Merge pull request #112 from Remi-Gau/remi-update_bids_validation

update bids validator version in CI

Author: Remi-Gau

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.github/workflows/moxunit.yml

@@ -11,17 +11,29 @@ jobs:
   build:
     runs-on: ubuntu-latest
     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: 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:

.gitignore

@@ -31,4 +31,3 @@ node_modules/*
 package-lock.json
 
 
-

.travis.yml

@@ -33,7 +33,7 @@ before_install:
   - travis_retry sudo apt-get -y install nodejs
   - travis_retry sudo apt-get -y install npm
   # Install BIDS-Validator
-  - sudo npm install -g [email protected].4
+  - sudo npm install -g [email protected].6
 
 install:
   # make octave file the JSONio submodule

README.md

@@ -101,23 +101,31 @@ Here are the naming templates used.
 
 -   Behavior
 
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv`
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json`
+```
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.tsv
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_beh.json
+```
 
 -   BOLD
 
-`sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
+```
+sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+```
 
 -   iEEG
 
-`sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json`
+```
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
+```
 
 -   EEG
 
-`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>`
-`sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json`
+```
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json
+```
 
 <!-- European data format (Each recording consisting of a .edf file)
 
@@ -136,14 +144,19 @@ Biosemi data format (Each recording consisting of a .bdf file) -->
 current format `<matches>_recording-eyetracking_physio.tsv.gz`
 
 future BEP format in a dedicated eyetracker folder
-`sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>`
+
+```
+sub-<participant_label>[_ses-<label>][_acq-<label>]_task-<task_label>_eyetrack.<manufacturer_specific_extension>
+```
 
 -   Stim and physio
 
-`<matches>[_recording-<label>]_physio.tsv.gz`
-`<matches>[_recording-<label>]_physio.json`
-`<matches>[_recording-<label>]_stim.tsv.gz`
-`<matches>[_recording-<label>]_stim.json`
+```
+<matches>[_recording-<label>]_physio.tsv.gz
+<matches>[_recording-<label>]_physio.json
+<matches>[_recording-<label>]_stim.tsv.gz
+<matches>[_recording-<label>]_stim.json
+```
 
 ### Change log
 

manualTests/test_createDataDictionary.m

@@ -71,7 +71,14 @@ function test_makeRawDataset()
     saveEventsFile('close', cfg, logFile);
 
     % add dummy stim data
-    stimLogFile = saveEventsFile('open_stim', cfg, logFile);
+    stimLogFile.extraColumns.Speed.length = 1;
+    stimLogFile.extraColumns.LHL24.length = 3;
+    stimLogFile.extraColumns.is_Fixation.length = 1;
+
+    stimLogFile.SamplingFrequency = cfg.mri.repetitionTime;
+    stimLogFile.StartTime = 0;
+
+    stimLogFile = saveEventsFile('open_stim', cfg, stimLogFile);
     for i = 1:100
         stimLogFile(i, 1).onset = cfg.mri.repetitionTime * i;
         stimLogFile(i, 1).trial_type = 'test';