From 90e1a1be50c8f810279aa903a64c1638cb0d2162 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 08:47:00 +0200
Subject: [PATCH 01/11] make printCredits shut up if we ask him

---
 checkCFG.m                 |  7 +--
 checkCppBidsDependencies.m |  4 +-
 printCreditsCppBids.m      | 93 +++++++++++++++++++++-----------------
 3 files changed, 57 insertions(+), 47 deletions(-)

diff --git a/checkCFG.m b/checkCFG.m
index 10337a5d..09ddfc9a 100644
--- a/checkCFG.m
+++ b/checkCFG.m
@@ -4,13 +4,13 @@
     % check that we have all the fields that we need in the experiment parameters
     % reuses a lot of code from the BIDS starter kit
 
-    checkCppBidsDependencies();
-
     if nargin < 1 || isempty(cfg)
         cfg = struct();
     end
+    
+    checkCppBidsDependencies(cfg);
 
-    %% set the cfg defaults
+    %% list the defaults to set
 
     fieldsToSet.verbose = false;
 
@@ -43,6 +43,7 @@
 
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
+    %% Set defaults
     cfg = setDefaultFields(cfg, fieldsToSet);
 
 end
diff --git a/checkCppBidsDependencies.m b/checkCppBidsDependencies.m
index 898f3c6d..3afc5dfb 100644
--- a/checkCppBidsDependencies.m
+++ b/checkCppBidsDependencies.m
@@ -1,4 +1,4 @@
-function checkCppBidsDependencies()
+function checkCppBidsDependencies(cfg)
     % checkCppBidsDependencies()
     %
     
@@ -10,7 +10,7 @@ function checkCppBidsDependencies()
     addpath(fullfile(pth, 'lib', 'utils'));
     addpath(fullfile(pth, 'subfun'));
 
-    printCreditsCppBids();
+    printCreditsCppBids(cfg);
 
 end
 
diff --git a/printCreditsCppBids.m b/printCreditsCppBids.m
index bfb3f252..189a064a 100644
--- a/printCreditsCppBids.m
+++ b/printCreditsCppBids.m
@@ -1,44 +1,53 @@
-function printCreditsCppBids()
-
-    version = '0.0.1';
-
-    contributors = { ...
-        'Rémi Gau', ...
-        'Marco Barilari', ...
-        'Ceren Battal'};
-
-    % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
-
-    repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
-
-    fprintf('\n\n');
-
-    disp('___________________________________________________');
-    disp('___________________________________________________');
-    disp('                                                   ');
-    disp('         ___ ___ ___   ___ ___ ___  ___            ');
-    disp('        / __| _ \ _ \ | _ )_ _|   \/ __|');
-    disp('       | (__|  _/  _/ | _ \| || |) \__ \');
-    disp('        \___|_| |_|   |___/___|___/|___/');
-    disp('                                                   ');
-
-    splash = 'Thank you for using the CPP BIDS - version %s. ';
-    fprintf(splash, version);
-    fprintf('\n\n');
-
-    fprintf('Current list of contributors includes:\n');
-    for iCont = 1:numel(contributors)
-        fprintf(' %s\n', contributors{iCont});
+function printCreditsCppBids(cfg)
+    
+    verbose = true;
+    if ~isempty(cfg) && isfield(cfg, 'verbose') && ~isempty(cfg.verbose)
+        verbose = cfg.verbose;
     end
-    fprintf('\b\n\n');
-
-    % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
-
-    fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
-
-    disp('___________________________________________________');
-    disp('___________________________________________________');
-
-    fprintf('\n\n');
-
+    
+    if verbose
+        
+        version = '0.0.1';
+        
+        contributors = { ...
+            'Rémi Gau', ...
+            'Marco Barilari', ...
+            'Ceren Battal'};
+        
+        % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
+        
+        repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
+        
+        fprintf('\n\n');
+        
+        disp('___________________________________________________');
+        disp('___________________________________________________');
+        disp('                                                   ');
+        disp('         ___ ___ ___   ___ ___ ___  ___            ');
+        disp('        / __| _ \ _ \ | _ )_ _|   \/ __|');
+        disp('       | (__|  _/  _/ | _ \| || |) \__ \');
+        disp('        \___|_| |_|   |___/___|___/|___/');
+        disp('                                                   ');
+        
+        splash = 'Thank you for using the CPP BIDS - version %s. ';
+        fprintf(splash, version);
+        fprintf('\n\n');
+        
+        fprintf('Current list of contributors includes:\n');
+        for iCont = 1:numel(contributors)
+            fprintf(' %s\n', contributors{iCont});
+        end
+        fprintf('\b\n\n');
+        
+        % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
+        
+        fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
+        
+        disp('___________________________________________________');
+        disp('___________________________________________________');
+        
+        fprintf('\n\n');
+        
+    end
+    
 end

From b6479f84cc4a98e8c074ecc23a5be899d7db255b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 08:47:34 +0200
Subject: [PATCH 02/11] rewrite test for checkCFG for mox unit

---
 tests/checkSubFields.m             |  29 ++++++
 tests/returnExpectedCfgStructure.m |  48 +++++++++
 tests/test_checkCFG.m              | 160 +++++++++--------------------
 3 files changed, 124 insertions(+), 113 deletions(-)
 create mode 100644 tests/checkSubFields.m
 create mode 100644 tests/returnExpectedCfgStructure.m

diff --git a/tests/checkSubFields.m b/tests/checkSubFields.m
new file mode 100644
index 00000000..764f4aff
--- /dev/null
+++ b/tests/checkSubFields.m
@@ -0,0 +1,29 @@
+function checkSubFields(expectedStructure, cfg)
+    % check that that the structures match
+    % if it fails it check from which subfield the error comes from
+    
+    try
+        
+        assertEqual(expectedStructure, cfg);
+        
+    catch ME
+        
+        if isstruct(expectedStructure)
+            
+            names = fieldnames(expectedStructure);
+            
+            for i = 1:numel(names)
+                
+                disp(names{i});
+                testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
+                
+            end
+            
+        end
+        
+        disp(expectedStructure);
+        disp(cfg);
+        
+        rethrow(ME);
+    end
+end
diff --git a/tests/returnExpectedCfgStructure.m b/tests/returnExpectedCfgStructure.m
new file mode 100644
index 00000000..41982a55
--- /dev/null
+++ b/tests/returnExpectedCfgStructure.m
@@ -0,0 +1,48 @@
+function expectedCfgStructure = returnExpectedCfgStructure()
+    
+    expectedCfgStructure.subject.subjectGrp = '';
+    expectedCfgStructure.subject.sessionNb = 1;
+    expectedCfgStructure.subject.askGrpSess = [true true];
+    
+    expectedCfgStructure.verbose = 0;
+    
+    expectedCfgStructure.fileName.task = '';
+    expectedCfgStructure.fileName.zeroPadding = 3;
+    expectedCfgStructure.fileName.dateFormat = 'yyyymmddHHMM';
+    
+    expectedCfgStructure.eyeTracker.do = false;
+    
+    expectedCfgStructure.mri.contrastEnhancement = [];
+    expectedCfgStructure.mri.phaseEncodingDirection = [];
+    expectedCfgStructure.mri.reconstruction = [];
+    expectedCfgStructure.mri.echo = [];
+    expectedCfgStructure.mri.acquisition = [];
+    expectedCfgStructure.mri.repetitionTime = [];
+    
+    expectedCfgStructure.bids.mri.RepetitionTime = [];
+    expectedCfgStructure.bids.mri.SliceTiming = '';
+    expectedCfgStructure.bids.mri.TaskName = '';
+    expectedCfgStructure.bids.mri.Instructions = '';
+    expectedCfgStructure.bids.mri.TaskDescription = '';
+    
+    expectedCfgStructure.bids.meg.TaskName = '';
+    expectedCfgStructure.bids.meg.SamplingFrequency = [];
+    expectedCfgStructure.bids.meg.PowerLineFrequency = [];
+    expectedCfgStructure.bids.meg.DewarPosition = [];
+    expectedCfgStructure.bids.meg.SoftwareFilters = [];
+    expectedCfgStructure.bids.meg.DigitizedLandmarks = [];
+    expectedCfgStructure.bids.meg.DigitizedHeadPoints = [];
+    
+    expectedCfgStructure.bids.datasetDescription.Name = '';
+    expectedCfgStructure.bids.datasetDescription.BIDSVersion =  '';
+    expectedCfgStructure.bids.datasetDescription.License = '';
+    expectedCfgStructure.bids.datasetDescription.Authors = {''};
+    expectedCfgStructure.bids.datasetDescription.Acknowledgements = '';
+    expectedCfgStructure.bids.datasetDescription.HowToAcknowledge = '';
+    expectedCfgStructure.bids.datasetDescription.Funding = {''};
+    expectedCfgStructure.bids.datasetDescription.ReferencesAndLinks = {''};
+    expectedCfgStructure.bids.datasetDescription.DatasetDOI = '';
+    
+    expectedCfgStructure = orderfields(expectedCfgStructure);
+    
+end
\ No newline at end of file
diff --git a/tests/test_checkCFG.m b/tests/test_checkCFG.m
index 8c2155ed..3768bdd0 100644
--- a/tests/test_checkCFG.m
+++ b/tests/test_checkCFG.m
@@ -1,147 +1,81 @@
-function test_checkCFG()
+function test_suite = test_checkCFG %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
+function test_checkCfgDefault()
+    
+    %% set up
     cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
     cfg = checkCFG(cfg);
-
-    expectedStructure = returnExpectedStructure();
+    
+    %% create test data
+    expectedStructure = returnExpectedCfgStructure();
     expectedStructure.dir.output = cfg.dir.output;
     expectedStructure.testingDevice = 'pc';
-
-    testSubFields(expectedStructure, cfg);
-
-    %%
-    fprintf('\n--------------------------------------------------------------------');
-
-    clear;
-
+    
+    %% test
+    checkSubFields(expectedStructure, cfg);
+    
+end
+    
+function test_checkCfgBasic()
+    
+    %% set up
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
+    
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-
+    
     cfg.task.name = 'test task';
-
+    
     cfg.dir.output = outputDir;
-
+    
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
-
+    
     cfg.mri.repetitionTime = 1.56;
-
+    
     cfg.testingDevice = 'mri';
-
+    
     cfg = checkCFG(cfg);
-
-    %%% test
-
-    % test data
-    expectedStructure = returnExpectedStructure();
+    
+    %% create test data
+    expectedStructure = returnExpectedCfgStructure();
     expectedStructure.subject.subjectNb = 1;
     expectedStructure.subject.runNb = 1;
-
+    
     expectedStructure.dir.output = outputDir;
-
+    
     expectedStructure.task.name = 'test task';
-
+    
     expectedStructure.testingDevice = 'mri';
-
+    
     expectedStructure.mri.repetitionTime = 1.56;
-
+    
     expectedStructure.fileName.task = 'testTask';
-
+    
     expectedStructure.bids.mri.RepetitionTime = 1.56;
     expectedStructure.bids.mri.TaskName = 'test Task';
-
+    
     expectedStructure.bids.meg.TaskName = 'test Task';
-
+    
     expectedStructure.bids.datasetDescription.Name = 'dummy';
     expectedStructure.bids.datasetDescription.BIDSVersion =  '1.0.0';
     expectedStructure.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
-
+    
     expectedStructure = orderfields(expectedStructure);
-
-    testSubFields(expectedStructure, cfg);
-
-    fprintf('\n');
-
-end
-
-function expectedStructure = returnExpectedStructure()
-
-    expectedStructure.subject.subjectGrp = '';
-    expectedStructure.subject.sessionNb = 1;
-    expectedStructure.subject.askGrpSess = [true true];
-
-    expectedStructure.verbose = 0;
-
-    expectedStructure.fileName.task = '';
-    expectedStructure.fileName.zeroPadding = 3;
-    expectedStructure.fileName.dateFormat = 'yyyymmddHHMM';
-
-    expectedStructure.eyeTracker.do = false;
-
-    expectedStructure.mri.contrastEnhancement = [];
-    expectedStructure.mri.phaseEncodingDirection = [];
-    expectedStructure.mri.reconstruction = [];
-    expectedStructure.mri.echo = [];
-    expectedStructure.mri.acquisition = [];
-    expectedStructure.mri.repetitionTime = [];
-
-    expectedStructure.bids.mri.RepetitionTime = [];
-    expectedStructure.bids.mri.SliceTiming = '';
-    expectedStructure.bids.mri.TaskName = '';
-    expectedStructure.bids.mri.Instructions = '';
-    expectedStructure.bids.mri.TaskDescription = '';
-
-    expectedStructure.bids.meg.TaskName = '';
-    expectedStructure.bids.meg.SamplingFrequency = [];
-    expectedStructure.bids.meg.PowerLineFrequency = [];
-    expectedStructure.bids.meg.DewarPosition = [];
-    expectedStructure.bids.meg.SoftwareFilters = [];
-    expectedStructure.bids.meg.DigitizedLandmarks = [];
-    expectedStructure.bids.meg.DigitizedHeadPoints = [];
-
-    expectedStructure.bids.datasetDescription.Name = '';
-    expectedStructure.bids.datasetDescription.BIDSVersion =  '';
-    expectedStructure.bids.datasetDescription.License = '';
-    expectedStructure.bids.datasetDescription.Authors = {''};
-    expectedStructure.bids.datasetDescription.Acknowledgements = '';
-    expectedStructure.bids.datasetDescription.HowToAcknowledge = '';
-    expectedStructure.bids.datasetDescription.Funding = {''};
-    expectedStructure.bids.datasetDescription.ReferencesAndLinks = {''};
-    expectedStructure.bids.datasetDescription.DatasetDOI = '';
-
-    expectedStructure = orderfields(expectedStructure);
-
+    
+    %% test
+    checkSubFields(expectedStructure, cfg);
+    
 end
 
-function testSubFields(expectedStructure, cfg)
-    % check that that the structures match
-    % if it fails it check from which subfield the error comes from
-
-    try
-
-        assert(isequal(expectedStructure, cfg));
-
-    catch ME
-
-        if isstruct(expectedStructure)
-
-            names = fieldnames(expectedStructure);
 
-            for i = 1:numel(names)
 
-                disp(names{i});
-                testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
-
-            end
-
-        end
-
-        expectedStructure;
-        cfg;
-
-        rethrow(ME);
-    end
-end

From d815e9e7476b80b617f36517384a89c9d1117465 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 09:18:05 +0200
Subject: [PATCH 03/11] add doc on tests and remove old testing function

---
 .gitignore       | 15 +++++++++---
 tests/README.md  | 23 ++++++++++++++++++
 tests/runTests.m | 63 ------------------------------------------------
 3 files changed, 35 insertions(+), 66 deletions(-)
 create mode 100644 tests/README.md
 delete mode 100644 tests/runTests.m

diff --git a/.gitignore b/.gitignore
index c1cac9ae..fef67417 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,14 +1,23 @@
-
+# exclude mac file
 *DS_Store
 
+# exclude matlab autosaves and octave workspace info
 *.m~
 *octave-workspace
 
 # exclude content of logfiles folders
+output/**
 *.tsv
 *.mat
 
-check_my_code_report.txt
+# exclude temp files from tests and coverage
+tests/coverage*
+tests/test_code_report.txt
 test_code_report.txt
 
-output/**
+# exclude report from check_my_code
+check_my_code_report.txt
+
+
+
+
diff --git a/tests/README.md b/tests/README.md
new file mode 100644
index 00000000..0559aa7f
--- /dev/null
+++ b/tests/README.md
@@ -0,0 +1,23 @@
+# how to run the tests
+
+- Install [MOxUnit for matlab and octave](https://github.com/MOxUnit/MOxUnit) to run the tests
+- Install [MOcov for matlab and octave](https://github.com/MOcov/MOcov) to get the code coverage
+- Make sure you are in the `tests` directory.
+- Run `moxunit_runtests` or `moxunit_runtests -verbose` to run the tests.
+
+This should tell you which tests pass or fail.
+  
+The following command would give more info and will give you HTML output in a `coverage_html` folder
+showing you which lines of code is or is not checked by your test suite.
+
+``` matlab
+success = moxunit_runtests(pwd, ... % the path where the tests are
+    '-verbose', ...
+    '-with_coverage', ...
+    '-cover', fullfile(pwd, '..'), ... % the path of the code whose coverage we want to estimate
+    '-cover_xml_file','coverage.xml', ...
+    '-cover_html_dir','coverage_html');
+```
+
+
+
diff --git a/tests/runTests.m b/tests/runTests.m
deleted file mode 100644
index 77ceecec..00000000
--- a/tests/runTests.m
+++ /dev/null
@@ -1,63 +0,0 @@
-function results = runTests(pth)
-    % Run tests
-    % List all the 'test_*.m' files located in the same directory as this
-    % function, run them and keep track of how many passed, failed or are
-    % incomplete.
-    % __________________________________________________________________________
-
-    % Copyright (C) 2019, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-    % Copyright (C) 2020--, CPP_BIDS developers
-
-    % -Get the path of where this file is located
-    if ~nargin
-        pth = fileparts(mfilename('fullpath'));
-    end
-
-    % -List all the 'test_*.m' files located in the same directory as this
-    % function
-    d = dir(pth);
-    d([d.isdir]) = [];
-    d(arrayfun(@(x) isempty(regexp(x.name, '^test_.*\.m$', 'once')), d)) = [];
-
-    results = struct('Passed', {}, 'Failed', {}, 'Incomplete', {}, 'Duration', {});
-    for i = 1:numel(d)
-
-        results(i).Failed = false;
-        results(i).Passed = false;
-        results(i).Incomplete = false;
-
-        tstart = tic;
-
-        % -Run each test file and catch error message in case of failure
-        try
-            fprintf('\n\n--------------------------------------------------------------------\n');
-            fprintf('%s', d(i).name(1:end - 2));
-            fprintf('\n--------------------------------------------------------------------\n');
-            feval(d(i).name(1:end - 2));
-            results(i).Passed = true;
-
-        catch err
-            results(i).Failed = true;
-            fprintf('\n%s', err.message);
-        end
-
-        results(i).Duration = toc(tstart);
-
-        fprintf('\n');
-
-    end
-
-    if ~nargout
-        fprintf(['Totals (%d tests):\n\t%d Passed, %d Failed, %d Incomplete.\n' ...
-            '\t%f seconds testing time.\n\n'], numel(results), nnz([results.Passed]), ...
-            nnz([results.Failed]), nnz([results.Incomplete]), sum([results.Duration]));
-        for i = 1:numel(d)
-            status = 'Incomplete';
-            if results(i).Passed
-                status = 'Passed';
-            elseif results(i).Failed
-                status = 'Failed';
-            end
-            fprintf('%s: %s\n', d(i).name(1:end - 2), status);
-        end
-    end

From f620894eaad8c51984ccc272e44ab0c6a03831b1 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 10:52:52 +0200
Subject: [PATCH 04/11] update all the tests to be used with mox unit

---
 tests/test_createBoldJson.m                |  26 +++--
 tests/test_createDataDictionary.m          |  35 ++++---
 tests/test_createDatasetDescription.m      |  22 +++--
 tests/test_createFilename.m                |  82 ++++++++-------
 tests/test_createTaskName.m                |  34 ++++++-
 tests/test_saveEventsFileInit.m            |  87 +++++++++-------
 tests/test_saveEventsFileOpen.m            | 110 +++++++++++----------
 tests/test_saveEventsFileOpenMultiColumn.m |  58 ++++++-----
 tests/test_saveEventsFileSave.m            |  55 ++++++-----
 tests/test_setDefaultFields.m              |  23 ++++-
 10 files changed, 326 insertions(+), 206 deletions(-)

diff --git a/tests/test_createBoldJson.m b/tests/test_createBoldJson.m
index 72348bfa..48629da1 100644
--- a/tests/test_createBoldJson.m
+++ b/tests/test_createBoldJson.m
@@ -1,15 +1,26 @@
-function test_createBoldJson()
+function test_suite = test_createBoldJson %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_createBoldJsonBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up 
 
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+    
     cfg.task.name = 'testtask';
+    
     cfg.dir.output = outputDir;
 
-    % cfg = struct();
     cfg.testingDevice = 'mri';
 
     cfg = createFilename(cfg);
@@ -18,14 +29,13 @@ function test_createBoldJson()
 
     createBoldJson(cfg);
 
-    %%% test part
-
-    % test data
+    %% data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
+    
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_bold_date-' ...
         cfg.fileName.date '.json'];
 
-    % check that the file has the right path and name
-    assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
+    %% test
+    assertTrue(exist(fullfile(funcDir, eventFilename), 'file') == 2);
 
 end
diff --git a/tests/test_createDataDictionary.m b/tests/test_createDataDictionary.m
index c9bf1a81..5c26006a 100644
--- a/tests/test_createDataDictionary.m
+++ b/tests/test_createDataDictionary.m
@@ -1,11 +1,18 @@
-function test_createDataDictionary()
+function test_suite = test_createDataDictionary %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
-    clear;
+function test_createDataDictionaryBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up
 
+    cfg.verbose = false;
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
     cfg.task.name = 'testtask';
@@ -21,20 +28,24 @@ function test_createDataDictionary()
 
     createDataDictionary(cfg, logFile);
 
-    %%% test part
-
-    % test data
+    %% check that the file has the right path and name
+    
+    % data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
         cfg.fileName.date '.json'];
 
-    % check that the file has the right path and name
-    assert(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
+    % test
+    assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
 
-    % check content
-    expectedStruct = bids.util.jsondecode(fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
+    %% check content
     actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
-
-    assert(isequal(expectedStruct, actualStruct));
+    
+    % data to test against
+    expectedStruct = bids.util.jsondecode(...
+        fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
+    
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
 
 end
diff --git a/tests/test_createDatasetDescription.m b/tests/test_createDatasetDescription.m
index 629fe432..1e2e0d89 100644
--- a/tests/test_createDatasetDescription.m
+++ b/tests/test_createDatasetDescription.m
@@ -1,10 +1,20 @@
-function test_createDatasetDescription()
+function test_suite = test_createDatasetDescription %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_createDatasetDescriptionBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up
 
     cfg.dir.output = outputDir;
+    
+    cfg.verbose = false;
 
     cfg.bids.datasetDescription.json.Name = 'dummy_dataset';
     cfg.bids.datasetDescription.json.BIDSVersion = '1.0.0';
@@ -15,13 +25,11 @@ function test_createDatasetDescription()
 
     createDatasetDescription(cfg);
 
-    %%% test part
-
-    % test data
+    %% data to test against
     directory = fullfile(outputDir, 'source');
     filename = 'dataset_description.json';
 
-    % check that the file has the right path and name
-    assert(exist(fullfile(directory, filename), 'file') == 2);
+    %% test
+    assertTrue(exist(fullfile(directory, filename), 'file') == 2);
 
 end
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index ebce891f..803ecd04 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -1,51 +1,60 @@
-function test_createFilename()
-    % test for filename creation and their directories
+function test_suite = test_createFilename %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
-    %% PC
+function test_createFilenameBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up
 
+    cfg.verbose = false;
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
     cfg.task.name = 'test task';
     cfg.dir.output = outputDir;
 
-    %%% run part
     cfg = createFilename(cfg);
 
-    %%% test part
-
-    % test data
+    %% data to test against
     behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
+    
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
+    
     eventFilename = ['sub-001_ses-001_task-testTask_run-001_events_date-'...
         cfg.fileName.date '.tsv'];
+    
     stimFilename =  ['sub-001_ses-001_task-testTask_run-001_stim_date-'...
         cfg.fileName.date '.tsv'];
 
+    %% test
+    
     % make sure the beh dir is created
-    assert(exist(behDir, 'dir') == 7);
+    assertTrue(exist(behDir, 'dir') == 7);
 
     % make sure the eyetracker dir is not created
-    assert(exist(eyetrackerDir, 'dir') == 0);
+    assertTrue(exist(eyetrackerDir, 'dir') == 0);
 
     % make sure the events filename is created
-    assert(strcmp(cfg.fileName.events, eventFilename));
+    assertEqual(cfg.fileName.events, eventFilename);
 
     % make sure the stim filename is created
-    assert(strcmp(cfg.fileName.stim, stimFilename));
+    assertEqual(cfg.fileName.stim, stimFilename);
 
-    %% fMRI and eye tracker
-    fprintf('\n--------------------------------------------------------------------');
+    
+end
 
-    clear;
+function test_createFilenameMriEyetracker()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up
 
+    cfg.verbose = false;
     cfg.subject.subjectGrp = 'ctrl';
     cfg.subject.subjectNb = 2;
     cfg.subject.sessionNb = 2;
@@ -58,37 +67,41 @@ function test_createFilename()
 
     cfg = createFilename(cfg);
 
-    %%% test part
-
-    % test data
+    %% data to test against
+    
     funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
+    
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
+    
     baseFilename = 'sub-ctrl002_ses-002_task-testTask';
+    
     eventFilename = ['sub-ctrl002_ses-002_task-testTask_run-002_events_date-' ...
         cfg.fileName.date '.tsv'];
+    
     eyetrackerFilename =  ['sub-ctrl002_ses-002_task-testTask_run-002_eyetrack_date-' ...
         cfg.fileName.date '.edf'];
 
+    %% tests
     % make sure the func dir is created
-    assert(exist(funcDir, 'dir') == 7);
+    assertTrue(exist(funcDir, 'dir') == 7);
 
     % make sure the eyetracker dir is created
-    assert(exist(eyetrackerDir, 'dir') == 7);
+    assertTrue(exist(eyetrackerDir, 'dir') == 7);
 
     % make sure the right filenames are created
-    assert(strcmp(cfg.fileName.base, baseFilename));
-    assert(strcmp(cfg.fileName.events, eventFilename));
-    assert(strcmp(cfg.fileName.eyetracker, eyetrackerFilename));
-
-    %% EEG
-    fprintf('\n--------------------------------------------------------------------');
-
-    clear;
+    assertEqual(cfg.fileName.base, baseFilename);
+    assertEqual(cfg.fileName.events, eventFilename);
+    assertEqual(cfg.fileName.eyetracker, eyetrackerFilename);
+    
+end
+    
+function test_createFilenameEeg()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up part
+    %% set up
 
+    cfg.verbose = false;
     cfg.subject.subjectGrp = 'blind';
     cfg.subject.subjectNb = 3;
     cfg.subject.sessionNb = 1;
@@ -100,10 +113,11 @@ function test_createFilename()
 
     cfg = createFilename(cfg);
 
-    %%% test part
-
-    % test data
+    %% data to test against
     eegDir = fullfile(outputDir, 'source', 'sub-blind003', 'ses-001', 'eeg');
 
+    %% test
     % make sure the func dir is created
-    assert(exist(eegDir, 'dir') == 7);
+    assertTrue(exist(eegDir, 'dir') == 7);
+
+end
\ No newline at end of file
diff --git a/tests/test_createTaskName.m b/tests/test_createTaskName.m
index 6f30fe35..40f14ef3 100644
--- a/tests/test_createTaskName.m
+++ b/tests/test_createTaskName.m
@@ -1,21 +1,33 @@
-function test_createTaskName()
-    %
+function test_suite = test_createTaskName %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
-    taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
+function test_createTaskNameRemoveInvalidCharacters()
 
+    %% set up 
+    
+    taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
+    
     [taskName, taskNameValid] = createTaskName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
-    assert(isempty(unvalidCharacters));
+    %% test
+    assertTrue(isempty(unvalidCharacters));
 
+    %% set up
     taskName = ' 09 visual task';
 
     [taskName, taskNameValid] = createTaskName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
-    assert(isempty(unvalidCharacters));
+    %% test
+    assertTrue(isempty(unvalidCharacters));
 
     taskName = 'foo bar';
     [taskName, taskNameValid] = createTaskName(taskName);
@@ -23,3 +35,15 @@ function test_createTaskName()
     assert(isequal(taskNameValid, 'fooBar'));
 
 end
+
+function test_createTaskNameCamelCase()
+
+    %% set up
+    taskName = 'foo bar';
+    [taskName, taskNameValid] = createTaskName(taskName);
+    
+    %% test
+    assertEqual(taskName, 'foo Bar');
+    assertEqual(taskNameValid, 'fooBar');
+
+end
diff --git a/tests/test_saveEventsFileInit.m b/tests/test_saveEventsFileInit.m
index ca0ecf02..ed86be99 100644
--- a/tests/test_saveEventsFileInit.m
+++ b/tests/test_saveEventsFileInit.m
@@ -1,55 +1,69 @@
-function test_saveEventsFileInit()
+function test_suite = test_saveEventsFileInit %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
-    %%
+function test_saveEventsFileInitBasic()
+    
+    %% set up 
 
-    %%% set up
+    cfg.verbose = false;
+    
     % make sure the dependencies are there
-    checkCFG();
-
-    %%% do stuff
+    checkCFG(cfg);
+    
     [logFile] = saveEventsFile('init');
-
-    %%% test section
+    
+    %% data to test against
     expectedStrcut(1).filename = '';
     expectedStrcut(1).extraColumns = [];
+    
+    %% test
+    assertEqual(expectedStrcut, logFile);
+    
+end
 
-    assert(isequal(expectedStrcut, logFile));
-
-    %%
-    fprintf('\n--------------------------------------------------------------------');
-
-    clear;
+function test_saveEventsFileInitExtraColumns()
+    
+    %% set up 
 
-    %%% set up
-    cfg = checkCFG();
+    cfg.verbose = false;
+    
+    cfg = checkCFG(cfg);
+    
     logFile.extraColumns = {'Speed'};
-
-    %%% do stuff
+    
     [logFile] = saveEventsFile('init', cfg, logFile);
-
-    %%% test section
+    
+    %% data to test against
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
     expectedStrcut(1).extraColumns.Speed.bids.Description = '';
     expectedStrcut(1).extraColumns.Speed.bids.Levels = '';
     expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
+    
+    %% test
+    assertEqual(expectedStrcut, logFile);
+    
+end
 
-    assert(isequal(expectedStrcut, logFile));
-
-    %%
-    fprintf('\n--------------------------------------------------------------------');
-
-    clear;
+function test_saveEventsFileInitExtraColumnsArray()
+    
+    %% set up 
 
-    %%% set up
-    cfg = checkCFG();
+    cfg.verbose = false;
+    
+    cfg = checkCFG(cfg);
+    
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
-
-    %%% do stuff
+    
     [logFile] = saveEventsFile('init', cfg, logFile);
-
-    %%% test section
+    
+    %% data to test against
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
     expectedStrcut(1).extraColumns.Speed.bids.Description = '';
@@ -60,9 +74,8 @@ function test_saveEventsFileInit()
     expectedStrcut(1).extraColumns.LHL24.bids.Description = '';
     expectedStrcut(1).extraColumns.LHL24.bids.Levels = '';
     expectedStrcut(1).extraColumns.LHL24.bids.TermURL = '';
-
-    assert(isequal(expectedStrcut, logFile));
-
-    fprintf('\n');
-
+    
+    %% test
+    assertEqual(expectedStrcut, logFile);
+    
 end
diff --git a/tests/test_saveEventsFileOpen.m b/tests/test_saveEventsFileOpen.m
index 032f5f47..e536a03d 100644
--- a/tests/test_saveEventsFileOpen.m
+++ b/tests/test_saveEventsFileOpen.m
@@ -1,91 +1,101 @@
-function test_saveEventsFileOpen()
-
-    %% Initialize file
-    clear;
+function test_suite = test_saveEventsFileOpen %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
+function test_saveEventsFileOpenBasic()
+    
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
-    %%% set up
-
+    
+    %% set up
+    
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+    
     cfg.task.name = 'testtask';
+    
     cfg.dir.output = outputDir;
-
+    
     cfg.testingDevice = 'mri';
-
-    %%% do stuff
-
+    
     cfg = createFilename(cfg);
-
+    
     % create the events file and header
     logFile = saveEventsFile('open', cfg);
-
+    
     % close the file
     saveEventsFile('close', cfg, logFile);
-
-    %%% test section
-
-    % test data
+    
+    %% data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
         cfg.fileName.date '.tsv'];
-
+    
     % check that the file has the right path and name
     assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
-
+    
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-
+    
+    %% test
     % check the extra columns of the header
-    assert(isequal(C{1}{1}, 'onset'));
-    assert(isequal(C{2}{1}, 'duration'));
-    assert(isequal(C{3}{1}, 'trial_type'));
-
-    %% check header writing with extra columns
-    fprintf('\n\n--------------------------------------------------------------------');
-
-    clear;
+    assertEqual(C{1}{1}, 'onset');
+    assertEqual(C{2}{1}, 'duration');
+    assertEqual(C{3}{1}, 'trial_type');
+    
+end
 
+function test_saveEventsFileOpenExtraColumns()
+    
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
-    %%% set up
-
+    
+    %% set up
+    
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
+    
     cfg.subject.runNb = 1;
+    
     cfg.task.name = 'testtask';
+    
     cfg.dir.output = outputDir;
-
+    
     cfg.testingDevice = 'mri';
-
-    % define the extra columns: they will be added to the tsv files in the order the user input them
-    logFile.extraColumns = {'Speed', 'is_Fixation'};
-
-    %%% do stuff
-
+    
     cfg = createFilename(cfg);
+    
+    % define the extra columns 
+    % they will be added to the tsv files in the order the user input them
+    logFile.extraColumns = {'Speed', 'is_Fixation'};
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
-
+    
     % close the file
     saveEventsFile('close', cfg, logFile);
-
-    %%% test section
-
+    
+    %% data to test against
+    
     % open the file
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
     eventFilename = cfg.fileName.events;
-
+    
     nbExtraCol = 2;
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-
+    
+    %% test
     % check the extra columns of the header
-    assert(isequal(C{1}{1}, 'onset'));
-    assert(isequal(C{2}{1}, 'duration'));
-    assert(isequal(C{3}{1}, 'trial_type'));
-    assert(isequal(C{4}{1}, 'Speed'));
-    assert(isequal(C{5}{1}, 'is_Fixation'));
-
+    assertEqual(C{1}{1}, 'onset');
+    assertEqual(C{2}{1}, 'duration');
+    assertEqual(C{3}{1}, 'trial_type');
+    assertEqual(C{4}{1}, 'Speed');
+    assertEqual(C{5}{1}, 'is_Fixation');
+    
 end
diff --git a/tests/test_saveEventsFileOpenMultiColumn.m b/tests/test_saveEventsFileOpenMultiColumn.m
index 69b0dc5b..66c826b0 100644
--- a/tests/test_saveEventsFileOpenMultiColumn.m
+++ b/tests/test_saveEventsFileOpenMultiColumn.m
@@ -1,53 +1,59 @@
-function test_saveEventsFileOpenMultiColumn()
-
-    %% check header writing with several columns for one variable
-    clear;
+function test_suite = test_saveEventsFileOpenMultiColumn %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
+function test_saveEventsFileOpenMultiColumnCheckHeader()
+    
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
-    %%% set up
-
+    
+    %% set up
+    
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+    
     cfg.task.name = 'testtask';
+    
     cfg.dir.output = outputDir;
-
+    
     cfg.testingDevice = 'mri';
-
+    
     cfg = createFilename(cfg);
-
+    
     % define the extra columns: here we specify how many columns we want for
     % each variable
     logFile.extraColumns.Speed.length = 1; % will set 1 columns with name Speed
     logFile.extraColumns.LHL24.length = 12; % will set 12 columns with names LHL24-01, LHL24-02, ...
     logFile.extraColumns.is_Fixation = []; % will set 1 columns with name is_Fixation
-
-    %%% do stuff
-
+    
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
-
+    
     % close the file
     saveEventsFile('close', cfg, logFile);
-
-    %%% test section
-
-    % check the extra columns of the header and some of the content
+    
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    
     eventFilename = cfg.fileName.events;
-
+    
     nbExtraCol = ...
         logFile(1).extraColumns.Speed.length + ...
         logFile(1).extraColumns.LHL24.length + ...
         logFile(1).extraColumns.is_Fixation.length;
-
+    
+    %% test
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-
+    
     % check the extra columns of the header
-    assert(isequal(C{4}{1}, 'Speed'));
-    assert(isequal(C{5}{1}, 'LHL24_01'));
-    assert(isequal(C{16}{1}, 'LHL24_12'));
-    assert(isequal(C{17}{1}, 'is_Fixation'));
-
+    assertEqual(C{4}{1}, 'Speed');
+    assertEqual(C{5}{1}, 'LHL24_01');
+    assertEqual(C{16}{1}, 'LHL24_12');
+    assertEqual(C{17}{1}, 'is_Fixation');
+    
 end
diff --git a/tests/test_saveEventsFileSave.m b/tests/test_saveEventsFileSave.m
index 9cc610c5..b49d5001 100644
--- a/tests/test_saveEventsFileSave.m
+++ b/tests/test_saveEventsFileSave.m
@@ -1,15 +1,24 @@
-function test_saveEventsFileSave()
+function test_suite = test_saveEventsFileSave %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
-    %%  write things in it
-    clear;
+function test_saveEventsFileSaveBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %%% set up
+    %% set up 
 
+    cfg.verbose = false;
+    
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+    
     cfg.task.name = 'testtask';
+    
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
@@ -23,8 +32,6 @@ function test_saveEventsFileSave()
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
 
-    %%% do stuff
-
     % ROW 2: normal events : all info is there
     logFile(1, 1).onset = 2;
     logFile(end, 1).trial_type = 'motion_up';
@@ -73,7 +80,7 @@ function test_saveEventsFileSave()
     % close the file
     saveEventsFile('close', cfg, logFile);
 
-    %%% test section
+    %% test
 
     % check the extra columns of the header and some of the content
     nbExtraCol = ...
@@ -82,34 +89,36 @@ function test_saveEventsFileSave()
         logFile(1).extraColumns.is_Fixation.length;
 
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
+    
     eventFilename = cfg.fileName.events;
+    
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
 
     % event 1/ ROW 2: check that values are entered correctly
-    assert(isequal(C{1}{2}, sprintf('%f', 2)));
-    assert(isequal(C{3}{2}, 'motion_up'));
-    assert(isequal(C{2}{2}, sprintf('%f', 3)));
-    assert(isequal(C{4}{2}, sprintf('%f', 2)));
-    assert(isequal(C{5}{2}, sprintf('%f', 1)));
-    assert(isequal(C{16}{2}, sprintf('%f', 12)));
-    assert(isequal(C{17}{2}, 'true'));
+    assertEqual(C{1}{2}, sprintf('%f', 2));
+    assertEqual(C{3}{2}, 'motion_up');
+    assertEqual(C{2}{2}, sprintf('%f', 3));
+    assertEqual(C{4}{2}, sprintf('%f', 2));
+    assertEqual(C{5}{2}, sprintf('%f', 1));
+    assertEqual(C{16}{2}, sprintf('%f', 12));
+    assertEqual(C{17}{2}, 'true');
 
     % event 2 / ROW 3: missing info replaced by nans
-    assert(isequal(C{4}{3}, 'n/a'));
-    assert(isequal(C{5}{3}, 'n/a'));
-    assert(isequal(C{16}{3}, 'n/a'));
-    assert(isequal(C{17}{3}, 'false'));
+    assertEqual(C{4}{3}, 'n/a');
+    assertEqual(C{5}{3}, 'n/a');
+    assertEqual(C{16}{3}, 'n/a');
+    assertEqual(C{17}{3}, 'false');
 
     % event 3 / ROW 4: missing info (duration is missing and speed is empty)
-    assert(isequal(C{2}{4}, 'n/a'));
-    assert(isequal(C{4}{4}, 'n/a'));
+    assertEqual(C{2}{4}, 'n/a');
+    assertEqual(C{4}{4}, 'n/a');
 
     % event 4-5 / ROW 5-6: skip empty events
-    assert(~isequal(C{1}{5}, 'n/a'));
+    assertTrue(~isequal(C{1}{5}, 'n/a'));
 
     % check values entered properly
-    assert(isequal(C{15}{5}, 'n/a'));
-    assert(isequal(C{16}{5}, 'n/a'));
+    assertEqual(C{15}{5}, 'n/a');
+    assertEqual(C{16}{5}, 'n/a');
 
 end
diff --git a/tests/test_setDefaultFields.m b/tests/test_setDefaultFields.m
index b0aea0fc..c327d148 100644
--- a/tests/test_setDefaultFields.m
+++ b/tests/test_setDefaultFields.m
@@ -1,19 +1,32 @@
-function test_setDefaultFields()
+function test_suite = test_setDefaultFields %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_setDefaultFieldsWrite()
 
+    %% set up
     structure = struct();
 
     fieldsToSet.field = 1;
 
     structure = setDefaultFields(structure, fieldsToSet);
 
+    %% data to test against
     expectedStructure.field = 1;
 
-    assert(isequal(expectedStructure, structure));
+    %% test
+    assertEqual(expectedStructure, structure);
+    
+end
 
-    fprintf('\n--------------------------------------------------------------------');
 
-    clear;
+function test_setDefaultFieldsNoOverwrite()
 
+    % set up
     structure.field.subfield_1 = 3;
 
     fieldsToSet.field.subfield_1 = 1;
@@ -21,9 +34,11 @@ function test_setDefaultFields()
 
     structure = setDefaultFields(structure, fieldsToSet);
 
+    % data to test against
     expectedStructure.field.subfield_1 = 3;
     expectedStructure.field.subfield_2 = 1;
 
+    % test
     assert(isequal(expectedStructure, structure));
 
 end

From 057b759c1502ed9fdc1e5a375755d464397a8915 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 10:54:15 +0200
Subject: [PATCH 05/11] make some functions shut up if we ask them

---
 createFilename.m | 120 +++++++++++++-------------
 saveEventsFile.m | 214 +++++++++++++++++++++++++----------------------
 2 files changed, 175 insertions(+), 159 deletions(-)

diff --git a/createFilename.m b/createFilename.m
index 88469cc8..3aa01c1a 100644
--- a/createFilename.m
+++ b/createFilename.m
@@ -11,34 +11,34 @@
     %
     %
     % See test_createFilename in the test folder for more details on how to use it.
-
+    
     cfg = checkCFG(cfg);
-
+    
     cfg.fileName.pattern = ['%0' num2str(cfg.fileName.zeroPadding) '.0f'];
     cfg.fileName.date = datestr(now, cfg.fileName.dateFormat);
-
+    
     if ~isfield(cfg, 'task')
         error('createFilename: missing a task name. i.e cfg.task.name');
     end
-
+    
     cfg = getModality(cfg);
-
+    
     cfg = createDirectories(cfg);
-
+    
     cfg = setSuffixes(cfg);
-
+    
     cfg = setFilenames(cfg);
-
+    
     talkToMe(cfg);
-
+    
     cfg = orderfields(cfg);
     cfg.fileName = orderfields(cfg.fileName);
     cfg.dir = orderfields(cfg.dir);
-
+    
 end
 
 function cfg = getModality(cfg)
-
+    
     switch lower(cfg.testingDevice)
         case 'pc'
             modality = 'beh';
@@ -53,52 +53,52 @@
         otherwise
             modality = 'beh';
     end
-
+    
     cfg.fileName.modality = modality;
-
+    
 end
 
 function [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg)
-
+    
     subjectGrp = cfg.subject.subjectGrp;
     subjectNb = cfg.subject.subjectNb;
     sessionNb = cfg.subject.sessionNb;
     modality = cfg.fileName.modality;
     taskName = cfg.fileName.task;
-
+    
     if isempty(sessionNb)
         sessionNb = 1;
     end
-
+    
 end
 
 function cfg = createDirectories(cfg)
-
+    
     [subjectGrp, subjectNb, sessionNb, modality] = extractInput(cfg);
-
+    
     pattern = cfg.fileName.pattern;
-
+    
     % output dir
     cfg.dir.outputSubject = fullfile ( ...
         cfg.dir.output, ...
         'source', ...
         ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
         ['ses-', sprintf(pattern, sessionNb)]);
-
+    
     [~, ~, ~] = mkdir(cfg.dir.output);
     [~, ~, ~] = mkdir(cfg.dir.outputSubject);
     [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, modality));
-
+    
     if cfg.eyeTracker.do
         [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, 'eyetracker'));
     end
-
+    
 end
 
 function cfg = setSuffixes(cfg)
-
+    
     cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
-
+    
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
         'contrastEnhancement', ...
@@ -107,7 +107,7 @@
         'echo', ...
         'acquisition'
         };
-
+    
     for iField = 1:numel(fields2Check)
         if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
@@ -116,81 +116,85 @@
                 ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
         end
     end
-
+    
     cfg.fileName.suffix = orderfields(cfg.fileName.suffix);
-
+    
 end
 
 function cfg = setFilenames(cfg)
-
+    
     [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg);
-
+    
     pattern = cfg.fileName.pattern;
-
+    
     runSuffix = cfg.fileName.suffix.run;
     acqSuffix = cfg.fileName.suffix.mri.acquisition ;
     ceSuffix = cfg.fileName.suffix.mri.contrastEnhancement ;
     dirSuffix = cfg.fileName.suffix.mri.phaseEncodingDirection ;
     recSuffix = cfg.fileName.suffix.mri.reconstruction ;
     echoSuffix = cfg.fileName.suffix.mri.echo;
-
+    
     thisDate = cfg.fileName.date;
-
+    
     cfg.fileName.datasetDescription = fullfile ( ...
         cfg.dir.output, ...
         'dataset_description.json');
-
+    
     % create base fileName
     fileNameBase = ...
         ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
         '_ses-', sprintf(pattern, sessionNb), ...
         '_task-', taskName];
     cfg.fileName.base = fileNameBase;
-
+    
     switch modality
-
+        
         case 'func'
-
+            
             cfg.fileName.events = ...
                 [fileNameBase, ...
                 acqSuffix, ceSuffix, ...
                 dirSuffix, recSuffix, ...
                 runSuffix, echoSuffix, ...
                 '_events_date-' thisDate '.tsv'];
-
+            
         otherwise
-
+            
             cfg.fileName.events = ...
                 [fileNameBase, runSuffix, '_events_date-' thisDate '.tsv'];
-
+            
     end
-
+    
     cfg.fileName.stim = strrep(cfg.fileName.events, 'events', 'stim');
-
+    
     if cfg.eyeTracker.do
         cfg.fileName.eyetracker = ...
             [fileNameBase, acqSuffix, ...
             runSuffix, '_eyetrack_date-' thisDate '.edf'];
     end
-
+    
 end
 
 function talkToMe(cfg)
-
-    fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
-        fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
-
-    fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
-        cfg.fileName.events);
-
-    if cfg.eyeTracker.do
-
-        fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
-            fullfile(cfg.dir.outputSubject, 'eyetracker'));
-
-        fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
-            cfg.fileName.eyetracker);
-
+    
+    if cfg.verbose
+        
+        fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
+            fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
+        
+        fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
+            cfg.fileName.events);
+        
+        if cfg.eyeTracker.do
+            
+            fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
+                fullfile(cfg.dir.outputSubject, 'eyetracker'));
+            
+            fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
+                cfg.fileName.eyetracker);
+            
+        end
+        
     end
-
+    
 end
diff --git a/saveEventsFile.m b/saveEventsFile.m
index 624b17dd..9ce5a01c 100644
--- a/saveEventsFile.m
+++ b/saveEventsFile.m
@@ -43,108 +43,104 @@
     % to true then this will tell you where the file is located.
     %
     % See test_saveEventsFile in the test folder for more details on how to use it.
-
+    
     if nargin < 1
         error('Missing action input');
     end
-
+    
     if nargin < 2
         cfg = struct();
     end
-
+    
     if nargin < 3 || isempty(logFile)
         logFile = checklLogFile('init');
     end
-
+    
     switch action
-
+        
         case 'init'
-
+            
             logFile = initializeExtraColumns(logFile);
-
+            
         case 'open'
-
+            
             logFile.filename = cfg.fileName.events;
-
+            
             logFile = initializeFile(cfg, logFile);
-
+            
         case 'open_stim'
-
+            
             logFile.filename = cfg.fileName.stim;
-
+            
             logFile = initializeFile(cfg, logFile);
-
+            
         case 'save'
-
+            
             checklLogFile('checkID', logFile);
             checklLogFile('type&size', logFile);
-
+            
             logFile = saveToLogFile(logFile);
-
+            
         case 'close'
-
+            
             checklLogFile('checkID', logFile);
-
+            
             % close txt log file
             fclose(logFile(1).fileID);
-
-            fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
-                fullfile( ...
-                cfg.dir.outputSubject, ...
-                cfg.fileName.modality, ...
-                logFile.filename));
-
+            
+            talkToMe(cfg, logFile);
+            
         otherwise
-
+            
             errorSaveEventsFile('unknownActionType');
-
+            
     end
-
+    
     logFile = resetLogFileVar(logFile);
-
+    
 end
 
 function logFile = checklLogFile(action, logFile, iEvent)
-
+    
     switch action
-
+        
         case 'init'
-
+            
             logFile = struct('filename', [], 'extraColumns', cell(1));
             logFile(1).filename = '';
-
+            
         case 'checkID'
-
+            
             if ~isfield(logFile(1), 'fileID') || isempty(logFile(1).fileID)
                 errorSaveEventsFile('missingFileID');
             end
-
+            
         case 'type&size'
-
+            
             if ~isstruct(logFile) || size(logFile, 2) > 1
                 errorSaveEventsFile('wrongLogSize');
             end
-
+            
         case 'fields'
-
+            
             for iFields = {'onset', 'trial_type', 'duration'}
                 if ~isfield(logFile, iFields) || isempty(logFile(iEvent).(iFields{1}))
                     logFile(iEvent).(iFields{1}) = nan;
                 end
             end
-
+            
             logFile = checkExtracolumns(logFile, iEvent);
-
+            
     end
-
+    
 end
 
 function logFile = initializeFile(cfg, logFile)
-
+    
     logFile = initializeExtraColumns(logFile);
-
+    
     createDataDictionary(cfg, logFile);
-
+    
     % Initialize txt logfiles and empty fields for the standard BIDS
     %  event file
     logFile.fileID = fopen( ...
@@ -153,36 +149,36 @@
         cfg.fileName.modality, ...
         logFile.filename), ...
         'w');
-
+    
     % print the basic BIDS columns
     fprintf(logFile.fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
-
+    
     printHeaderExtraColumns(logFile);
-
+    
     % next line so we start printing at the right place
     fprintf(logFile.fileID, '\n');
-
+    
 end
 
 function printHeaderExtraColumns(logFile)
     % print any extra column specified by the user
-
+    
     [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile);
-
+    
     for iExtraColumn = 1:numel(namesExtraColumns)
-
+        
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
-
+        
         for iCol = 1:nbCol
-
+            
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
-
+            
             fprintf(logFile.fileID, '\t%s', headerName);
-
+            
         end
-
+        
     end
-
+    
 end
 
 function logFile = checkExtracolumns(logFile, iEvent)
@@ -190,24 +186,24 @@ function printHeaderExtraColumns(logFile)
     % if the field we are looking for does not exist or is empty in the
     % action logFile structure we will write a n/a
     % otherwise we write its content
-
+    
     namesExtraColumns = returnNamesExtraColumns(logFile);
-
+    
     for iExtraColumn = 1:numel(namesExtraColumns)
-
+        
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
-
+        
         data = 'n/a';
         if isfield(logFile, namesExtraColumns{iExtraColumn})
             data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
         end
-
+        
         data = checkInput(data);
-
+        
         data = nanPadding(data, nbCol);
-
+        
         logFile(iEvent).(namesExtraColumns{iExtraColumn}) = data;
-
+        
         if any(isnan(data))
             warning('Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
@@ -215,22 +211,22 @@ function printHeaderExtraColumns(logFile)
             warning('Missing %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
         end
-
+        
     end
-
+    
 end
 
 function data = checkInput(data)
     % check the data to write
     % default will be 'n/a' for chars and NaN for numeric data
     % for numeric data that don't have the expected length, it will be padded with NaNs
-
+    
     if islogical(data) && data
         data = 'true';
     elseif islogical(data) && ~data
         data = 'false';
     end
-
+    
     if ischar(data) && isempty(data) || strcmp(data, ' ')
         data = 'n/a';
     elseif isempty(data)
@@ -238,15 +234,15 @@ function printHeaderExtraColumns(logFile)
         % numeric valur has the right length and needs to be nan padded
         data = nan;
     end
-
+    
 end
 
 function data = nanPadding(data, expectedLength)
-
+    
     if nargin < 2
         expectedLength = [];
     end
-
+    
     if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
         padding = expectedLength - max(size(data));
         data(end + 1:end + padding) = nan(1, padding);
@@ -254,56 +250,56 @@ function printHeaderExtraColumns(logFile)
         warning('A field for this event is longer than expected. Truncating the extra values.');
         data = data(1:expectedLength);
     end
-
+    
 end
 
 function logFile = saveToLogFile(logFile)
-
+    
     % appends to the logfile all the data stored in the structure
     % first with the standard BIDS data and then any extra things
     for iEvent = 1:size(logFile, 1)
-
+        
         logFile = checklLogFile('fields', logFile, iEvent);
-
+        
         onset = logFile(iEvent).onset;
         duration = logFile(iEvent).duration;
         trial_type = logFile(iEvent).trial_type;
-
+        
         if isnan(onset) || ischar(onset) || any(isempty({onset trial_type})) || ...
                 strcmp(trial_type, 'n/a')
-
+            
             warning('\nSkipping saving this event.\n onset: %f \n trial_type: %s\n', ...
                 onset, ...
                 trial_type);
-
+            
         else
-
+            
             printData(logFile(1).fileID, onset);
             printData(logFile(1).fileID, duration);
             printData(logFile(1).fileID, trial_type);
-
+            
             printExtraColumns(logFile, iEvent);
-
+            
             fprintf(logFile(1).fileID, '\n');
-
+            
         end
     end
-
+    
 end
 
 function printExtraColumns(logFile, iEvent)
     % loops through the extra columns and print them
-
+    
     namesExtraColumns = returnNamesExtraColumns(logFile);
-
+    
     for iExtraColumn = 1:numel(namesExtraColumns)
-
+        
         data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
-
+        
         printData(logFile(1).fileID, data);
-
+        
     end
-
+    
 end
 
 function printData(output, data)
@@ -323,37 +319,53 @@ function printData(output, data)
 end
 
 function logFile = resetLogFileVar(logFile)
-
+    
     logFile(2:end) = [];
-
+    
     namesColumns = {'onset', 'duration', 'trial_type'};
     namesExtraColumns = returnNamesExtraColumns(logFile);
     namesColumns = cat(2, namesColumns, namesExtraColumns');
-
+    
     for iColumn = 1:numel(namesColumns)
-
+        
         if isfield(logFile, namesColumns{iColumn})
             logFile = rmfield(logFile, namesColumns{iColumn});
         end
-
+        
     end
-
+    
 end
 
 function errorSaveEventsFile(identifier)
-
+    
     switch identifier
         case 'unknownActionType'
             errorStruct.message = 'unknown action for saveEventsFile';
-
+            
         case 'missingFileID'
             errorStruct.message = 'logFile must contain a valid fileID field';
-
+            
         case 'wrongLogSize'
             errorStruct.message = 'logFile must be a nx1 structure';
-
+            
     end
-
+    
     errorStruct.identifier = ['saveEventsFile:' identifier];
     error(errorStruct);
 end
+
+function talkToMe(cfg, logFile)
+    
+    if cfg.verbose
+        
+        fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
+            fullfile( ...
+            cfg.dir.outputSubject, ...
+            cfg.fileName.modality, ...
+            logFile.filename));
+        
+    end
+    
+end
+
+

From 00912ab205e122b86dd688475edc21fe5828aec0 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 12:44:48 +0200
Subject: [PATCH 06/11] update tests doc

update testing doc
---
 tests/README.md | 74 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/tests/README.md b/tests/README.md
index 0559aa7f..673cc339 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -7,6 +7,8 @@
 
 This should tell you which tests pass or fail.
   
+## code coverage
+
 The following command would give more info and will give you HTML output in a `coverage_html` folder
 showing you which lines of code is or is not checked by your test suite.
 
@@ -18,6 +20,78 @@ success = moxunit_runtests(pwd, ... % the path where the tests are
     '-cover_xml_file','coverage.xml', ...
     '-cover_html_dir','coverage_html');
 ```
+This will return a clear underestimation of the code coverage as the the code in dependencies in the `lib` folder
+are also included in this report.
+
+If you want to get a slightly more accurate estimate you should run the following.
+
+I have not been able to find a way to exclude certain files without breaking some tests.
+
+```matlab
+coverage = mocov( ...
+    '-expression', 'moxunit_runtests()', ...
+    '-verbose', ...
+    '-cover', fullfile(pwd, '..'), ...
+    '-cover_exclude', '*jsonread.m', ...
+    '-cover_exclude', '*json*code.m', ...
+    '-cover_exclude', '*Contents.m', ...
+    '-cover_exclude', '*report.m', ...
+    '-cover_exclude', '*layout.m', ...
+    '-cover_exclude', '*query.m', ...
+    '-cover_exclude', '*private*', ...
+    '-cover_exclude', '*util*', ...
+    '-cover_exclude', '*Tests*', ...
+    '-cover_exclude', '*tests*', ...
+    '-cover_exclude', '*test_*', ...
+    '-cover_xml_file','coverage.xml', ...
+    '-cover_html_dir','coverage_html')
+```
+
+
+## Adding more tests
+
+You can use the following function template to write more tests.
+
+
+```matlab
+function test_suite = test_functionToTest()
+    % This top function is necessary for mox unit to run tests. 
+    % DO NOT CHANGE IT except to adapt the name of the function.
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
 
+function test_functionToTestBasic()
 
+    %% set up
+
+
+    %% data to test against
+    
+
+    %% test
+    % assertTrue( );
+    % assertFalse( );
+    % assertEqual( );
+
+end
+
+function test_functionToTestUseCase1()
+
+    %% set up
+
+
+    %% data to test against
+    
+
+    %% test
+    % assertTrue( );
+    % assertFalse( );
+    % assertEqual( );
+
+end
+```
 

From e20affcd91c4ee7440448715f6a677e40b72f09d Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 12:53:58 +0200
Subject: [PATCH 07/11] update continuous integration

- create github action workflow
- remove travis
---
 .github/workflows/moxunit.yml | 26 ++++++++++++++++++++++++++
 .travis.yml                   |  6 +++---
 2 files changed, 29 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/moxunit.yml

diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
new file mode 100644
index 00000000..14884735
--- /dev/null
+++ b/.github/workflows/moxunit.yml
@@ -0,0 +1,26 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+    - uses: agahkarakuzu/moxunit-action@master
+      with:
+        src: src
+        with_coverage: true
+        cover_xml_file: coverage.xml
+    - uses: codecov/codecov-action@v1
+      with:
+       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+       file:  coverage.xml # optional
+       flags: unittests # optional
+       name: codecov-umbrella # optional
+       fail_ci_if_error: true # optional (default = false)
diff --git a/.travis.yml b/.travis.yml
index 94ba9f97..51fdee5e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -34,9 +34,9 @@ before_script:
 
 jobs:
   include:
-    - stage: "Tests" 
-      name: "Unit and integration Tests"
-      script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
+    # - stage: "Tests" 
+    #   name: "Unit and integration Tests"
+    #   script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
     - stage: "BIDS validator"
       name: "Create and check dataset"
       script: cd manualTests && octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders

From 02adeef653c108a6b583d823cc06123cffa50d92 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 12:58:35 +0200
Subject: [PATCH 08/11] add trigger to action on PRs

---
 .github/workflows/moxunit.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
index 14884735..a7c72eb6 100644
--- a/.github/workflows/moxunit.yml
+++ b/.github/workflows/moxunit.yml
@@ -4,6 +4,9 @@ on:
   push:
     branches:
       - master
+  pull_request:
+    branches: '*'
+    
 jobs:
   build:
     runs-on: ubuntu-latest

From d6dd167b4cd8ca6e8ed6db21730e71f34b713fb2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 13:13:55 +0200
Subject: [PATCH 09/11] update github action

---
 .github/workflows/moxunit.yml | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
index a7c72eb6..e426698f 100644
--- a/.github/workflows/moxunit.yml
+++ b/.github/workflows/moxunit.yml
@@ -6,7 +6,7 @@ on:
       - master
   pull_request:
     branches: '*'
-    
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,14 +15,15 @@ jobs:
       with:
         submodules: true
         fetch-depth: 1
-    - uses: agahkarakuzu/moxunit-action@master
+    - name: MOxUnit Action
+      uses: joergbrech/moxunit-action@v1.1
       with:
-        src: src
+        tests: tests
         with_coverage: true
         cover_xml_file: coverage.xml
-    - uses: codecov/codecov-action@v1
+    - name: Code coverage
+      uses: codecov/codecov-action@v1
       with:
-       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
        file:  coverage.xml # optional
        flags: unittests # optional
        name: codecov-umbrella # optional

From 2fc70ca1f9f61c087299619bec8f2a211f683fdc Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 13:19:25 +0200
Subject: [PATCH 10/11] mh autofix

---
 checkCFG.m                                 |   2 +-
 checkCppBidsDependencies.m                 |   2 +-
 convertSourceToRaw.m                       |   2 +-
 createFilename.m                           | 102 +++++------
 printCreditsCppBids.m                      |  32 ++--
 saveEventsFile.m                           | 202 ++++++++++-----------
 subfun/returnHeaderName.m                  |   2 +-
 subfun/returnNamesExtraColumns.m           |   2 +-
 tests/checkSubFields.m                     |  22 +--
 tests/returnExpectedCfgStructure.m         |  22 +--
 tests/test_checkCFG.m                      |  55 +++---
 tests/test_createBoldJson.m                |  10 +-
 tests/test_createDataDictionary.m          |   8 +-
 tests/test_createDatasetDescription.m      |   2 +-
 tests/test_createFilename.m                |  25 ++-
 tests/test_createTaskName.m                |   8 +-
 tests/test_saveEventsFileInit.m            |  46 ++---
 tests/test_saveEventsFileOpen.m            |  64 +++----
 tests/test_saveEventsFileOpenMultiColumn.m |  34 ++--
 tests/test_saveEventsFileSave.m            |  12 +-
 tests/test_setDefaultFields.m              |   3 +-
 21 files changed, 325 insertions(+), 332 deletions(-)

diff --git a/checkCFG.m b/checkCFG.m
index 09ddfc9a..a1563897 100644
--- a/checkCFG.m
+++ b/checkCFG.m
@@ -7,7 +7,7 @@
     if nargin < 1 || isempty(cfg)
         cfg = struct();
     end
-    
+
     checkCppBidsDependencies(cfg);
 
     %% list the defaults to set
diff --git a/checkCppBidsDependencies.m b/checkCppBidsDependencies.m
index 3afc5dfb..aef02a1a 100644
--- a/checkCppBidsDependencies.m
+++ b/checkCppBidsDependencies.m
@@ -1,7 +1,7 @@
 function checkCppBidsDependencies(cfg)
     % checkCppBidsDependencies()
     %
-    
+
     pth = fileparts(mfilename('fullpath'));
 
     checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
diff --git a/convertSourceToRaw.m b/convertSourceToRaw.m
index e6e7df5a..aad85f16 100644
--- a/convertSourceToRaw.m
+++ b/convertSourceToRaw.m
@@ -6,7 +6,7 @@ function convertSourceToRaw(cfg)
     % - creates dummy README and CHANGE file
     % - copy source dir to raw dir
     % - remove the date suffix (_date-YYYYMMDDHHMM) from the files where it is present
-    % 
+    %
 
     sourceDir = fullfile(cfg.dir.output, 'source');
     rawDir = fullfile(cfg.dir.output, 'rawdata');
diff --git a/createFilename.m b/createFilename.m
index 3aa01c1a..8f73628a 100644
--- a/createFilename.m
+++ b/createFilename.m
@@ -11,34 +11,34 @@
     %
     %
     % See test_createFilename in the test folder for more details on how to use it.
-    
+
     cfg = checkCFG(cfg);
-    
+
     cfg.fileName.pattern = ['%0' num2str(cfg.fileName.zeroPadding) '.0f'];
     cfg.fileName.date = datestr(now, cfg.fileName.dateFormat);
-    
+
     if ~isfield(cfg, 'task')
         error('createFilename: missing a task name. i.e cfg.task.name');
     end
-    
+
     cfg = getModality(cfg);
-    
+
     cfg = createDirectories(cfg);
-    
+
     cfg = setSuffixes(cfg);
-    
+
     cfg = setFilenames(cfg);
-    
+
     talkToMe(cfg);
-    
+
     cfg = orderfields(cfg);
     cfg.fileName = orderfields(cfg.fileName);
     cfg.dir = orderfields(cfg.dir);
-    
+
 end
 
 function cfg = getModality(cfg)
-    
+
     switch lower(cfg.testingDevice)
         case 'pc'
             modality = 'beh';
@@ -53,52 +53,52 @@
         otherwise
             modality = 'beh';
     end
-    
+
     cfg.fileName.modality = modality;
-    
+
 end
 
 function [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg)
-    
+
     subjectGrp = cfg.subject.subjectGrp;
     subjectNb = cfg.subject.subjectNb;
     sessionNb = cfg.subject.sessionNb;
     modality = cfg.fileName.modality;
     taskName = cfg.fileName.task;
-    
+
     if isempty(sessionNb)
         sessionNb = 1;
     end
-    
+
 end
 
 function cfg = createDirectories(cfg)
-    
+
     [subjectGrp, subjectNb, sessionNb, modality] = extractInput(cfg);
-    
+
     pattern = cfg.fileName.pattern;
-    
+
     % output dir
     cfg.dir.outputSubject = fullfile ( ...
         cfg.dir.output, ...
         'source', ...
         ['sub-' subjectGrp, sprintf(pattern, subjectNb)], ...
         ['ses-', sprintf(pattern, sessionNb)]);
-    
+
     [~, ~, ~] = mkdir(cfg.dir.output);
     [~, ~, ~] = mkdir(cfg.dir.outputSubject);
     [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, modality));
-    
+
     if cfg.eyeTracker.do
         [~, ~, ~] = mkdir(fullfile(cfg.dir.outputSubject, 'eyetracker'));
     end
-    
+
 end
 
 function cfg = setSuffixes(cfg)
-    
+
     cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
-    
+
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
         'contrastEnhancement', ...
@@ -107,7 +107,7 @@
         'echo', ...
         'acquisition'
         };
-    
+
     for iField = 1:numel(fields2Check)
         if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
@@ -116,85 +116,85 @@
                 ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
         end
     end
-    
+
     cfg.fileName.suffix = orderfields(cfg.fileName.suffix);
-    
+
 end
 
 function cfg = setFilenames(cfg)
-    
+
     [subjectGrp, subjectNb, sessionNb, modality, taskName] = extractInput(cfg);
-    
+
     pattern = cfg.fileName.pattern;
-    
+
     runSuffix = cfg.fileName.suffix.run;
     acqSuffix = cfg.fileName.suffix.mri.acquisition ;
     ceSuffix = cfg.fileName.suffix.mri.contrastEnhancement ;
     dirSuffix = cfg.fileName.suffix.mri.phaseEncodingDirection ;
     recSuffix = cfg.fileName.suffix.mri.reconstruction ;
     echoSuffix = cfg.fileName.suffix.mri.echo;
-    
+
     thisDate = cfg.fileName.date;
-    
+
     cfg.fileName.datasetDescription = fullfile ( ...
         cfg.dir.output, ...
         'dataset_description.json');
-    
+
     % create base fileName
     fileNameBase = ...
         ['sub-', subjectGrp, sprintf(pattern, subjectNb), ...
         '_ses-', sprintf(pattern, sessionNb), ...
         '_task-', taskName];
     cfg.fileName.base = fileNameBase;
-    
+
     switch modality
-        
+
         case 'func'
-            
+
             cfg.fileName.events = ...
                 [fileNameBase, ...
                 acqSuffix, ceSuffix, ...
                 dirSuffix, recSuffix, ...
                 runSuffix, echoSuffix, ...
                 '_events_date-' thisDate '.tsv'];
-            
+
         otherwise
-            
+
             cfg.fileName.events = ...
                 [fileNameBase, runSuffix, '_events_date-' thisDate '.tsv'];
-            
+
     end
-    
+
     cfg.fileName.stim = strrep(cfg.fileName.events, 'events', 'stim');
-    
+
     if cfg.eyeTracker.do
         cfg.fileName.eyetracker = ...
             [fileNameBase, acqSuffix, ...
             runSuffix, '_eyetrack_date-' thisDate '.edf'];
     end
-    
+
 end
 
 function talkToMe(cfg)
-    
+
     if cfg.verbose
-        
+
         fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
             fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
-        
+
         fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
             cfg.fileName.events);
-        
+
         if cfg.eyeTracker.do
-            
+
             fprintf(1, '\nEyetracking data will be saved in this directory:\n\t%s\n', ...
                 fullfile(cfg.dir.outputSubject, 'eyetracker'));
-            
+
             fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
                 cfg.fileName.eyetracker);
-            
+
         end
-        
+
     end
-    
+
 end
diff --git a/printCreditsCppBids.m b/printCreditsCppBids.m
index 189a064a..ab1e19d8 100644
--- a/printCreditsCppBids.m
+++ b/printCreditsCppBids.m
@@ -1,25 +1,25 @@
 function printCreditsCppBids(cfg)
-    
+
     verbose = true;
     if ~isempty(cfg) && isfield(cfg, 'verbose') && ~isempty(cfg.verbose)
         verbose = cfg.verbose;
     end
-    
+
     if verbose
-        
+
         version = '0.0.1';
-        
+
         contributors = { ...
             'Rémi Gau', ...
             'Marco Barilari', ...
             'Ceren Battal'};
-        
+
         % DOI_URL = 'https://doi.org/10.5281/zenodo.3554331.';
-        
+
         repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS';
-        
+
         fprintf('\n\n');
-        
+
         disp('___________________________________________________');
         disp('___________________________________________________');
         disp('                                                   ');
@@ -28,26 +28,26 @@ function printCreditsCppBids(cfg)
         disp('       | (__|  _/  _/ | _ \| || |) \__ \');
         disp('        \___|_| |_|   |___/___|___/|___/');
         disp('                                                   ');
-        
+
         splash = 'Thank you for using the CPP BIDS - version %s. ';
         fprintf(splash, version);
         fprintf('\n\n');
-        
+
         fprintf('Current list of contributors includes:\n');
         for iCont = 1:numel(contributors)
             fprintf(' %s\n', contributors{iCont});
         end
         fprintf('\b\n\n');
-        
+
         % fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
-        
+
         fprintf('For bug report, suggestions or contributions see: \n %s\n\n', repoURL);
-        
+
         disp('___________________________________________________');
         disp('___________________________________________________');
-        
+
         fprintf('\n\n');
-        
+
     end
-    
+
 end
diff --git a/saveEventsFile.m b/saveEventsFile.m
index 9ce5a01c..5f7388e9 100644
--- a/saveEventsFile.m
+++ b/saveEventsFile.m
@@ -43,104 +43,104 @@
     % to true then this will tell you where the file is located.
     %
     % See test_saveEventsFile in the test folder for more details on how to use it.
-    
+
     if nargin < 1
         error('Missing action input');
     end
-    
+
     if nargin < 2
         cfg = struct();
     end
-    
+
     if nargin < 3 || isempty(logFile)
         logFile = checklLogFile('init');
     end
-    
+
     switch action
-        
+
         case 'init'
-            
+
             logFile = initializeExtraColumns(logFile);
-            
+
         case 'open'
-            
+
             logFile.filename = cfg.fileName.events;
-            
+
             logFile = initializeFile(cfg, logFile);
-            
+
         case 'open_stim'
-            
+
             logFile.filename = cfg.fileName.stim;
-            
+
             logFile = initializeFile(cfg, logFile);
-            
+
         case 'save'
-            
+
             checklLogFile('checkID', logFile);
             checklLogFile('type&size', logFile);
-            
+
             logFile = saveToLogFile(logFile);
-            
+
         case 'close'
-            
+
             checklLogFile('checkID', logFile);
-            
+
             % close txt log file
             fclose(logFile(1).fileID);
-            
+
             talkToMe(cfg, logFile);
-            
+
         otherwise
-            
+
             errorSaveEventsFile('unknownActionType');
-            
+
     end
-    
+
     logFile = resetLogFileVar(logFile);
-    
+
 end
 
 function logFile = checklLogFile(action, logFile, iEvent)
-    
+
     switch action
-        
+
         case 'init'
-            
+
             logFile = struct('filename', [], 'extraColumns', cell(1));
             logFile(1).filename = '';
-            
+
         case 'checkID'
-            
+
             if ~isfield(logFile(1), 'fileID') || isempty(logFile(1).fileID)
                 errorSaveEventsFile('missingFileID');
             end
-            
+
         case 'type&size'
-            
+
             if ~isstruct(logFile) || size(logFile, 2) > 1
                 errorSaveEventsFile('wrongLogSize');
             end
-            
+
         case 'fields'
-            
+
             for iFields = {'onset', 'trial_type', 'duration'}
                 if ~isfield(logFile, iFields) || isempty(logFile(iEvent).(iFields{1}))
                     logFile(iEvent).(iFields{1}) = nan;
                 end
             end
-            
+
             logFile = checkExtracolumns(logFile, iEvent);
-            
+
     end
-    
+
 end
 
 function logFile = initializeFile(cfg, logFile)
-    
+
     logFile = initializeExtraColumns(logFile);
-    
+
     createDataDictionary(cfg, logFile);
-    
+
     % Initialize txt logfiles and empty fields for the standard BIDS
     %  event file
     logFile.fileID = fopen( ...
@@ -149,36 +149,36 @@
         cfg.fileName.modality, ...
         logFile.filename), ...
         'w');
-    
+
     % print the basic BIDS columns
     fprintf(logFile.fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
-    
+
     printHeaderExtraColumns(logFile);
-    
+
     % next line so we start printing at the right place
     fprintf(logFile.fileID, '\n');
-    
+
 end
 
 function printHeaderExtraColumns(logFile)
     % print any extra column specified by the user
-    
+
     [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile);
-    
+
     for iExtraColumn = 1:numel(namesExtraColumns)
-        
+
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
-        
+
         for iCol = 1:nbCol
-            
+
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
-            
+
             fprintf(logFile.fileID, '\t%s', headerName);
-            
+
         end
-        
+
     end
-    
+
 end
 
 function logFile = checkExtracolumns(logFile, iEvent)
@@ -186,24 +186,24 @@ function printHeaderExtraColumns(logFile)
     % if the field we are looking for does not exist or is empty in the
     % action logFile structure we will write a n/a
     % otherwise we write its content
-    
+
     namesExtraColumns = returnNamesExtraColumns(logFile);
-    
+
     for iExtraColumn = 1:numel(namesExtraColumns)
-        
+
         nbCol = returnNbColumns(logFile, namesExtraColumns{iExtraColumn});
-        
+
         data = 'n/a';
         if isfield(logFile, namesExtraColumns{iExtraColumn})
             data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
         end
-        
+
         data = checkInput(data);
-        
+
         data = nanPadding(data, nbCol);
-        
+
         logFile(iEvent).(namesExtraColumns{iExtraColumn}) = data;
-        
+
         if any(isnan(data))
             warning('Missing some %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
@@ -211,22 +211,22 @@ function printHeaderExtraColumns(logFile)
             warning('Missing %s data for this event.', namesExtraColumns{iExtraColumn});
             disp(logFile(iEvent));
         end
-        
+
     end
-    
+
 end
 
 function data = checkInput(data)
     % check the data to write
     % default will be 'n/a' for chars and NaN for numeric data
     % for numeric data that don't have the expected length, it will be padded with NaNs
-    
+
     if islogical(data) && data
         data = 'true';
     elseif islogical(data) && ~data
         data = 'false';
     end
-    
+
     if ischar(data) && isempty(data) || strcmp(data, ' ')
         data = 'n/a';
     elseif isempty(data)
@@ -234,15 +234,15 @@ function printHeaderExtraColumns(logFile)
         % numeric valur has the right length and needs to be nan padded
         data = nan;
     end
-    
+
 end
 
 function data = nanPadding(data, expectedLength)
-    
+
     if nargin < 2
         expectedLength = [];
     end
-    
+
     if ~isempty(expectedLength) && isnumeric(data) && max(size(data)) < expectedLength
         padding = expectedLength - max(size(data));
         data(end + 1:end + padding) = nan(1, padding);
@@ -250,56 +250,56 @@ function printHeaderExtraColumns(logFile)
         warning('A field for this event is longer than expected. Truncating the extra values.');
         data = data(1:expectedLength);
     end
-    
+
 end
 
 function logFile = saveToLogFile(logFile)
-    
+
     % appends to the logfile all the data stored in the structure
     % first with the standard BIDS data and then any extra things
     for iEvent = 1:size(logFile, 1)
-        
+
         logFile = checklLogFile('fields', logFile, iEvent);
-        
+
         onset = logFile(iEvent).onset;
         duration = logFile(iEvent).duration;
         trial_type = logFile(iEvent).trial_type;
-        
+
         if isnan(onset) || ischar(onset) || any(isempty({onset trial_type})) || ...
                 strcmp(trial_type, 'n/a')
-            
+
             warning('\nSkipping saving this event.\n onset: %f \n trial_type: %s\n', ...
                 onset, ...
                 trial_type);
-            
+
         else
-            
+
             printData(logFile(1).fileID, onset);
             printData(logFile(1).fileID, duration);
             printData(logFile(1).fileID, trial_type);
-            
+
             printExtraColumns(logFile, iEvent);
-            
+
             fprintf(logFile(1).fileID, '\n');
-            
+
         end
     end
-    
+
 end
 
 function printExtraColumns(logFile, iEvent)
     % loops through the extra columns and print them
-    
+
     namesExtraColumns = returnNamesExtraColumns(logFile);
-    
+
     for iExtraColumn = 1:numel(namesExtraColumns)
-        
+
         data = logFile(iEvent).(namesExtraColumns{iExtraColumn});
-        
+
         printData(logFile(1).fileID, data);
-        
+
     end
-    
+
 end
 
 function printData(output, data)
@@ -319,53 +319,51 @@ function printData(output, data)
 end
 
 function logFile = resetLogFileVar(logFile)
-    
+
     logFile(2:end) = [];
-    
+
     namesColumns = {'onset', 'duration', 'trial_type'};
     namesExtraColumns = returnNamesExtraColumns(logFile);
     namesColumns = cat(2, namesColumns, namesExtraColumns');
-    
+
     for iColumn = 1:numel(namesColumns)
-        
+
         if isfield(logFile, namesColumns{iColumn})
             logFile = rmfield(logFile, namesColumns{iColumn});
         end
-        
+
     end
-    
+
 end
 
 function errorSaveEventsFile(identifier)
-    
+
     switch identifier
         case 'unknownActionType'
             errorStruct.message = 'unknown action for saveEventsFile';
-            
+
         case 'missingFileID'
             errorStruct.message = 'logFile must contain a valid fileID field';
-            
+
         case 'wrongLogSize'
             errorStruct.message = 'logFile must be a nx1 structure';
-            
+
     end
-    
+
     errorStruct.identifier = ['saveEventsFile:' identifier];
     error(errorStruct);
 end
 
 function talkToMe(cfg, logFile)
-    
+
     if cfg.verbose
-        
+
         fprintf(1, '\nData were saved in this file:\n\n%s\n\n', ...
             fullfile( ...
             cfg.dir.outputSubject, ...
             cfg.fileName.modality, ...
             logFile.filename));
-        
-    end
-    
-end
 
+    end
 
+end
diff --git a/subfun/returnHeaderName.m b/subfun/returnHeaderName.m
index 1caff806..2401ea0d 100644
--- a/subfun/returnHeaderName.m
+++ b/subfun/returnHeaderName.m
@@ -1,7 +1,7 @@
 function headerName = returnHeaderName(columnName, nbCol, iCol)
     % headerName = returnHeaderName(columnName, nbCol, iCol)
     %
-    
+
     if nbCol == 1
         headerName = sprintf('%s', columnName);
     else
diff --git a/subfun/returnNamesExtraColumns.m b/subfun/returnNamesExtraColumns.m
index 502d2e57..ada0791c 100644
--- a/subfun/returnNamesExtraColumns.m
+++ b/subfun/returnNamesExtraColumns.m
@@ -1,7 +1,7 @@
 function [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile)
     % [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile)
     %
-    
+
     namesExtraColumns = [];
 
     if isfield(logFile, 'extraColumns') && ~isempty(logFile(1).extraColumns)
diff --git a/tests/checkSubFields.m b/tests/checkSubFields.m
index 764f4aff..a6b8cb7e 100644
--- a/tests/checkSubFields.m
+++ b/tests/checkSubFields.m
@@ -1,29 +1,29 @@
 function checkSubFields(expectedStructure, cfg)
     % check that that the structures match
     % if it fails it check from which subfield the error comes from
-    
+
     try
-        
+
         assertEqual(expectedStructure, cfg);
-        
+
     catch ME
-        
+
         if isstruct(expectedStructure)
-            
+
             names = fieldnames(expectedStructure);
-            
+
             for i = 1:numel(names)
-                
+
                 disp(names{i});
                 testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
-                
+
             end
-            
+
         end
-        
+
         disp(expectedStructure);
         disp(cfg);
-        
+
         rethrow(ME);
     end
 end
diff --git a/tests/returnExpectedCfgStructure.m b/tests/returnExpectedCfgStructure.m
index 41982a55..749338ae 100644
--- a/tests/returnExpectedCfgStructure.m
+++ b/tests/returnExpectedCfgStructure.m
@@ -1,30 +1,30 @@
 function expectedCfgStructure = returnExpectedCfgStructure()
-    
+
     expectedCfgStructure.subject.subjectGrp = '';
     expectedCfgStructure.subject.sessionNb = 1;
     expectedCfgStructure.subject.askGrpSess = [true true];
-    
+
     expectedCfgStructure.verbose = 0;
-    
+
     expectedCfgStructure.fileName.task = '';
     expectedCfgStructure.fileName.zeroPadding = 3;
     expectedCfgStructure.fileName.dateFormat = 'yyyymmddHHMM';
-    
+
     expectedCfgStructure.eyeTracker.do = false;
-    
+
     expectedCfgStructure.mri.contrastEnhancement = [];
     expectedCfgStructure.mri.phaseEncodingDirection = [];
     expectedCfgStructure.mri.reconstruction = [];
     expectedCfgStructure.mri.echo = [];
     expectedCfgStructure.mri.acquisition = [];
     expectedCfgStructure.mri.repetitionTime = [];
-    
+
     expectedCfgStructure.bids.mri.RepetitionTime = [];
     expectedCfgStructure.bids.mri.SliceTiming = '';
     expectedCfgStructure.bids.mri.TaskName = '';
     expectedCfgStructure.bids.mri.Instructions = '';
     expectedCfgStructure.bids.mri.TaskDescription = '';
-    
+
     expectedCfgStructure.bids.meg.TaskName = '';
     expectedCfgStructure.bids.meg.SamplingFrequency = [];
     expectedCfgStructure.bids.meg.PowerLineFrequency = [];
@@ -32,7 +32,7 @@
     expectedCfgStructure.bids.meg.SoftwareFilters = [];
     expectedCfgStructure.bids.meg.DigitizedLandmarks = [];
     expectedCfgStructure.bids.meg.DigitizedHeadPoints = [];
-    
+
     expectedCfgStructure.bids.datasetDescription.Name = '';
     expectedCfgStructure.bids.datasetDescription.BIDSVersion =  '';
     expectedCfgStructure.bids.datasetDescription.License = '';
@@ -42,7 +42,7 @@
     expectedCfgStructure.bids.datasetDescription.Funding = {''};
     expectedCfgStructure.bids.datasetDescription.ReferencesAndLinks = {''};
     expectedCfgStructure.bids.datasetDescription.DatasetDOI = '';
-    
+
     expectedCfgStructure = orderfields(expectedCfgStructure);
-    
-end
\ No newline at end of file
+
+end
diff --git a/tests/test_checkCFG.m b/tests/test_checkCFG.m
index 3768bdd0..80656a23 100644
--- a/tests/test_checkCFG.m
+++ b/tests/test_checkCFG.m
@@ -7,75 +7,72 @@
 end
 
 function test_checkCfgDefault()
-    
+
     %% set up
     cfg.dir.output = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
     cfg = checkCFG(cfg);
-    
+
     %% create test data
     expectedStructure = returnExpectedCfgStructure();
     expectedStructure.dir.output = cfg.dir.output;
     expectedStructure.testingDevice = 'pc';
-    
+
     %% test
     checkSubFields(expectedStructure, cfg);
-    
+
 end
-    
+
 function test_checkCfgBasic()
-    
+
     %% set up
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-    
+
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'test task';
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
-    
+
     cfg.mri.repetitionTime = 1.56;
-    
+
     cfg.testingDevice = 'mri';
-    
+
     cfg = checkCFG(cfg);
-    
+
     %% create test data
     expectedStructure = returnExpectedCfgStructure();
     expectedStructure.subject.subjectNb = 1;
     expectedStructure.subject.runNb = 1;
-    
+
     expectedStructure.dir.output = outputDir;
-    
+
     expectedStructure.task.name = 'test task';
-    
+
     expectedStructure.testingDevice = 'mri';
-    
+
     expectedStructure.mri.repetitionTime = 1.56;
-    
+
     expectedStructure.fileName.task = 'testTask';
-    
+
     expectedStructure.bids.mri.RepetitionTime = 1.56;
     expectedStructure.bids.mri.TaskName = 'test Task';
-    
+
     expectedStructure.bids.meg.TaskName = 'test Task';
-    
+
     expectedStructure.bids.datasetDescription.Name = 'dummy';
     expectedStructure.bids.datasetDescription.BIDSVersion =  '1.0.0';
     expectedStructure.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
-    
+
     expectedStructure = orderfields(expectedStructure);
-    
+
     %% test
     checkSubFields(expectedStructure, cfg);
-    
-end
-
-
 
+end
diff --git a/tests/test_createBoldJson.m b/tests/test_createBoldJson.m
index 48629da1..769d7148 100644
--- a/tests/test_createBoldJson.m
+++ b/tests/test_createBoldJson.m
@@ -10,15 +10,15 @@ function test_createBoldJsonBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %% set up 
+    %% set up
 
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
-    
+
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
@@ -31,7 +31,7 @@ function test_createBoldJsonBasic()
 
     %% data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
-    
+
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_bold_date-' ...
         cfg.fileName.date '.json'];
 
diff --git a/tests/test_createDataDictionary.m b/tests/test_createDataDictionary.m
index 5c26006a..dc8f5ed2 100644
--- a/tests/test_createDataDictionary.m
+++ b/tests/test_createDataDictionary.m
@@ -29,7 +29,7 @@ function test_createDataDictionaryBasic()
     createDataDictionary(cfg, logFile);
 
     %% check that the file has the right path and name
-    
+
     % data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
@@ -40,11 +40,11 @@ function test_createDataDictionaryBasic()
 
     %% check content
     actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
-    
+
     % data to test against
-    expectedStruct = bids.util.jsondecode(...
+    expectedStruct = bids.util.jsondecode( ...
         fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
-    
+
     % test
     assertTrue(isequal(expectedStruct, actualStruct));
 
diff --git a/tests/test_createDatasetDescription.m b/tests/test_createDatasetDescription.m
index 1e2e0d89..c4664eb0 100644
--- a/tests/test_createDatasetDescription.m
+++ b/tests/test_createDatasetDescription.m
@@ -13,7 +13,7 @@ function test_createDatasetDescriptionBasic()
     %% set up
 
     cfg.dir.output = outputDir;
-    
+
     cfg.verbose = false;
 
     cfg.bids.datasetDescription.json.Name = 'dummy_dataset';
diff --git a/tests/test_createFilename.m b/tests/test_createFilename.m
index 803ecd04..772a536a 100644
--- a/tests/test_createFilename.m
+++ b/tests/test_createFilename.m
@@ -22,17 +22,17 @@ function test_createFilenameBasic()
 
     %% data to test against
     behDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'beh');
-    
+
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'eyetracker');
-    
+
     eventFilename = ['sub-001_ses-001_task-testTask_run-001_events_date-'...
         cfg.fileName.date '.tsv'];
-    
+
     stimFilename =  ['sub-001_ses-001_task-testTask_run-001_stim_date-'...
         cfg.fileName.date '.tsv'];
 
     %% test
-    
+
     % make sure the beh dir is created
     assertTrue(exist(behDir, 'dir') == 7);
 
@@ -45,7 +45,6 @@ function test_createFilenameBasic()
     % make sure the stim filename is created
     assertEqual(cfg.fileName.stim, stimFilename);
 
-    
 end
 
 function test_createFilenameMriEyetracker()
@@ -68,16 +67,16 @@ function test_createFilenameMriEyetracker()
     cfg = createFilename(cfg);
 
     %% data to test against
-    
+
     funcDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'func');
-    
+
     eyetrackerDir = fullfile(outputDir, 'source', 'sub-ctrl002', 'ses-002', 'eyetracker');
-    
+
     baseFilename = 'sub-ctrl002_ses-002_task-testTask';
-    
+
     eventFilename = ['sub-ctrl002_ses-002_task-testTask_run-002_events_date-' ...
         cfg.fileName.date '.tsv'];
-    
+
     eyetrackerFilename =  ['sub-ctrl002_ses-002_task-testTask_run-002_eyetrack_date-' ...
         cfg.fileName.date '.edf'];
 
@@ -92,9 +91,9 @@ function test_createFilenameMriEyetracker()
     assertEqual(cfg.fileName.base, baseFilename);
     assertEqual(cfg.fileName.events, eventFilename);
     assertEqual(cfg.fileName.eyetracker, eyetrackerFilename);
-    
+
 end
-    
+
 function test_createFilenameEeg()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
@@ -120,4 +119,4 @@ function test_createFilenameEeg()
     % make sure the func dir is created
     assertTrue(exist(eegDir, 'dir') == 7);
 
-end
\ No newline at end of file
+end
diff --git a/tests/test_createTaskName.m b/tests/test_createTaskName.m
index 40f14ef3..f3aac9a4 100644
--- a/tests/test_createTaskName.m
+++ b/tests/test_createTaskName.m
@@ -8,10 +8,10 @@
 
 function test_createTaskNameRemoveInvalidCharacters()
 
-    %% set up 
-    
+    %% set up
+
     taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
-    
+
     [taskName, taskNameValid] = createTaskName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
@@ -41,7 +41,7 @@ function test_createTaskNameCamelCase()
     %% set up
     taskName = 'foo bar';
     [taskName, taskNameValid] = createTaskName(taskName);
-    
+
     %% test
     assertEqual(taskName, 'foo Bar');
     assertEqual(taskNameValid, 'fooBar');
diff --git a/tests/test_saveEventsFileInit.m b/tests/test_saveEventsFileInit.m
index ed86be99..d56fe165 100644
--- a/tests/test_saveEventsFileInit.m
+++ b/tests/test_saveEventsFileInit.m
@@ -7,62 +7,62 @@
 end
 
 function test_saveEventsFileInitBasic()
-    
-    %% set up 
+
+    %% set up
 
     cfg.verbose = false;
-    
+
     % make sure the dependencies are there
     checkCFG(cfg);
-    
+
     [logFile] = saveEventsFile('init');
-    
+
     %% data to test against
     expectedStrcut(1).filename = '';
     expectedStrcut(1).extraColumns = [];
-    
+
     %% test
     assertEqual(expectedStrcut, logFile);
-    
+
 end
 
 function test_saveEventsFileInitExtraColumns()
-    
-    %% set up 
+
+    %% set up
 
     cfg.verbose = false;
-    
+
     cfg = checkCFG(cfg);
-    
+
     logFile.extraColumns = {'Speed'};
-    
+
     [logFile] = saveEventsFile('init', cfg, logFile);
-    
+
     %% data to test against
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
     expectedStrcut(1).extraColumns.Speed.bids.Description = '';
     expectedStrcut(1).extraColumns.Speed.bids.Levels = '';
     expectedStrcut(1).extraColumns.Speed.bids.TermURL = '';
-    
+
     %% test
     assertEqual(expectedStrcut, logFile);
-    
+
 end
 
 function test_saveEventsFileInitExtraColumnsArray()
-    
-    %% set up 
+
+    %% set up
 
     cfg.verbose = false;
-    
+
     cfg = checkCFG(cfg);
-    
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
-    
+
     [logFile] = saveEventsFile('init', cfg, logFile);
-    
+
     %% data to test against
     expectedStrcut(1).extraColumns.Speed.length = 1;
     expectedStrcut(1).extraColumns.Speed.bids.LongName = '';
@@ -74,8 +74,8 @@ function test_saveEventsFileInitExtraColumnsArray()
     expectedStrcut(1).extraColumns.LHL24.bids.Description = '';
     expectedStrcut(1).extraColumns.LHL24.bids.Levels = '';
     expectedStrcut(1).extraColumns.LHL24.bids.TermURL = '';
-    
+
     %% test
     assertEqual(expectedStrcut, logFile);
-    
+
 end
diff --git a/tests/test_saveEventsFileOpen.m b/tests/test_saveEventsFileOpen.m
index e536a03d..134f6ffe 100644
--- a/tests/test_saveEventsFileOpen.m
+++ b/tests/test_saveEventsFileOpen.m
@@ -7,89 +7,89 @@
 end
 
 function test_saveEventsFileOpenBasic()
-    
+
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-    
+
     %% set up
-    
+
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'mri';
-    
+
     cfg = createFilename(cfg);
-    
+
     % create the events file and header
     logFile = saveEventsFile('open', cfg);
-    
+
     % close the file
     saveEventsFile('close', cfg, logFile);
-    
+
     %% data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
     eventFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
         cfg.fileName.date '.tsv'];
-    
+
     % check that the file has the right path and name
     assert(exist(fullfile(funcDir, eventFilename), 'file') == 2);
-    
+
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-    
+
     %% test
     % check the extra columns of the header
     assertEqual(C{1}{1}, 'onset');
     assertEqual(C{2}{1}, 'duration');
     assertEqual(C{3}{1}, 'trial_type');
-    
+
 end
 
 function test_saveEventsFileOpenExtraColumns()
-    
+
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-    
+
     %% set up
-    
+
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
-    
+
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'mri';
-    
+
     cfg = createFilename(cfg);
-    
-    % define the extra columns 
+
+    % define the extra columns
     % they will be added to the tsv files in the order the user input them
     logFile.extraColumns = {'Speed', 'is_Fixation'};
 
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
-    
+
     % close the file
     saveEventsFile('close', cfg, logFile);
-    
+
     %% data to test against
-    
+
     % open the file
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
     eventFilename = cfg.fileName.events;
-    
+
     nbExtraCol = 2;
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-    
+
     %% test
     % check the extra columns of the header
     assertEqual(C{1}{1}, 'onset');
@@ -97,5 +97,5 @@ function test_saveEventsFileOpenExtraColumns()
     assertEqual(C{3}{1}, 'trial_type');
     assertEqual(C{4}{1}, 'Speed');
     assertEqual(C{5}{1}, 'is_Fixation');
-    
+
 end
diff --git a/tests/test_saveEventsFileOpenMultiColumn.m b/tests/test_saveEventsFileOpenMultiColumn.m
index 66c826b0..05e63f41 100644
--- a/tests/test_saveEventsFileOpenMultiColumn.m
+++ b/tests/test_saveEventsFileOpenMultiColumn.m
@@ -7,53 +7,53 @@
 end
 
 function test_saveEventsFileOpenMultiColumnCheckHeader()
-    
+
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-    
+
     %% set up
-    
+
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
-    
+
     cfg.dir.output = outputDir;
-    
+
     cfg.testingDevice = 'mri';
-    
+
     cfg = createFilename(cfg);
-    
+
     % define the extra columns: here we specify how many columns we want for
     % each variable
     logFile.extraColumns.Speed.length = 1; % will set 1 columns with name Speed
     logFile.extraColumns.LHL24.length = 12; % will set 12 columns with names LHL24-01, LHL24-02, ...
     logFile.extraColumns.is_Fixation = []; % will set 1 columns with name is_Fixation
-    
+
     % create the events file and header
     logFile = saveEventsFile('open', cfg, logFile);
-    
+
     % close the file
     saveEventsFile('close', cfg, logFile);
-    
+
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
-    
+
     eventFilename = cfg.fileName.events;
-    
+
     nbExtraCol = ...
         logFile(1).extraColumns.Speed.length + ...
         logFile(1).extraColumns.LHL24.length + ...
         logFile(1).extraColumns.is_Fixation.length;
-    
+
     %% test
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
-    
+
     % check the extra columns of the header
     assertEqual(C{4}{1}, 'Speed');
     assertEqual(C{5}{1}, 'LHL24_01');
     assertEqual(C{16}{1}, 'LHL24_12');
     assertEqual(C{17}{1}, 'is_Fixation');
-    
+
 end
diff --git a/tests/test_saveEventsFileSave.m b/tests/test_saveEventsFileSave.m
index b49d5001..514aee75 100644
--- a/tests/test_saveEventsFileSave.m
+++ b/tests/test_saveEventsFileSave.m
@@ -10,15 +10,15 @@ function test_saveEventsFileSaveBasic()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
 
-    %% set up 
+    %% set up
 
     cfg.verbose = false;
-    
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
-    
+
     cfg.task.name = 'testtask';
-    
+
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
@@ -89,9 +89,9 @@ function test_saveEventsFileSaveBasic()
         logFile(1).extraColumns.is_Fixation.length;
 
     funcDir = fullfile(cfg.dir.outputSubject, cfg.fileName.modality);
-    
+
     eventFilename = cfg.fileName.events;
-    
+
     FID = fopen(fullfile(funcDir, eventFilename), 'r');
     C = textscan(FID, repmat('%s', 1, nbExtraCol + 3), 'Delimiter', '\t', 'EndOfLine', '\n');
 
diff --git a/tests/test_setDefaultFields.m b/tests/test_setDefaultFields.m
index c327d148..39ca05d4 100644
--- a/tests/test_setDefaultFields.m
+++ b/tests/test_setDefaultFields.m
@@ -20,9 +20,8 @@ function test_setDefaultFieldsWrite()
 
     %% test
     assertEqual(expectedStructure, structure);
-    
-end
 
+end
 
 function test_setDefaultFieldsNoOverwrite()
 

From 14baca80614b34a7a7db22fa47e684b0a78b137f Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 1 Aug 2020 17:17:16 +0200
Subject: [PATCH 11/11] reorganize for github actions

---
 .github/workflows/moxunit.yml                 |  2 +
 .gitignore                                    |  4 +-
 .travis.yml                                   |  6 +-
 checkCppBidsDependencies.m                    | 27 -------
 .../manualTests => manualTests}/miss_hit.cfg  |  0
 .../testData/eventsDataDictionary.json        |  0
 .../test_createDataDictionary.m               |  4 +
 .../test_makeRawDataset.m                     |  8 +-
 .../test_userInput.m                          |  0
 checkCFG.m => src/checkCFG.m                  |  0
 src/checkCppBidsDependencies.m                | 39 +++++++++
 .../convertSourceToRaw.m                      |  4 +-
 createBoldJson.m => src/createBoldJson.m      |  0
 .../createDataDictionary.m                    |  0
 .../createDatasetDescription.m                |  0
 createFilename.m => src/createFilename.m      |  0
 src/miss_hit.cfg                              |  3 +
 .../printCreditsCppBids.m                     |  0
 saveEventsFile.m => src/saveEventsFile.m      |  0
 {subfun => src/subfun}/createTaskName.m       |  0
 .../subfun}/initializeExtraColumns.m          |  0
 {subfun => src/subfun}/returnHeaderName.m     |  0
 .../subfun}/returnNamesExtraColumns.m         |  0
 {subfun => src/subfun}/returnNbColumns.m      |  0
 {subfun => src/subfun}/setDefaultFields.m     |  0
 {subfun => src/subfun}/transferInfoToBids.m   |  0
 userInputs.m => src/userInputs.m              |  0
 tests/checkSubFields.m                        | 29 -------
 tests/returnExpectedCfgStructure.m            | 48 -----------
 tests/test_checkCFG.m                         | 79 +++++++++++++++++++
 30 files changed, 139 insertions(+), 114 deletions(-)
 delete mode 100644 checkCppBidsDependencies.m
 rename {tests/manualTests => manualTests}/miss_hit.cfg (100%)
 rename {tests => manualTests}/testData/eventsDataDictionary.json (100%)
 rename {tests => manualTests}/test_createDataDictionary.m (99%)
 rename {tests/manualTests => manualTests}/test_makeRawDataset.m (92%)
 rename {tests/manualTests => manualTests}/test_userInput.m (100%)
 rename checkCFG.m => src/checkCFG.m (100%)
 create mode 100644 src/checkCppBidsDependencies.m
 rename convertSourceToRaw.m => src/convertSourceToRaw.m (92%)
 rename createBoldJson.m => src/createBoldJson.m (100%)
 rename createDataDictionary.m => src/createDataDictionary.m (100%)
 rename createDatasetDescription.m => src/createDatasetDescription.m (100%)
 rename createFilename.m => src/createFilename.m (100%)
 create mode 100644 src/miss_hit.cfg
 rename printCreditsCppBids.m => src/printCreditsCppBids.m (100%)
 rename saveEventsFile.m => src/saveEventsFile.m (100%)
 rename {subfun => src/subfun}/createTaskName.m (100%)
 rename {subfun => src/subfun}/initializeExtraColumns.m (100%)
 rename {subfun => src/subfun}/returnHeaderName.m (100%)
 rename {subfun => src/subfun}/returnNamesExtraColumns.m (100%)
 rename {subfun => src/subfun}/returnNbColumns.m (100%)
 rename {subfun => src/subfun}/setDefaultFields.m (100%)
 rename {subfun => src/subfun}/transferInfoToBids.m (100%)
 rename userInputs.m => src/userInputs.m (100%)
 delete mode 100644 tests/checkSubFields.m
 delete mode 100644 tests/returnExpectedCfgStructure.m

diff --git a/.github/workflows/moxunit.yml b/.github/workflows/moxunit.yml
index e426698f..16a9ee9c 100644
--- a/.github/workflows/moxunit.yml
+++ b/.github/workflows/moxunit.yml
@@ -19,11 +19,13 @@ jobs:
       uses: joergbrech/moxunit-action@v1.1
       with:
         tests: tests
+        src: src
         with_coverage: true
         cover_xml_file: coverage.xml
     - name: Code coverage
       uses: codecov/codecov-action@v1
       with:
+       token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
        file:  coverage.xml # optional
        flags: unittests # optional
        name: codecov-umbrella # optional
diff --git a/.gitignore b/.gitignore
index fef67417..51fd1392 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,7 +6,9 @@
 *octave-workspace
 
 # exclude content of logfiles folders
-output/**
+tests/output/*
+manualTests/output/*
+output/*
 *.tsv
 *.mat
 
diff --git a/.travis.yml b/.travis.yml
index 51fdee5e..16d3b453 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -29,8 +29,10 @@ install:
   - sudo npm install -g bids-validator
 
 before_script:
+  # Add to src functions to path
+  - octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath ();"
   # Change current directory
-  - cd tests
+  - cd manualTests
 
 jobs:
   include:
@@ -39,7 +41,7 @@ jobs:
     #   script: octave $OCTFLAGS --eval "results = runTests; assert(all(~[results.Failed]))"
     - stage: "BIDS validator"
       name: "Create and check dataset"
-      script: cd manualTests && octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
+      script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
     - stage: "Linter"
       name: "miss_hit"
       script: cd .. && mh_style `pwd`
diff --git a/checkCppBidsDependencies.m b/checkCppBidsDependencies.m
deleted file mode 100644
index aef02a1a..00000000
--- a/checkCppBidsDependencies.m
+++ /dev/null
@@ -1,27 +0,0 @@
-function checkCppBidsDependencies(cfg)
-    % checkCppBidsDependencies()
-    %
-
-    pth = fileparts(mfilename('fullpath'));
-
-    checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
-    checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
-
-    addpath(fullfile(pth, 'lib', 'utils'));
-    addpath(fullfile(pth, 'subfun'));
-
-    printCreditsCppBids(cfg);
-
-end
-
-function checkSubmodule(pth)
-    % If external dir is empty throw an exception
-    % and ask user to update submodules.
-    if numel(dir(pth)) <= 2 % Means that the external is empty
-        error(['Git submodules are not cloned!', ...
-              'Try this in your terminal:', ...
-              ' git submodule update --recursive ']);
-    else
-        addpath(pth);
-    end
-end
diff --git a/tests/manualTests/miss_hit.cfg b/manualTests/miss_hit.cfg
similarity index 100%
rename from tests/manualTests/miss_hit.cfg
rename to manualTests/miss_hit.cfg
diff --git a/tests/testData/eventsDataDictionary.json b/manualTests/testData/eventsDataDictionary.json
similarity index 100%
rename from tests/testData/eventsDataDictionary.json
rename to manualTests/testData/eventsDataDictionary.json
diff --git a/tests/test_createDataDictionary.m b/manualTests/test_createDataDictionary.m
similarity index 99%
rename from tests/test_createDataDictionary.m
rename to manualTests/test_createDataDictionary.m
index dc8f5ed2..d1f71138 100644
--- a/tests/test_createDataDictionary.m
+++ b/manualTests/test_createDataDictionary.m
@@ -13,9 +13,12 @@ function test_createDataDictionaryBasic()
     %% set up
 
     cfg.verbose = false;
+
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+
     cfg.task.name = 'testtask';
+
     cfg.dir.output = outputDir;
 
     cfg.testingDevice = 'mri';
@@ -32,6 +35,7 @@ function test_createDataDictionaryBasic()
 
     % data to test against
     funcDir = fullfile(outputDir, 'source', 'sub-001', 'ses-001', 'func');
+
     jsonFilename = ['sub-001_ses-001_task-testtask_run-001_events_date-' ...
         cfg.fileName.date '.json'];
 
diff --git a/tests/manualTests/test_makeRawDataset.m b/manualTests/test_makeRawDataset.m
similarity index 92%
rename from tests/manualTests/test_makeRawDataset.m
rename to manualTests/test_makeRawDataset.m
index e3ca4b3d..51b30262 100644
--- a/tests/manualTests/test_makeRawDataset.m
+++ b/manualTests/test_makeRawDataset.m
@@ -1,9 +1,5 @@
 function test_makeRawDataset()
 
-    fprintf('\n\n--------------------------------------------------------------------\n\n');
-
-    clear;
-
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
     if isdir(outputDir)
@@ -16,7 +12,9 @@ function test_makeRawDataset()
 
     cfg.subject.subjectNb = 1;
     cfg.subject.runNb = 1;
+
     cfg.task.name = 'testtask';
+
     cfg.dir.output = outputDir;
 
     cfg.bids.datasetDescription.Name = 'dummy';
@@ -77,7 +75,7 @@ function test_makeRawDataset()
     funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
     copyfile( ...
-        fullfile('..', '..', 'dummyData', 'dummyData.nii.gz'), ...
+        fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
 
     %%
diff --git a/tests/manualTests/test_userInput.m b/manualTests/test_userInput.m
similarity index 100%
rename from tests/manualTests/test_userInput.m
rename to manualTests/test_userInput.m
diff --git a/checkCFG.m b/src/checkCFG.m
similarity index 100%
rename from checkCFG.m
rename to src/checkCFG.m
diff --git a/src/checkCppBidsDependencies.m b/src/checkCppBidsDependencies.m
new file mode 100644
index 00000000..03dfd92f
--- /dev/null
+++ b/src/checkCppBidsDependencies.m
@@ -0,0 +1,39 @@
+function checkCppBidsDependencies(cfg)
+    % checkCppBidsDependencies()
+    %
+
+    GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE');
+
+    if strcmp(GITHUB_WORKSPACE, '/github/workspace')
+
+        pth = GITHUB_WORKSPACE;
+        addpath(fullfile(pth, 'lib', 'JSONio'));
+        addpath(fullfile(pth, 'lib', 'bids-matlab'));
+
+    elseif isempty(GITHUB_WORKSPACE)  % local
+
+        pth = fullfile(fileparts(mfilename('fullpath')), '..');
+        checkSubmodule(fullfile(pth, 'lib', 'JSONio'));
+        checkSubmodule(fullfile(pth, 'lib', 'bids-matlab'));
+
+        addpath(fullfile(pth, 'src', 'subfun'));
+
+    end
+
+    addpath(fullfile(pth, 'lib', 'utils'));
+
+    printCreditsCppBids(cfg);
+
+end
+
+function checkSubmodule(pth)
+    % If external dir is empty throw an exception
+    % and ask user to update submodules.
+    if numel(dir(pth)) <= 2 % Means that the external is empty
+        error(['Git submodules are not cloned!', ...
+            'Try this in your terminal:', ...
+            ' git submodule update --recursive ']);
+    else
+        addpath(pth);
+    end
+end
diff --git a/convertSourceToRaw.m b/src/convertSourceToRaw.m
similarity index 92%
rename from convertSourceToRaw.m
rename to src/convertSourceToRaw.m
index aad85f16..bc73606a 100644
--- a/convertSourceToRaw.m
+++ b/src/convertSourceToRaw.m
@@ -13,10 +13,10 @@ function convertSourceToRaw(cfg)
 
     % add dummy readme and change file
     copyfile(fullfile( ...
-        fileparts(mfilename('fullpath')), 'dummyData', 'README'), ...
+        fileparts(mfilename('fullpath')), '..', 'dummyData', 'README'), ...
         sourceDir);
     copyfile(fullfile( ...
-        fileparts(mfilename('fullpath')), 'dummyData', 'CHANGES'), ...
+        fileparts(mfilename('fullpath')), '..', 'dummyData', 'CHANGES'), ...
         sourceDir);
 
     copyfile(sourceDir, rawDir);
diff --git a/createBoldJson.m b/src/createBoldJson.m
similarity index 100%
rename from createBoldJson.m
rename to src/createBoldJson.m
diff --git a/createDataDictionary.m b/src/createDataDictionary.m
similarity index 100%
rename from createDataDictionary.m
rename to src/createDataDictionary.m
diff --git a/createDatasetDescription.m b/src/createDatasetDescription.m
similarity index 100%
rename from createDatasetDescription.m
rename to src/createDatasetDescription.m
diff --git a/createFilename.m b/src/createFilename.m
similarity index 100%
rename from createFilename.m
rename to src/createFilename.m
diff --git a/src/miss_hit.cfg b/src/miss_hit.cfg
new file mode 100644
index 00000000..fce7fa45
--- /dev/null
+++ b/src/miss_hit.cfg
@@ -0,0 +1,3 @@
+line_length: 100
+regex_function_name: "[a-z]+(([A-Z]){1}[A-Za-z]+)*"
+suppress_rule: "copyright_notice"
\ No newline at end of file
diff --git a/printCreditsCppBids.m b/src/printCreditsCppBids.m
similarity index 100%
rename from printCreditsCppBids.m
rename to src/printCreditsCppBids.m
diff --git a/saveEventsFile.m b/src/saveEventsFile.m
similarity index 100%
rename from saveEventsFile.m
rename to src/saveEventsFile.m
diff --git a/subfun/createTaskName.m b/src/subfun/createTaskName.m
similarity index 100%
rename from subfun/createTaskName.m
rename to src/subfun/createTaskName.m
diff --git a/subfun/initializeExtraColumns.m b/src/subfun/initializeExtraColumns.m
similarity index 100%
rename from subfun/initializeExtraColumns.m
rename to src/subfun/initializeExtraColumns.m
diff --git a/subfun/returnHeaderName.m b/src/subfun/returnHeaderName.m
similarity index 100%
rename from subfun/returnHeaderName.m
rename to src/subfun/returnHeaderName.m
diff --git a/subfun/returnNamesExtraColumns.m b/src/subfun/returnNamesExtraColumns.m
similarity index 100%
rename from subfun/returnNamesExtraColumns.m
rename to src/subfun/returnNamesExtraColumns.m
diff --git a/subfun/returnNbColumns.m b/src/subfun/returnNbColumns.m
similarity index 100%
rename from subfun/returnNbColumns.m
rename to src/subfun/returnNbColumns.m
diff --git a/subfun/setDefaultFields.m b/src/subfun/setDefaultFields.m
similarity index 100%
rename from subfun/setDefaultFields.m
rename to src/subfun/setDefaultFields.m
diff --git a/subfun/transferInfoToBids.m b/src/subfun/transferInfoToBids.m
similarity index 100%
rename from subfun/transferInfoToBids.m
rename to src/subfun/transferInfoToBids.m
diff --git a/userInputs.m b/src/userInputs.m
similarity index 100%
rename from userInputs.m
rename to src/userInputs.m
diff --git a/tests/checkSubFields.m b/tests/checkSubFields.m
deleted file mode 100644
index a6b8cb7e..00000000
--- a/tests/checkSubFields.m
+++ /dev/null
@@ -1,29 +0,0 @@
-function checkSubFields(expectedStructure, cfg)
-    % check that that the structures match
-    % if it fails it check from which subfield the error comes from
-
-    try
-
-        assertEqual(expectedStructure, cfg);
-
-    catch ME
-
-        if isstruct(expectedStructure)
-
-            names = fieldnames(expectedStructure);
-
-            for i = 1:numel(names)
-
-                disp(names{i});
-                testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
-
-            end
-
-        end
-
-        disp(expectedStructure);
-        disp(cfg);
-
-        rethrow(ME);
-    end
-end
diff --git a/tests/returnExpectedCfgStructure.m b/tests/returnExpectedCfgStructure.m
deleted file mode 100644
index 749338ae..00000000
--- a/tests/returnExpectedCfgStructure.m
+++ /dev/null
@@ -1,48 +0,0 @@
-function expectedCfgStructure = returnExpectedCfgStructure()
-
-    expectedCfgStructure.subject.subjectGrp = '';
-    expectedCfgStructure.subject.sessionNb = 1;
-    expectedCfgStructure.subject.askGrpSess = [true true];
-
-    expectedCfgStructure.verbose = 0;
-
-    expectedCfgStructure.fileName.task = '';
-    expectedCfgStructure.fileName.zeroPadding = 3;
-    expectedCfgStructure.fileName.dateFormat = 'yyyymmddHHMM';
-
-    expectedCfgStructure.eyeTracker.do = false;
-
-    expectedCfgStructure.mri.contrastEnhancement = [];
-    expectedCfgStructure.mri.phaseEncodingDirection = [];
-    expectedCfgStructure.mri.reconstruction = [];
-    expectedCfgStructure.mri.echo = [];
-    expectedCfgStructure.mri.acquisition = [];
-    expectedCfgStructure.mri.repetitionTime = [];
-
-    expectedCfgStructure.bids.mri.RepetitionTime = [];
-    expectedCfgStructure.bids.mri.SliceTiming = '';
-    expectedCfgStructure.bids.mri.TaskName = '';
-    expectedCfgStructure.bids.mri.Instructions = '';
-    expectedCfgStructure.bids.mri.TaskDescription = '';
-
-    expectedCfgStructure.bids.meg.TaskName = '';
-    expectedCfgStructure.bids.meg.SamplingFrequency = [];
-    expectedCfgStructure.bids.meg.PowerLineFrequency = [];
-    expectedCfgStructure.bids.meg.DewarPosition = [];
-    expectedCfgStructure.bids.meg.SoftwareFilters = [];
-    expectedCfgStructure.bids.meg.DigitizedLandmarks = [];
-    expectedCfgStructure.bids.meg.DigitizedHeadPoints = [];
-
-    expectedCfgStructure.bids.datasetDescription.Name = '';
-    expectedCfgStructure.bids.datasetDescription.BIDSVersion =  '';
-    expectedCfgStructure.bids.datasetDescription.License = '';
-    expectedCfgStructure.bids.datasetDescription.Authors = {''};
-    expectedCfgStructure.bids.datasetDescription.Acknowledgements = '';
-    expectedCfgStructure.bids.datasetDescription.HowToAcknowledge = '';
-    expectedCfgStructure.bids.datasetDescription.Funding = {''};
-    expectedCfgStructure.bids.datasetDescription.ReferencesAndLinks = {''};
-    expectedCfgStructure.bids.datasetDescription.DatasetDOI = '';
-
-    expectedCfgStructure = orderfields(expectedCfgStructure);
-
-end
diff --git a/tests/test_checkCFG.m b/tests/test_checkCFG.m
index 80656a23..f82a1171 100644
--- a/tests/test_checkCFG.m
+++ b/tests/test_checkCFG.m
@@ -76,3 +76,82 @@ function test_checkCfgBasic()
     checkSubFields(expectedStructure, cfg);
 
 end
+
+function expectedCfgStructure = returnExpectedCfgStructure()
+
+    expectedCfgStructure.subject.subjectGrp = '';
+    expectedCfgStructure.subject.sessionNb = 1;
+    expectedCfgStructure.subject.askGrpSess = [true true];
+
+    expectedCfgStructure.verbose = 0;
+
+    expectedCfgStructure.fileName.task = '';
+    expectedCfgStructure.fileName.zeroPadding = 3;
+    expectedCfgStructure.fileName.dateFormat = 'yyyymmddHHMM';
+
+    expectedCfgStructure.eyeTracker.do = false;
+
+    expectedCfgStructure.mri.contrastEnhancement = [];
+    expectedCfgStructure.mri.phaseEncodingDirection = [];
+    expectedCfgStructure.mri.reconstruction = [];
+    expectedCfgStructure.mri.echo = [];
+    expectedCfgStructure.mri.acquisition = [];
+    expectedCfgStructure.mri.repetitionTime = [];
+
+    expectedCfgStructure.bids.mri.RepetitionTime = [];
+    expectedCfgStructure.bids.mri.SliceTiming = '';
+    expectedCfgStructure.bids.mri.TaskName = '';
+    expectedCfgStructure.bids.mri.Instructions = '';
+    expectedCfgStructure.bids.mri.TaskDescription = '';
+
+    expectedCfgStructure.bids.meg.TaskName = '';
+    expectedCfgStructure.bids.meg.SamplingFrequency = [];
+    expectedCfgStructure.bids.meg.PowerLineFrequency = [];
+    expectedCfgStructure.bids.meg.DewarPosition = [];
+    expectedCfgStructure.bids.meg.SoftwareFilters = [];
+    expectedCfgStructure.bids.meg.DigitizedLandmarks = [];
+    expectedCfgStructure.bids.meg.DigitizedHeadPoints = [];
+
+    expectedCfgStructure.bids.datasetDescription.Name = '';
+    expectedCfgStructure.bids.datasetDescription.BIDSVersion =  '';
+    expectedCfgStructure.bids.datasetDescription.License = '';
+    expectedCfgStructure.bids.datasetDescription.Authors = {''};
+    expectedCfgStructure.bids.datasetDescription.Acknowledgements = '';
+    expectedCfgStructure.bids.datasetDescription.HowToAcknowledge = '';
+    expectedCfgStructure.bids.datasetDescription.Funding = {''};
+    expectedCfgStructure.bids.datasetDescription.ReferencesAndLinks = {''};
+    expectedCfgStructure.bids.datasetDescription.DatasetDOI = '';
+
+    expectedCfgStructure = orderfields(expectedCfgStructure);
+
+end
+
+function checkSubFields(expectedStructure, cfg)
+    % check that that the structures match
+    % if it fails it check from which subfield the error comes from
+
+    try
+
+        assertEqual(expectedStructure, cfg);
+
+    catch ME
+
+        if isstruct(expectedStructure)
+
+            names = fieldnames(expectedStructure);
+
+            for i = 1:numel(names)
+
+                disp(names{i});
+                testSubFields(expectedStructure.(names{i}), cfg.(names{i}));
+
+            end
+
+        end
+
+        disp(expectedStructure);
+        disp(cfg);
+
+        rethrow(ME);
+    end
+end