Merge tag 'v1.0.0'

Author: CerenB

.travis.yml

@@ -1,32 +1,39 @@
 # Travis CI (https://travis-ci.org/)
+# This will only work on your repo if you have an account on travis and you
+# have set it up to run continuous integration on this this repo
+
+# Linux distribution (bionic beaver)
+dist: bionic
+
+# Language and version
+language: python
+python:
+  - "3.6" # current default Python on Travis CI
 
-language: c
-dist: bionic # based on bionic beaver ubuntu distribution
 cache:
   apt: true # only works with Pro version
 
 env:
-  global: # define environment variables for bash
+  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
+  # Install octave
   - travis_retry sudo apt-get -y install octave
   - travis_retry sudo apt-get -y install liboctave-dev
-  # install javascript
+  # Install javascript node and node package manager necessary to run the validator
   - 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 BIDS-Validator
+  - sudo npm install -g bids-validator
+  # Install miss_hit linter
+  - pip3 install miss_hit
 
 install:
   # 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
@@ -36,11 +43,9 @@ before_script:
 
 jobs:
   include:
-    - stage: "BIDS validator"
-      name: "Create and check dataset"
+    - name: "BIDS validator: create and check dataset"
       script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/rawdata/ --ignoreNiftiHeaders
-    - stage: "Linter"
-      name: "miss_hit"
-      script: cd .. && mh_style `pwd`
-      
-    
+    - name: "miss_hit: checking code quality"
+      script: mh_metric . --ci
+    - name: "miss_hit: checking code style"
+      script: mh_style .

README.md

@@ -59,8 +59,7 @@ sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-2020072915
 ##  2. <a name='Documentation'></a>Documentation
 
 - [Installation](./docs/installation.md)
-- [How to use it](./docs/usage.md)
-- [Jupyter notebooks](./notebooks/README.md)
+- [How to use it: jupyter notebooks](./notebooks)
 - [Functions description](./docs/functions_description.md)
 
 ##  3. <a name='Contributing'></a>Contributing
@@ -77,6 +76,13 @@ Feel free to open issues to report a bug and ask for improvements.
 
 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`
+
 -   BOLD
 
 `sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]`
@@ -88,15 +94,37 @@ Here are the naming templates used.
 -   EEG
 
 `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)
+
+BrainVision Core Data Format (Each recording consisting of a .vhdr, .vmrk, .eeg file triplet)
+
+The format used by the MATLAB toolbox EEGLAB (Each recording consisting of a .set file with an optional .fdt file)
+
+Biosemi data format (Each recording consisting of a .bdf file) -->
+
+
 
 -   MEG
 
 ???
 
 -   Eyetracker
 
+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>`
 
+-   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`
+
 ###  3.3. <a name='Contributors'></a>Contributors ✨
 
 Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

docs/functions_description.md

@@ -5,8 +5,8 @@
 * 2. [createFilename](#createFilename)
 * 3. [saveEventsFile](#saveEventsFile)
 * 4. [checkCFG](#checkCFG)
-* 5. [CFG content](#CFGcontent)
-* 6. [createBoldJson](#createBoldJson)
+	* 4.1. [CFG content](#CFGcontent)
+* 5. [createBoldJson](#createBoldJson)
 
 <!-- vscode-markdown-toc-config
 	numbering=true
@@ -57,7 +57,7 @@ If the user DOES NOT provide `onset`, `trial_type`, this events will be skipped.
 
 Check that we have all the fields that we need in the experiment parameters.
 
-##  5. <a name='CFGcontent'></a>CFG content
+###  4.1. <a name='CFGcontent'></a>CFG content
 
 ```matlab
 % The following can be modified by users but their effect might
@@ -123,7 +123,7 @@ cfg.fileName.datasetDescription
 
 ```
 
-##  6. <a name='createBoldJson'></a>createBoldJson
+##  5. <a name='createBoldJson'></a>createBoldJson
 
 ```
 createBoldJson(cfg)

docs/usage.md

@@ -0,0 +1,11 @@
+*_beh.*
+*_eeg.*
+*_ieeg.*
+*_meg.*
+
+# *_beh.tsv
+# *_eeg.edf
+# *_ieeg.edf
+# *_meg.fif
+
+# *_bold.nii.gz

manualTests/dummyData/.bidsignore

@@ -1,3 +1,10 @@
+# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
-regex_function_name: "(test_[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
-suppress_rule: "copyright_notice"
+regex_function_name: "((test_[a-z]+)|[a-z]+)(([A-Z]){1}[A-Za-z]+)*"
+suppress_rule: "copyright_notice"
+
+# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
+metric "cnest": limit 4
+metric "file_length": limit 500
+metric "cyc": limit 15
+metric "parameters": limit 5

manualTests/miss_hit.cfg

@@ -1,12 +1,12 @@
-function test_suite = test_createBoldJson %#ok<*STOUT>
+function test_suite = test_createJson %#ok<*STOUT>
     try % assignment of 'localfunctions' is necessary in Matlab >= 2016
         test_functions = localfunctions(); %#ok<*NASGU>
     catch % no problem; early Matlab versions can use initTestSuite fine
     end
     initTestSuite;
 end
 
-function test_createBoldJsonExtra()
+function test_createJsonExtra()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
 
@@ -29,7 +29,7 @@ function test_createBoldJsonExtra()
 
     extraInfo = struct('extraInfo', struct('nestedExtraInfo', 'something extra'));
 
-    createBoldJson(cfg, extraInfo);
+    createJson(cfg, extraInfo);
 
     %% check content
     fileName = strrep(cfg.fileName.events, '_events', '_bold');