Remove remaining dependencies on MATLAB toolboxes - Githubissues

JeschkeLab / DeerLab-Matlab

Data analysis and method development toolbox for dipolar EPR spectroscopy

MIT License

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Remove remaining dependencies on MATLAB toolboxes #9

Closed luisfabib closed 4 years ago

luisfabib commented 4 years ago

In order for the DOE to be usable with the core MATLAB product without any additional (purchaseable) toolbox the following dependencies must be eliminated::

Optimization toolbox - need to find good open-source alternatives to the fmincon, lsqnonlin, ...
Statistics and Machine Learning toolbox - the sensitivity analysis function now requires the pdist map, this must be changed by an open-source alternative

The functionality does not need to be removed, and toolbox-dependent functions can be used optionally.

luisfabib commented 4 years ago

All reamining dependencies have been removed in the following commits:

Optimization Toolbox

https://github.com/luisfabib/DeerAnalysis2/commit/640c2498a9fdd89a9c823a31c1bfca7d1953b087 & https://github.com/luisfabib/DeerAnalysis2/commit/56370d7853e4c9500df270d0df13ccce7be75612 : The fmincon and lsqnonlin solvers used for the fitparamodel function now have open-source alternatives fminsearchbnd and nlsqbnd, respectively. If the toolbox is available, the MATLAB solvers will be used by default, otherwise the open-source solvers will be set as default.

Statistics and Machine Learning toolbox

https://github.com/luisfabib/DeerAnalysis2/commit/0d0cb80fa8a002a985992b4dc57f97bc53fba97e & https://github.com/luisfabib/DeerAnalysis2/commit/48e00eac3f2b7ad02cb79c3d56cc8f1dac7312dd : The prctile and pdist functions from the toolbox have been locally implemented.