Author: bugman
Date: Wed Jul 2 09:42:32 2014
New Revision: 24392
URL: http://svn.gna.org/viewcvs/relax?rev=24392&view=rev
Log:
Merged revisions 24354-24355,24361,24365,24380-24383,24386 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r24354 | bugman | 2014-06-27 18:13:27 +0200 (Fri, 27 Jun 2014) | 16 lines
Numpy version 1.6 or higher is now required to be able to run relax.
This follows from the series of messages:
- http://www.mail-archive.com/relax-devel@xxxxxxx/msg06288.html,
- http://www.mail-archive.com/relax-devel@xxxxxxx/msg06289.html,
- http://www.mail-archive.com/relax-devel@xxxxxxx/msg06327.html,
- http://www.mail-archive.com/relax-devel@xxxxxxx/msg06335.html.
If too many users complain, maybe this change can be reverted later. This
minimal numpy version is
needed for many of the speed ups going in the relaxation dispersion and
frame order analyses. It is
required for the numpy ufunc out arguments and for the numpy.eigsum()
function. These will likely
be used in other analyses in the future for improving the speed of relax,
so it might affect users
of other analyses later on.
........
r24355 | bugman | 2014-06-27 18:14:26 +0200 (Fri, 27 Jun 2014) | 3 lines
Updated the numpy minimal dependency in the installation chapter of the
manual to version 1.6.
........
r24361 | bugman | 2014-06-30 10:16:57 +0200 (Mon, 30 Jun 2014) | 5 lines
Added better epydoc sectioning to the lib.dispersion.ns_cpmg_2site_expanded
module docstring.
This is to better separate the original scripts used to document the code
evolution.
........
r24365 | bugman | 2014-06-30 18:10:09 +0200 (Mon, 30 Jun 2014) | 6 lines
Created the very basic structure.com user function for calculating the
centre of mass.
This is to simply allow an easy interface to the
pipe_control.structure.mass.pipe_centre_of_mass()
function.
........
r24380 | bugman | 2014-07-01 17:04:41 +0200 (Tue, 01 Jul 2014) | 6 lines
Empty lines are now handled by the lib.structure.pdb_write.record()
function.
By supplying the remark as None, empty lines can now be created in the
REMARK section of a PDB file.
This can be used for nicer formatting.
........
r24381 | bugman | 2014-07-01 17:08:16 +0200 (Tue, 01 Jul 2014) | 8 lines
Expansion of the REMARK section of the PDB file created for the internal
structural object.
This is visible when using the structure.write_pdb user function, as well
as the many other user
functions which create PDB files. The relax version as well as the file
creation date are now
recorded in the PDB file. This extra information should be very useful.
Empty lines in the REMARK
section improve the formatting.
........
r24382 | bugman | 2014-07-01 17:16:30 +0200 (Tue, 01 Jul 2014) | 5 lines
Fixes for the Diffusion_tensor system tests due to the recent PDB file
changes.
Prior to the comparison of the generated PDB files, all REMARK PDB lines
are now stripped out.
........
r24383 | bugman | 2014-07-01 17:30:56 +0200 (Tue, 01 Jul 2014) | 6 lines
Fixes for all system tests failing due to the expanded and improved PDB
REMARK section.
The system tests now remove all REMARK records prior to comparing file
contents. The special
strip_remarks() system test method has been created to simplify the
stripping process.
........
r24386 | bugman | 2014-07-02 09:06:16 +0200 (Wed, 02 Jul 2014) | 10 lines
Fix for the software verification tests.
The recent expansion and improvements of the REMARK records created by the
internal structural
object PDB writing method imported the relax version to place this
information into the PDB files.
However this breaks the relax library design, as shown by the verification
tests. Instead the relax
version information is being taken from the
lib.structure.internal.object.RELAX_VERSION variable.
This defaults to None, however the version module now sets this variable
directly when it is
imported so that it is always set to the current relax version when running
relax.
........
Modified:
branches/disp_spin_speed/ (props changed)
branches/disp_spin_speed/dep_check.py
branches/disp_spin_speed/docs/latex/install.tex
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
branches/disp_spin_speed/lib/structure/internal/object.py
branches/disp_spin_speed/lib/structure/pdb_write.py
branches/disp_spin_speed/pipe_control/structure/main.py
branches/disp_spin_speed/test_suite/system_tests/diffusion_tensor.py
branches/disp_spin_speed/test_suite/system_tests/structure.py
branches/disp_spin_speed/user_functions/structure.py
branches/disp_spin_speed/version.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/disp_spin_speed/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/dep_check.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/docs/latex/install.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/latex/install.tex?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/internal/object.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/pdb_write.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/pipe_control/structure/main.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/diffusion_tensor.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/structure.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/user_functions/structure.py?rev=24392&r1=24391&r2=24392&view=diff
Modified: branches/disp_spin_speed/version.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/version.py?rev=24392&r1=24391&r2=24392&view=diff
r24392 - in /branches/disp_spin_speed: ./ docs/latex/ lib/dispersion/ lib/structure/ lib/structure/internal/ pipe_control/st...