tapas_physio_check_spm_batch_editor_integration should honour spm_get_defaults('tbx') for possible toolbox installation paths

[gdevenyi]

When initializing PhysIO, tapas checks a hardcoded path: https://github.com/translationalneuromodeling/tapas/blob/master/PhysIO/code/utils/tapas_physio_check_spm_batch_editor_integration.m#L40

But I have separately managed toolbox directories, by adding this file to the startup path:

$ cat spm_my_defaults.m 
global defaults
defaults.tbx.dir{end+1} = fullfile(fileparts(mfilename('fullpath')),"PhysIO","toolbox") ;

Where toolbox contains the linked code/ directory, named PhysIO

This is to enable lmod (https://lmod.readthedocs.io/en/latest/) to (potentially) manage multiple parallel versions of toolboxes for users.

[mrikasper]

Dear Gabriel,

Thank you for the feedback and pointing us to the lmod system. How would I go about this? Checking every directory in the defaults.tbx.dir cell array and its subdirectories?

Just out of curiosity: Do you have an example of using different versions of SPM toolboxes with lmod?

All the best, Lars

[gdevenyi]

How would I go about this? Checking every directory in the defaults.tbx.dir cell array and its subdirectories?

Yes I think that would resolve this particular check for my implementation.

Just out of curiosity: Do you have an example of using different versions of SPM toolboxes with lmod?

The spm startup code will find and load any spm_my_defaults.m file it finds on the MATLABPATH: https://github.com/neurodebian/spm12/blob/master/spm_defaults.m#L200-L236

So my lmod modules consist of: prepend_path( "MATLABPATH", "/path/to/tapas/<VERSION>/install")

Which then contains a spm_my_defaults.m with matlab code I provided above, appending a dir to the toolbox path which contains the toolbox.

If I want different versions, I just create a different /path/to/tapas/<VERSION>/install and place that version there.

For full details I have the skeleton of my lmod system here, https://github.com/DouglasNeuroInformatics/software_quarantine/blob/master/software/tapas/6.0.1/module

There's no examples for multiple versions yet explicitly because this is a fresh rebuild transitioning from environment-modules (TCL) to lmod (lua)

[gdevenyi]

Also P.S. thank you so much for properly releasing and versioning your software. So many popular MATLAB/SPM toolboxes make zero attempt to track changes, or even have anything in a version control system.

[mrikasper]

Dear Gabriel,

That's great to hear. I have changed tapas_physio_check_spm_batch_editor_integration in the physio branch following your feedback. Could you please check whether it fulfills your needs? If we are quick, it might make it into the upcoming release.

All the best, Lars

[gdevenyi]

tapas_init now works without any code modifications:

Checking Matlab PhysIO paths, SPM paths and Batch Editor integration now...
Checking Matlab PhysIO paths now...added PhysIO path recursively: /tmp/tapas/PhysIO/code
Checking Matlab SPM path now...OK.
Checking whether PhysIO/code folder is a subfolder of SPM/toolbox (or a link within there)...Defaults settings have been modified by file(s):
  /tmp/tapas/spm_my_defaults.m
Modified fields: tbx 

One small thing, there's a missing newline after the "..."