Merge remote-tracking branch 'cpp-lln-lab/master'

Author: CerenB

.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/[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
+       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

@@ -1,42 +1,47 @@
 # Travis CI (https://travis-ci.org/)
 
 language: c
-dist: bionic
+dist: bionic # based on bionic beaver ubuntu distribution
 cache:
   apt: true # only works with Pro version
 
 env:
-  global:
+  global: # define environment variables for bash
     - OCTFLAGS="--no-gui --no-window-system --silent"
 
 before_install:
   - travis_retry sudo apt-get -y -qq update
+  # install octave
   - travis_retry sudo apt-get -y install octave
   - travis_retry sudo apt-get -y install liboctave-dev
+  # install javascript
   - travis_retry sudo apt-get -y install nodejs
   - travis_retry sudo apt-get -y install npm
+  # install miss_hit linter
   - cd .. && git clone https://github.com/florianschanda/miss_hit.git && export PATH=$PATH:`pwd`/miss_hit && cd CPP_BIDS
 
 
 install:
-  # make octave file for JSONio
+  # make octave file the JSONio submodule
   - cd lib/JSONio; mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS; cd ../..
   - octave $OCTFLAGS --eval "addpath (pwd); savepath ();"
   # Install BIDS-Validator
   - 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`