Open main menu

Changes

Relax 3.3.3

No change in size, 12:56, 24 November 2014
Tracker links with full descriptions.
* 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)bug #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.
<section begin=bugfixes/>
* Fix for bug #22961 ([https://gna.org/bugs/?22961)bug #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.
Trusted, Bureaucrats
4,223

edits