to the currently calculated values to catch any
accidental changes in the future.
+ * Fixes for the proportions of the align_tensor.matrix_angle user
function GUI wizard.
+ * Expanded the 'irreducible 5D' text in the
align_tensor.matrix_angles and align_tensor.svd user functions. This now
explains that these are the coefficients for the spherical harmonic
decomposition.
+ * Improved the text for the irreducible tensor notation in the
align_tensor.display user function.
+ * Formatting fix for the magnetic susceptibility tensor part of the
align_tensor.display user function.
+ * More improvements for the align_tensor.matrix_angles user function
description.
+ * Epydoc docstring fixes and expansion for the
lib.io.sort_filenames() function.
+ * Epydoc docstring fixes for the lib.spectrum.nmrpipe module. This
is for the API documentation at http://www.nmr-relax.com/api/index.html. The
show_apod_rmsd_to_file() and show_apod_rmsd_dir_to_files() function
docstrings have both been modified.
+ * Epydoc docstring fixes for the pipe_control.opendx.map() function.
This is for
http://www.nmr-relax.com/api/3.3/pipe_control.opendx-module.html#map. The
fixes include whitespace and textwrapping changes.
+ * Python 2.5 fix for the align_tensor.display user function. The
new irreducible spherical tensor coefficient printout was failing as the
float.real variable was introduced from Python 2.6 onwards.
+ * Shifted the structure checks into their own module. This shifts
the special check_structure Check object from pipe_control.structure.main
into the new checks module. It allows the check to be performed by other
modules in the pipe_control.structure package.
+ * Added the missing_error keyword argument to the
pipe_centre_of_mass() function. This is from the pipe_control.structure.mass
module. The new keyword controls what happens with the absence of structural
data. The pipe_control.structure.checks.check_structure() function is now
being used to either throw a warning and return [0, 0, 0] or to raise a
RelaxError.
+ * Fix for the new unit tests - Python 2.5 floats do not have a
'real' property.
+
+
+ Bugfixes:
+ * Fix for bug #22961 (https://gna.org/bugs/?22961), the failure of
relaxation data loading with the message "IndexError: list index out of
range". The bug was found by Julien Orts. It is triggered by loading
relaxation data from a file containing spin name information and supplying
the spin ID using the spin name to restrict data loading to a spin subset.
To solve the problem, the pipe_control.relax_data.pack_data() function has
been redesigned. Now the selection union concept of Chris MacRaild's
selection object is being used by joining the spin ID constructed from the
data file and the user supplied spin ID with '&', and using this to isolate
the correct spin system.
+ * Big Python 3 bug fix for the dep_check module for the detection of
the NMRPipe showApod software. The showApod program was falsely detected as
always not being present when using Python 3. This is because the output of
the program was being tested using string comparisons. However the output
from programs obtained from the subprocess module is no longer strings but
rather byte-arrays in Python 3. Therefore the byte-array is not being
converted to text if Python 3 is being used, allowing the showApod software
to be detected.
+ * Python 3 bug fix for the lib.spectrum.nmrpipe.show_apod_extract()
function. The subprocess module output from the showApod program, or any
software, is a byte array in Python 3 rather than text. This is now detected
and the byte array converted to text before any processing.
+ * Bug fix for the lib.structure.angles.angles_*() functions for odd
increments. This affects the PDB representations of the diffusion tensor and
frame order when the number of increments in the respective user functions is
set to an odd number. It really only affects the frame_order.pdb_model user
functions, as the number of increments cannot be set in any of the other user
functions (structure.create_diff_tensor_pdb, structure.create_rotor_pdb,
structure.create_vector_dist, n_state_model.cone_pdb).
+
+
+
Version 3.3.2
(13 November 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.2
Modified: branches/frame_order_cleanup/docs/devel/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/docs/devel/Release_Checklist?rev=26723&r1=26722&r2=26723&view=diff
==============================================================================
--- branches/frame_order_cleanup/docs/devel/Release_Checklist (original)
+++ branches/frame_order_cleanup/docs/devel/Release_Checklist Tue Nov 25
20:13:17 2014
@@ -200,7 +200,7 @@
- For all bugs, support requests, and tasks, make links to the trackers
including the full description in the link. (for vim, go to the start of the
text and use the register: "3dwr[/_<80>kb)^Mi ^[pxr]").
- Make links to the relax manual for all user functions (Vim register:
"v/[ ,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html
^[pa]^[/user function^M", then search for
"www.nmr-relax.com\/manual\/[a-z0-9_]*\.\|html" and replace all '.'.)
- - Make internal links for all relax versions.
+ - Make internal links for all relax versions (search for
"[1-3]\.[0-9]*\.[0-9]*").
- Convert all symbols/parameters to use wiki formatting.
- Convert all model names to internal wiki links (vi search
"\<m[0-9]\>\|\<tm[0-9]\>\|No Rex\|R2eff\|LM63\|LM63 3-site\|CR72\|CR72
full\|IT99\|TSMFK01\|B14\|B14 full\|NS CPMG\|MMQ CR72\|NS
MMQ\|M61\|DPL94\|TP02\|TAP03\|MP05\|NS R1rho\|BK13").
- Add as many links as possible to the API documentation (to help users
dive into the relax code and to help with search engine indexing).
@@ -225,7 +225,7 @@
The steps are:
- Log into Gna! and go to https://gna.org/news/submit.php?group=relax.
- - Cut and paste all of the wiki text. Delete the initial lower case
title formatting text, the final 'See also' section, and any wiki markup.
+ - Cut and paste all of the wiki text. Delete the initial lower case
title formatting text, the final 'Links', 'Announcements' and 'See also'
sections, and any wiki markup.
- Add a paragraph before the 'Download' paragraph with the text 'For the
official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.1.'.
- Use the Savane markup to format the text (recipe #236,
https://gna.org/cookbook/?func=detailitem&item_id=236).
- As the Savane markup for sectioning is the same as the wiki, the
section titles = Description =, = Download =, and = Full list of changes = do
not need to be modified (except changing the text 'CHANGES file' to 'Full
list of changes' and deleting the metadata). The same for the subtitles ==
Features ==, == Changes ==, and == Bugfixes ==.
r26723 - in /branches/frame_order_cleanup: ./ docs/CHANGES docs/devel/Release_Checklist