Merge branch 'master' of https://github.com/cpp-lln-lab/CPP_BIDS

Author: Remi-Gau

.all-contributorsrc

@@ -61,6 +61,16 @@
         "ideas",
         "test"
       ]
+    },
+    {
+      "login": "iqrashahzad14",
+      "name": "iqrashahzad14",
+      "avatar_url": "https://avatars.githubusercontent.com/u/75671348?v=4",
+      "profile": "https://github.com/iqrashahzad14",
+      "contributions": [
+        "bug",
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/bids_validator.yml

@@ -0,0 +1,45 @@
+name: BIDS validator
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: ['master']
+
+env:
+  OCTFLAGS: --no-gui --no-window-system --silent
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Make jsonread for octave
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install octave
+        sudo apt-get -y install liboctave-dev
+        cd lib/JSONio
+        mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
+        cd ..
+
+    - name: Update octave path
+      run: |
+        octave $OCTFLAGS --eval "addpath(pwd); savepath();"
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'lib'))); savepath();"
+        octave $OCTFLAGS --eval "addpath(genpath(fullfile(pwd, 'src'))); savepath();"
+
+    - name: Install BIDS validator
+      run: |
+        sudo npm install -g bids-validator@1.6.2
+
+    - name: Create dummy dataset and validate it
+      run: |
+        cd tests/manualTests
+        octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders

.github/workflows/check_markdown.yml

@@ -7,11 +7,11 @@ on:
     branches:
       - master
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
-    - uses: gaurav-nelson/github-action-markdown-link-check@v1
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/check_md_links.yml

@@ -5,8 +5,7 @@ on:
     branches:
       - master
   pull_request:
-    branches: '*'
-
+    branches: ['*']
 jobs:
   build:
 

.github/workflows/miss_hit.yml

@@ -1,16 +1,16 @@
-name: MOxUnit
+name: tests and coverage
 
 on:
   push:
     branches:
       - master
       - dev
   pull_request:
-    branches: '*'
+    branches: ['*']
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
 
     - uses: actions/checkout@v2
@@ -21,17 +21,18 @@ jobs:
     - name: Make jsonread for octave
       run: |
         sudo apt-get -y -qq update
-        sudo apt-get -y install octave 
+        sudo apt-get -y install octave
         sudo apt-get -y install liboctave-dev
         cd lib/JSONio
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
-      # cd ../..
 
     - name: MOxUnit Action
-      uses: joergbrech/moxunit-action@v1.1
+      uses: joergbrech/moxunit-action@master
       with:
-        tests: tests
-        src: src
+        tests: tests # files or directories containing the MOxUnit test cases
+        src: src # directories to be added to the Octave search path before running the tests.
+        ext: tests/utils # External resources to add to the search put (excluded from coverage)
+        # data: # Directory for test data
         with_coverage: true
         cover_xml_file: coverage.xml
 

.github/workflows/moxunit.yml .github/workflows/run_tests.yml.github/workflows/moxunit.yml renamed to .github/workflows/run_tests.yml

@@ -0,0 +1,44 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_version
+      name: mh_version
+      entry: mh_style
+      args: [-v]
+      verbose: true
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    # - id: mh_style
+    #   name: mh_style
+    #   entry: mh_style
+    #   args: [--process-slx, --fix]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_metric
+    #   name: mh_metric
+    #   entry: mh_metric
+    #   args: [--ci]
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit_core]
+
+    # - id: mh_lint
+    #   name: mh_lint
+    #   entry: mh_lint
+    #   files: ^(.*\.(m|slx))$
+    #   language: python
+    #   additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.2.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

.pre-commit-config.yaml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt