reduce number of warning in tests

Author: Remi-Gau

bidspm.m

@@ -13,18 +13,18 @@ function bidspm(varargin)
 
   defaultAction = 'init';
 
-  isEmptyOrCellstr = @(x) isempty(x) || iscellstr(x);
+  isEmptyOrCellstr = @(x) isempty(x) || isstring(x);
   isFileOrStruct = @(x) isstruct(x) || exist(x, 'file') == 2;
 
   isLogical = @(x) islogial(x) && numel(x) == 1;
   isChar = @(x) ischar(x);
   isPositiveScalar = @(x) isnumeric(x) && numel(x) == 1 && x >= 0;
 
-  isDir = @(x) isdir(x);
+  isFolder = @(x) isfolder(x);
 
-  isCellStr = @(x) iscellstr(x);
+  isCellStr = @(x) isstring(x);
 
-  isLowLevelActionOrDir = @(x) (ismember(x, low_level_actions()) || isdir(x));
+  isLowLevelActionOrDir = @(x) (ismember(x, low_level_actions()) || isfolder(x));
 
   addOptional(args, 'bids_dir', pwd, isLowLevelActionOrDir);
 
@@ -48,7 +48,7 @@ function bidspm(varargin)
   addParameter(args, 'ignore', {}, isEmptyOrCellstr);
 
   % stats only
-  addParameter(args, 'preproc_dir', pwd, isDir);
+  addParameter(args, 'preproc_dir', pwd, isFolder);
   addParameter(args, 'model_file', struct([]), isFileOrStruct);
   addParameter(args, 'roi_based', false, isLogical);
   % group level stats only
@@ -384,7 +384,7 @@ function initBidspm(dev)
   opt.verbosity = 2;
   opt.msg.color = '';
 
-  octaveVersion = '4.0.3';
+  octaveVersion = '6.4.0';
   matlabVersion = '8.6.0';
 
   % octave packages
@@ -547,6 +547,11 @@ function run_tests()
 
   bidspm('action', 'dev');
 
+  % to reduce noise in the output
+  if isOctave
+    warning('off', 'setGraphicWindow:noGraphicWindow');
+  end
+
   cd(fileparts(mfilename('fullpath')));
 
   if isGithubCi
@@ -566,8 +571,7 @@ function run_tests()
   folderToCover = fullfile(pwd, 'src');
   testFolder = fullfile(pwd, 'tests', subfolder);
 
-  success = moxunit_runtests( ...
-                             testFolder, ...
+  success = moxunit_runtests(testFolder, ...
                              '-verbose', '-recursive', '-with_coverage', ...
                              '-cover', folderToCover, ...
                              '-cover_xml_file', 'coverage.xml', ...

demos/MoAE/moae_fmriprep.m

@@ -22,6 +22,10 @@
 addpath(fullfile(pwd, '..', '..'));
 bidspm();
 
+if isOctave
+  warning('off', 'setGraphicWindow:noGraphicWindow');
+end
+
 % Getting the raw dataset
 download_data = true;
 download_moae_ds(download_data);

demos/MoAE/test_moae.m

@@ -22,11 +22,15 @@
 
 addpath(fullfile(WD, '..', '..'));
 
+bidspm();
 if download_data
-  bidspm();
   download_moae_ds(download_data, clean);
 end
 
+if isOctave
+  warning('off', 'setGraphicWindow:noGraphicWindow');
+end
+
 optionsFile = fullfile(WD, 'options', 'options_task-auditory.json');
 
 space = {'IXI549Space'

demos/face_repetition/test_face_rep.m

@@ -15,11 +15,16 @@
 
 addpath(fullfile(WD, '..', '..'));
 
+bidspm();
+
 if download_data
-  bidspm();
   download_face_rep_ds(download_data);
 end
 
+if isOctave
+  warning('off', 'setGraphicWindow:noGraphicWindow');
+end
+
 optionsFile = fullfile(WD, 'options', 'options_task-facerepetition.json');
 
 model_file = fullfile(WD, 'models', 'model-faceRepetition_smdl.json');

mlc_config.json

@@ -21,12 +21,12 @@
 
   % (C) Copyright 2020 bidspm developers
 
-  isDir = @(x) isdir(x);
+  isFolder = @(x) isfolder(x);
 
   args = inputParser;
 
   addRequired(args, 'opt', @isstruct);
-  addRequired(args, 'bidsDir', isDir);
+  addRequired(args, 'bidsDir', isFolder);
 
   try
     parse(args, varargin{:});

src/IO/getData.m

@@ -17,12 +17,12 @@ function anatomicalQA(opt)
 
   % (C) Copyright 2020 bidspm developers
 
-  if ~opt.QA.anat.do
-    return
-  end
-
   if isOctave()
     warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.');
+    opt.QA.anat.do = false;
+  end
+
+  if ~opt.QA.anat.do
     return
   end
 

src/QA/anatomicalQA.m

@@ -16,6 +16,10 @@ function anatomicalQALesion(opt)
 
   if isOctave()
     warning('\nanatomicalQA is not yet supported on Octave. This step will be skipped.');
+    opt.QA.anat.do = false;
+  end
+
+  if ~opt.QA.anat.do
     return
   end
 

src/QA/anatomicalQALesion.m

@@ -109,7 +109,7 @@ function functionalQA(opt)
                     ']'];
           pattern = ['^', prefix, 'sub-', subLabel];
           if ~strcmp(sessions{iSes}, '')
-            pattern = [pattern, '_ses-', sessions{iSes}];
+            pattern = [pattern, '_ses-', sessions{iSes}]; %#ok<*AGROW>
           end
           pattern = [pattern, '.*', '_task-' thisTask, '.*'];
           if ~strcmp(runs{iRun}, '')

src/QA/functionalQA.m

@@ -158,7 +158,7 @@
 
   icell(1).levels = 1;
 
-  assert(iscellstr(icell.scans));
+  assert(isstring(icell.scans));
 
   matlabbatch = returnFactorialDesignBatch(matlabbatch, rfxDir, icell, thisGroup);