try to standardize order of input arguments into functions

[Remi-Gau]

[marcobarilari]

wait until the repo is safe with more tests

[Remi-Gau]

input arguments

Suggestion for ordering: from more general to more specific

BIDS > opt > subject > session > run

• BIDS (from getData) restrict the set of possible analysis one can run to this BIDS data set
• opt restricts this set even further
• subject / session / run even more

% OK
varargout = getInfo(BIDS, opt, subID, info, varargin)

% not OK
varargout = getInfo(subID, BIDS, opt, info, varargin) 

output arguments

Try to return them in order of importance first and in order of appearance otherwise.

exceptions

If function creates or modifies a batch then matlabbatch is the first argin and first argout.

If a function performs an "action" to be chosen from a one of several strings (with a switch statement), this string comes as first argin or second if matlabbatch is first.

This applies even for optional argument. <--- not sure about that one.

% OK
varargout = getInfo('filename', BIDS, opt, subID, varargin)
[matlabbatch, voxDim] = setBatchRealign(matlabbatch, [action = 'realign',] BIDS, opt, subID)

% not OK
varargout = getInfo(BIDS, opt, subID, 'filename', varargin) % 'filename' is the name of the "action" or the info to get in this case
[matlabbatch, voxDim] = setBatchRealign(BIDS, opt, subID, matlabbatch, [action = 'realign']) % batch and action should go first

@marcobarilari @CerenB

Does this make sense?