Merge pull request #157 from cpp-lln-lab/release_candidate_2.0

Release candidate 2.0

.gitattributes

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

.github/workflows/check_markdown.yml

@@ -0,0 +1,34 @@
+name: Check Markdown
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - uses: actions/setup-node@v2
+      with:
+        node-version: '10'
+
+    - name: Install dependencies and check markdown
+      run: |
+        npm install `cat npm-requirements.txt`
+        npx remark README.md --frail  
+        npx remark ./notebooks/ --frail
+        npx remark ./tests/ --frail
+        npx remark ./docs/ --frail
+
+

.github/workflows/check_md_links.yml

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

.github/workflows/miss_hit.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - dev
   pull_request:
     branches: '*'
 
@@ -28,12 +27,16 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        pip3 install install miss_hit
+        pip3 install -r requirements.txt
 
-    - name: Miss_hit code quality
+    - name: MISS_HIT Code style
       run: |
-        mh_metric . --ci
+        mh_style --process-slx
 
-    - name: Miss_hit code style
+    - name: MISS_HIT Metrics
       run: |
-        mh_style .
+        mh_metric --ci
+
+    - name: MISS_HIT Bug finder
+      run: |
+        mh_lint

.github/workflows/moxunit.yml

@@ -1,27 +1,40 @@
-name: CI
+name: MOxUnit
 
 on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches: '*'
 
 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/moxunit-action@v1.1
       with:
         tests: tests
         src: src
         with_coverage: true
         cover_xml_file: coverage.xml
+
     - name: Code coverage
       uses: codecov/codecov-action@v1
       with:

.gitignore

@@ -23,8 +23,20 @@ tests/*.tsv*
 check_my_code_report.txt
 
 # jupyter notebook checkpoints
-.ipynb_checkpoints
-*/.ipynb_checkpoints/*
+notebooks/.ipynb_checkpoints/*
+notebooks/source/*
+notebooks/output/*
+notebooks/new_experiment/*
 
+# ignore node js files
+node_modules/*
+package-lock.json
 
+# visual studio code stuff
+.vscode
 
+# virtual env
+cpp_bids/*
+
+# documentation
+docs/build/*

.readthedocs.yml

@@ -0,0 +1,26 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  builder: html
+  fail_on_warning: true
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements.txt

.travis.yml

@@ -3,17 +3,12 @@
 # have set it up to run continuous integration on this this repo
 
 # Linux distribution (bionic beaver)
-dist: bionic
+dist: focal
 
 # Language and version
 language: node_js
 node_js:
-  - "10"
-
-cache:
-  apt: true # only works with Pro version
-  directories:
-  - node_modules # NPM packages for the remark markdown linter
+  - "11"
 
 branches:
   only:  # only run the CI for those branches 
@@ -33,7 +28,7 @@ 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 bids-validator@1.5.4
+  - sudo npm install -g bids-validator@1.5.7
 
 install:
   # make octave file the JSONio submodule
@@ -51,12 +46,3 @@ jobs:
 
     - name: "BIDS validator: create and check dataset"
       script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
-
-    - name: "Check markdown"
-      before_script:
-        - npm install `cat npm-requirements.txt`
-      script:
-        - remark README.md --frail
-        - remark ./notebooks/ --frail
-        - remark ./tests/ --frail
-        - remark ./docs/ --frail

.zenodo.json

@@ -0,0 +1,35 @@
+{
+  "title": "CPP_BIDS",
+  "description": "A lightweight Octave/MATLAB toolbox to help create BIDS data sets from source.",
+  "creators": [
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Gau, Rémi",
+      "orcid": "0000-0002-1535-9767"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Barilari, Marco",
+      "orcid": "0000-0002-3313-3120"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Battal, Ceren",
+      "orcid": "0000-0002-9844-7630"
+    },
+    {
+      "affiliation": "Université Catholique de Louvain",
+      "name": "Lenc, Thomas",
+      "orcid": "0000-0001-5796-1388"
+    }
+  ],
+  "keywords": [
+    "BIDS",
+    "brain imaging data structure",
+    "neuroscience",
+    "MATLAB",
+    "Octave"
+  ],
+  "license": "MIT license",
+  "upload_type": "software"
+}

README.md

@@ -4,6 +4,14 @@
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb)
 
+**Documentation**
+
+[![Documentation Status: stable](https://readthedocs.org/projects/cpp-bids/badge/?version=stable)](https://cpp-bids.readthedocs.io/en/stable/?badge=stable)
+
+**Cite it**
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4007674.svg)](https://doi.org/10.5281/zenodo.4007674)
+
 **Unit tests and coverage**
 
 [![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_BIDS/actions)
@@ -19,7 +27,7 @@
 
 [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
 
-* * *
+---
 
 # CPP_BIDS
 
@@ -44,42 +52,24 @@ A set of function for matlab and octave to create
 structure and filenames for the output of behavioral, EEG, fMRI, eyetracking
 studies.
 
-## Output format
-
-### Modality agnostic aspect
-
-Subjects, session and run number labels will be numbers with zero padding up to
-3 values (e.g subject 1 will become `sub-001`).
-
-A session folder will ALWAYS be created even if not requested (default will be
-`ses-001`).
-
-Task labels will be printed in camelCase in the filenames.
-
-Time stamps are added directly in the filename by adding a suffix
-`_date-YYYYMMDDHHMM` which makes the file name non-BIDS compliant. This was
-added to prevent overwriting files in case a certain run needs to be done a
-second time because of a crash (Some of us are paranoid about keeping even
-cancelled runs during my experiments). This suffix should be removed to make the
-data set BIDS compliant. See `convertSourceToRaw.m` for more details.
-
-For example:
-
-```bash
-sub-090/ses-003/sub-090_ses-003_task-auditoryTask_run-023_events_date-202007291536.tsv
-```
-
 ## Documentation
 
 -   [Installation](./docs/installation.md)
 -   [How to use it: jupyter notebooks](./notebooks)
--   [Functions description](./docs/functions-description.md)
+-   [General documentation](https://cpp-bids.readthedocs.io/en/dev/index.html)
 
 ## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.
 
-### Guidestyle
+If you want to contribute, have a look at our
+[contributing guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md)
+that are meant to guide you and help you get started. If something is not clear
+or you get stuck: it is more likely we did not do good enough a job at
+explaining things. So do not hesitate to open an issue, just to ask for
+clarification.
+
+### Style guide
 
 -   We use camelCase.
 
@@ -97,23 +87,31 @@ 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`
+```bash
+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]`
+```bash
+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`
+```bash
+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`
+```bash
+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)
 
@@ -132,14 +130,19 @@ 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>`
+
+```bash
+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`
+```bash
+<matches>[_recording-<label>]_physio.tsv.gz
+<matches>[_recording-<label>]_physio.json
+<matches>[_recording-<label>]_stim.tsv.gz
+<matches>[_recording-<label>]_stim.json
+```
 
 ### Change log
 
@@ -164,6 +167,7 @@ Thanks goes to these wonderful people
 
 <!-- markdownlint-enable -->
 <!-- prettier-ignore-end -->
+
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
 This project follows the