Merge pull request #221 from cpp-lln-lab/dev

[REL] 2.2.0

Author: Remi-Gau

.all-contributorsrc

@@ -7,7 +7,7 @@
   "contributors": [
     {
       "login": "CerenB",
-      "name": "CerenB",
+      "name": "Ceren Battal",
       "avatar_url": "https://avatars1.githubusercontent.com/u/10451654?v=4",
       "profile": "https://github.com/CerenB",
       "contributions": [
@@ -21,7 +21,7 @@
     },
     {
       "login": "marcobarilari",
-      "name": "marcobarilari",
+      "name": "Marco Barilari",
       "avatar_url": "https://avatars3.githubusercontent.com/u/38101692?v=4",
       "profile": "https://github.com/marcobarilari",
       "contributions": [
@@ -64,7 +64,7 @@
     },
     {
       "login": "iqrashahzad14",
-      "name": "iqrashahzad14",
+      "name": "Iqra Shahzad",
       "avatar_url": "https://avatars.githubusercontent.com/u/75671348?v=4",
       "profile": "https://github.com/iqrashahzad14",
       "contributions": [

.github/dependabot.yml

@@ -1,4 +1,3 @@
-
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2

.github/release-drafter.yml

@@ -0,0 +1,5 @@
+template: |
+  ## Release Notes
+
+  ## CHANGES
+  $CHANGES

.github/workflows/bids_validator.yml

@@ -2,23 +2,26 @@ name: BIDS validator
 
 on:
   push:
-    branches:
-      - master
+    branches: ['master', 'main', 'dev']
   pull_request:
-    branches: ['master']
+    branches: ['*']
 
 env:
   OCTFLAGS: --no-gui --no-window-system --silent
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
 
+    - uses: actions/setup-node@v3
+      with:
+        node-version: '14'
+
     - uses: actions/checkout@v3
       with:
         submodules: true
-        fetch-depth: 1
+        fetch-depth: 0
 
     - name: Make jsonread for octave
       run: |
@@ -37,9 +40,10 @@ jobs:
 
     - name: Install BIDS validator
       run: |
-        sudo npm install -g bids-validator@1.6.2
+        sudo npm install -g bids-validator
 
     - name: Create dummy dataset and validate it
       run: |
         cd tests/manualTests
-        octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
+        octave $OCTFLAGS --eval "test_makeRawDataset"
+        bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders

.github/workflows/check_md_links.yml

@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: ['*']
 

.github/workflows/miss_hit.yml

@@ -10,7 +10,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
 
     - uses: actions/checkout@v3
@@ -27,11 +27,11 @@ jobs:
         mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
 
     - name: MOxUnit Action
-      uses: joergbrech/moxunit-action@master
+      uses: joergbrech/moxunit-action@v1.2.0
       with:
         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)
+        ext: tests/utils lib # 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/run_tests.yml

@@ -1,42 +1,77 @@
 # exclude mac file
 *DS_Store
 
-# exclude matlab autosaves and octave workspace info
-*.m~
-*octave-workspace
-
 # exclude content of logfiles folders
-*output*
+output
+
 *.mat
 
 # exclude temp files from tests and coverage
 *test_code_report.txt
+test_report.log
 *coverage*
+check_my_code_report.txt
 
 *filteredBy*
 
 tests/*.nii*
 tests/*.json*
 tests/*.tsv*
 
-# exclude report from check_my_code
-check_my_code_report.txt
+*_cfg.json
 
 # jupyter notebook checkpoints
-notebooks/.ipynb_checkpoints/*
+.ipynb_checkpoints
 notebooks/source/*
-notebooks/output/*
 notebooks/new_experiment/*
 
 # ignore node js files
-node_modules/*
+node_modules
+package.json
 package-lock.json
 
 # visual studio code stuff
 .vscode
 
 # virtual env
 cpp_bids/*
+env
 
 # documentation
 docs/build/*
+
+## MATLAB / OCTAVE gitignore template
+
+# From : https://github.com/github/gitignore/blob/master/Global/MATLAB.gitignore
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace

.github/workflows/update_submodules.yml

@@ -1,7 +1,7 @@
 [submodule "lib/bids-matlab"]
 	path = lib/bids-matlab
 	url = https://github.com/bids-standard/bids-matlab.git
-	branch = master
+	branch = dev
 [submodule "lib/JSONio"]
 	path = lib/JSONio
 	url = https://github.com/gllmflndn/JSONio.git