Set up MOxunit and MOcov

.github/workflows/moxunit.yml

@@ -0,0 +1,32 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+    - name: MOxUnit Action
+      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
+       fail_ci_if_error: true # optional (default = false)

.gitignore

@@ -1,14 +1,25 @@
-
+# exclude mac file
 *DS_Store
 
+# exclude matlab autosaves and octave workspace info
 *.m~
 *octave-workspace
 
 # exclude content of logfiles folders
+tests/output/*
+manualTests/output/*
+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
+
+
+
+

.travis.yml

@@ -29,17 +29,19 @@ 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:
-    - 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
+      script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
     - stage: "Linter"
       name: "miss_hit"
       script: cd .. && mh_style `pwd`

manualTests/test_createDataDictionary.m

@@ -0,0 +1,55 @@
+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
+
+function test_createDataDictionaryBasic()
+
+    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);
+
+    logFile.extraColumns.Speed.length = 1;
+    logFile.extraColumns.LHL24.length = 3;
+    logFile = saveEventsFile('init', cfg, logFile);
+
+    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-' ...
+        cfg.fileName.date '.json'];
+
+    % test
+    assertTrue(exist(fullfile(funcDir, jsonFilename), 'file') == 2);
+
+    %% check content
+    actualStruct = bids.util.jsondecode(fullfile(funcDir, jsonFilename));
+
+    % data to test against
+    expectedStruct = bids.util.jsondecode( ...
+        fullfile(pwd, 'testData', 'eventsDataDictionary.json'));
+
+    % test
+    assertTrue(isequal(expectedStruct, actualStruct));
+
+end

tests/manualTests/test_makeRawDataset.m → 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));
 
     %%

checkCFG.m → src/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
 
-    %% set the cfg defaults
+    checkCppBidsDependencies(cfg);
+
+    %% list the defaults to set
 
     fieldsToSet.verbose = false;
 
@@ -43,6 +43,7 @@
 
     fieldsToSet = transferInfoToBids(fieldsToSet, cfg);
 
+    %% Set defaults
     cfg = setDefaultFields(cfg, fieldsToSet);
 
 end

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

convertSourceToRaw.m → src/convertSourceToRaw.m

@@ -6,17 +6,17 @@ 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');
 
     % 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);

createFilename.m → src/createFilename.m

@@ -177,19 +177,23 @@
 
 function talkToMe(cfg)
 
-    fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
-        fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
+    if cfg.verbose
 
-    fprintf(1, '\nData will be saved in this file:\n\t%s\n', ...
-        cfg.fileName.events);
+        fprintf(1, '\nData will be saved in this directory:\n\t%s\n', ...
+            fullfile(cfg.dir.outputSubject, cfg.fileName.modality));
 
-    if cfg.eyeTracker.do
+        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 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);
+            fprintf(1, '\nEyetracking data will be saved in this file:\n\t%s\n', ...
+                cfg.fileName.eyetracker);
+
+        end
 
     end
 

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"