Trusted, Bureaucrats
4,228
edits
Changes
Lots more external API links.
* Updated the Mac OS X framework setting up instruction document. New sections have been added for the nose and matplotlib Python packages, as nose is needed for the numpy and scipy testing frameworks and matplotlib might be a useful optional dependency in the future. The mpy4py section has been updated to avoid the non-framework fink version of mpicc which cannot produce universal binaries. A few other parts also have small edits.
* Removed the Freecode section from the release checklist as Freecode has been permanently shut down. The old relax links are still there (http://freecode.com/projects/nmr-relax), but Freecode is dead (http://freecode.com/about).
* Fix for the [http://www.nmr-relax.com/api/3.3/lib.structure.internal.molecules.MolContainer-class.html#last_residue internal structural object MolContainer.last_residue() method]. This can now operate when no structural information is present, returning 0 instead of resulting in an IndexError.
* Updated the script for finding unused imports in the relax source code. Now the file name is only printed for Python files which have unused imports.
* Completely removed all mentions of Freecode from the release document. The old relax links are still there ([http://freecode.com/projects/nmr-relax)old relax links are still there], but Freecode is dead ([http://freecode.com/about)Freecode is dead].
* Updated the minfx version in the release checklist document to [https://gna.org/forum/forum.php?forum_id=2471 1.0.8]. This version has not been released yet, but it will include important fixes and additions for constrained parallelised grid searches.
* Fix for a broken link in the development chapter of the relax manual.
* Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax manual. The [[B14]] model links to http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken as the B in [[B14]] was capitalised.
* Sent in the verbosity argument value to the [http://home.gna.org/minfx/minfx.grid-module.html#grid_split minfx.grid.grid_split() function]. The minfx function in the next release ([https://gna.org/forum/forum.php?forum_id=2471 1.0.8]) will now be more verbose, so this will help with user feedback when running the model-free analysis on a cluster or multi-core system using MPI.
* The [http://www.nmr-relax.com/manual/time.html time user function] now uses the chronometer Oxygen icon in the GUI.
* Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings. This is for the pipe_control.minimise module.
* More docstring line wrapping removal from [http://www.nmr-relax.com/api/3.3/pipe_control.minimise-module.html pipe_control.minimise].* Bug fix for the parameter units descriptions. This only affects a few rare parameters. The [http://www.nmr-relax.com/api/3.3/specific_analyses.parameter_object.Param_list-class.html#units specific analysis API parameter object units() method ] was incorrectly checking if the units value is a function - it was checking the parameter conversion factor instead.
* Modified the [http://www.nmr-relax.com/manual/align_tensor_init.html align_tensor.init user function] so that the parameters are now optional. This allows alignment tensors to be initialised without specifying the parameter values for that tensor.
* Modified profiling script to have different number of NCYC points per frequency. This is to complicate the data, so any erroneous reshaping of data is discovered. It is expected, that experiments can have different number of NCYC points per spectrometer frequency. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis].
* Initial try to alter the [http://www.nmr-relax.com/api/3.3/target_functions.relax_disp.Dispersion-class.html#calc_CR72_chi2 target function calc_CR72_chi2]. This is the first test to restructure the arrays, to allow for higher dimensional computation. All numpy arrays have to have same shape to allow to multiply together. The dimensions should be [ei][si][mi][oi][di]. [Experiment][spins][spec. frq][offset][disp points]. This is complicated with number of disp point can change per spectrometer frequency. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis]. This implementation brings a high overhead. The first test shows no winning of time. The creation of arrays takes all the time.
* Temporary changed the lib/dispersion/cr72.py function to unsafe state. This change turns-off all the safety measures, since they have to be re-implemented for higher dimensional structures.
* Altered profiling script to report cumulative timings and save to temporary files. [https://gna.org/task/?7807 Task #7807: Speed-up of dispersion models for clustered analysis]. This indeed shows that the efficiency has gone down.