reorganize for github actions

Author: Remi-Gau

.github/workflows/moxunit.yml

@@ -19,11 +19,13 @@ jobs:
       uses: joergbrech/[email protected]
       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

.gitignore

@@ -6,7 +6,9 @@
 *octave-workspace
 
 # exclude content of logfiles folders
-output/**
+tests/output/*
+manualTests/output/*
+output/*
 *.tsv
 *.mat
 

.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`

checkCppBidsDependencies.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'];
 

tests/manualTests/miss_hit.cfg renamed to manualTests/miss_hit.cfg

@@ -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));
 
     %%