Trusted, Bureaucrats
4,228
edits
Changes
Jump to navigation
Jump to search
→Changes: Formatting of ^[[?1034h.
* Modified the Relax_disp.test_sprangers_data_to_mmq_cr72 system test to pass on certain systems. This test fails on 32-bit Linux (and probably other systems as well). To fix the test, the k<sub>ex</sub> values are all divided by 100 before checking them to 4 decimal places of accuracy.
* Improved how the relax installation path is determined in the status object. If the path cannot be found, the current working directory is then checked if it is where relax is installed. This is needed when importing modules outside of relax.
* Hack to permanently eliminate the <code><nowiki>^[[?1034h </nowiki></code> escape code being produced on Linux systems. This is produced by importing the readline module. The escape code will be sent to STDOUT every time relax is executed, so it will be present in all log files. The problem is the TERM environmental variable being set to 'xterm'. The hack simply sets TERM to an empty string.* More hacks for permanently eliminating the <code><nowiki>^[[?1034h </nowiki></code> escape code being produced on Linux systems. This is a nasty feature of the GNU readline library. It is now also turned off in the dep_check module, suppressing <code><nowiki>^[[?1034h </nowiki></code> in Python scripts which import only parts of relax.
* 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@gna.org/msg06288.html, http://www.mail-archive.com/relax-devel@gna.org/msg06289.html, http://www.mail-archive.com/relax-devel@gna.org/msg06327.html, and http://www.mail-archive.com/relax-devel@gna.org/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.
* Updated the numpy minimal dependency in the installation chapter of the manual to version 1.6.
* The internal structural object add_molecule() and has_molecule() methods are now model specific. This allows for finer control of structural object.
* Created the new [http://www.nmr-relax.com/api/3.2/lib.structure.files-module.html lib.structure.files module]. This currently contains the single find_pdb_files() function which will be used to find all *.pdb, *.pdb.gz and *.pdb.bz2 versions of the PDB file in a given path.
* Fix for the breakage of the relax help system. This was reported at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481. The problem was that the TERM environmental variable was turned off to avoid the GNU readline library on Linux systems emitting the <code><nowiki>^[[?1034h </nowiki></code> escape code. See the message at http://thread.gmane.org/gmane.science.nmr.relax.devel/6481/focus=6489 for more details. However the Python help system obviously requires this environmental variable. Now only if the TERM variable is set to 'xterm' will it be reset, and to 'linux' instead of the blank string "". This does not affect any relax releases.
<section end=changes/>
