5.7.0 - #273

Running into some problems with toolbox initialization when testing this.

For example:

FAIL - aatest_ds000114_fmri.m aatest_ds000114_fmri.m had an error: Too many input arguments. in /Users/peellelab/automaticanalysis/aa_tools/toolboxes/bwtClass.m (line 23) in /Users/peellelab/automaticanalysis/aa_tools/toolboxes/aas_inittoolbox.m (line 22) in /Users/peellelab/automaticanalysis/aa_engine/aa_init.m (line 119) in /Users/peellelab/automaticanalysis/aa_engine/aa_doprocessing.m (line 79) in /Users/peellelab/automaticanalysis/developer/testscripts/aatest_ds000114_fmri.m (line 75) in /Users/peellelab/automaticanalysis/developer/aa_test.m (line 156) in /Users/peellelab/automaticanalysis/developer/aa_test.m (line 121)

I suspect this is a parameter file issue. Here is my current bwt toolbox setup:

<toolbox desc='Toolbox with implemented interface in extrafunctions/toolboxes' ui='custom'>
    <name desc='Name corresponding to the name of the interface without the "Class" suffix' ui='text'>bwt</name>
    <dir ui='dir'>/Users/peellelab/MATLAB_THIRDPARTY/BrainWavelet</dir>
</toolbox>

My previous version had an extraparameters block that I removed (cf. aap_parameters_defaults_CBSU.xml). However, aa also crashes if the extraparameter block is present.

I am afraid I forgot to update your toolboxes. The doKeepInPath parameter has been removed because it has no effect. This was the missing bit to make the code and the documentation fully aligned. It did not raise a flag because they are not part of the CI (yet - WIP).
I have updated them.

That seems to have got it working.

Thanks much.

I am sorry for the lack of transparency.

Thanks, @jones-michael-s. However, I'd rather first sort out the new tests including AROMA and scrubbing. I think I have sorted them out. I currently run the test on my repo, and if it passes, I submit a PR.
So, please, hold off with merging this one.

I take a look at the conflict.
I probably have to resync the central master to this branch and update the new toolbox classes, as well. Please, wait for a new CI test before merging.

Now it is ready to be merged.