[INFRA] switch to moxunit for tests

[Remi-Gau]

This is an extension of the PR #100 and should probably be merged after.

This should fix #44

---

For reviewers:

I had to silence one test that fails with octave and not matlab.

We have some slight differences in behavior between the 2 on some queries that I would like to "fix" but I would need someone to cross check that they can reproduce them.

If they are reproducible, I would suggest to open an issue about that but to still merge that PR so we can move forward.

[Remi-Gau]

EDIT: now fixed

---

hum...

Trying to list several directories to add to the path of the MOxUnit github action give some weird results.

    - name: MOxUnit Action
      uses: joergbrech/moxunit-action@master
      with:
        tests: tests
        src: +bids 
        ext: JSONio tests/utils      # < ------ External resources to add to the search put (excluded from coverage)
        with_coverage: true
        cover_xml_file: coverage.xml

This fails:
https://github.com/bids-standard/bids-matlab/pull/108/checks?check_run_id=1694214979

The setup phase of the action gives this:

addpath(genpath("/github/workspace/JSONio tests/utils"));

This does not seem to be the expected behavior.

Opening an issue on the github action repo.

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[Remi-Gau]

OK there is one assert that now fails for some unknown reason.

  pth_bids_example = get_test_data_dir();
  
  BIDS = bids.layout(fullfile(pth_bids_example, '7t_trt'));

  %   test
  mods = {'anat', 'fmap', 'func'};
  
  assert(isequal(bids.query(BIDS, 'modalities'), mods));
  assert(isequal(bids.query(BIDS, 'modalities', 'sub', '01'), mods));
  assert(isequal(bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '1'), mods));
  
  % assert(isequal(bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '2'), mods(2:3)));
  % this now fails on octave 4.2.2 but not on Matlab
  %
  % On octave this gives:
  % 
  % bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '2')
  %
  % ans =
  % {
  %   [1,1] = anat
  %   [1,2] = fmap
  %   [1,3] = func
  % }

[Remi-Gau]

I am tempted to say we should try to put in place some sort of input validation with more meaningful error messages to make the behavior between matlab and octace more consistent.

This is the kind of output on the parts that fails

With matlab

>> BIDS = bids.layout(fullfile(pwd, 'tests', 'bids-examples', '7t_trt'));

>> bids.query(BIDS, 'subjects')
ans =
  1×22 cell array
  Columns 1 through 12
    '01'    '02'    '03'    '04'    '05'    '06'    '07'    '08'    '09'    '10'    '11'    '12'
  Columns 13 through 22
    '13'    '14'    '15'    '16'    '17'    '18'    '19'    '20'    '21'    '22'

>> bids.query(BIDS, 'sessions', 'sub', '01')
ans =
  1×2 cell array
    '1'    '2'

% the following should at leat throw a warning 
%   that subject label should be a string
>> bids.query(BIDS, 'modalities', 'sub', 1)
ans =
  0×0 empty cell array

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '')
ans =
  0×0 empty cell array

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', [])
ans =
  0×0 empty cell array

>> bids.query(BIDS, 'modalities', 'sub', '01')
ans =
  1×3 cell array
    'anat'    'fmap'    'func'

% the following should at leat throw a warning
%    that session '01' does not exist with a list of the valid sessions
>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '01')
ans =
  0×0 empty cell array

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '1')
ans =
  1×3 cell array
    'anat'    'fmap'    'func'

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '2')
ans =
  1×2 cell array
    'fmap'    'func'

With octave

>> BIDS = bids.layout(fullfile(pwd, 'tests', 'bids-examples', '7t_trt'));

>> bids.query(BIDS, 'subjects')
ans =
{
  [1,1] = 01
  [1,2] = 02
  [1,3] = 03
  [1,4] = 04
  [1,5] = 05
  [1,6] = 06
  [1,7] = 07
  [1,8] = 08
  [1,9] = 09
  [1,10] = 10
  [1,11] = 11
  [1,12] = 12
  [1,13] = 13
  [1,14] = 14
  [1,15] = 15
  [1,16] = 16
  [1,17] = 17
  [1,18] = 18
  [1,19] = 19
  [1,20] = 20
  [1,21] = 21
  [1,22] = 22
}

>> bids.query(BIDS, 'sessions', 'sub', '01')
ans =
{
  [1,1] = 1
  [1,2] = 2
}

Asking for modalities on sessions that do not exist return the same thing. (??)

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '02')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '12')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '023')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

Both of the following return empty cell arrays in matlab.
We can have an error on the second and third one but they should be more informative.

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', [])
error: Invalid call to lookup.  Correct usage is:

 -- IDX = lookup (TABLE, Y)
 -- IDX = lookup (TABLE, Y, OPT)
error: called from
    print_usage at line 91 column 5
    ismember at line 116 column 10
    query at line 82 column 15

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', 2)
error: Invalid call to lookup.  Correct usage is:

 -- IDX = lookup (TABLE, Y)
 -- IDX = lookup (TABLE, Y, OPT)
error: called from
    print_usage at line 91 column 5
    ismember at line 116 column 10
    query at line 82 column 15

This is the part of the test that goes "BOINK" as session 2 only has fmap and func.

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '1')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

>> bids.query(BIDS, 'modalities', 'sub', '01', 'ses', '2')
ans =
{
  [1,1] = anat
  [1,2] = fmap
  [1,3] = func
}

[Remi-Gau]

Unless I hear otherwise I will merge this in 2 days: this is mostly infrastructure related but it should make our lives easier moving forward.