Merge pull request #109 from Remi-Gau/dev

getting ready for a version bump: v1.1.0

.github/workflows/check_md_links.yml

@@ -0,0 +1,18 @@
+name: Check Markdown links
+
+# checking for any dead links in markdown files
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches: '*'
+
+jobs:
+  markdown-link-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - uses: gaurav-nelson/github-action-markdown-link-check@v1

.github/workflows/miss_hit.yml

@@ -0,0 +1,39 @@
+name: miss_hit
+
+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: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install install miss_hit
+
+    - name: Miss_hit code quality
+      run: |
+        mh_metric . --ci
+
+    - name: Miss_hit code style
+      run: |
+        mh_style .

.gitignore

@@ -7,13 +7,14 @@
 
 # exclude content of logfiles folders
 *output*
-*.tsv
 *.mat
 
 # exclude temp files from tests and coverage
 *test_code_report.txt
 *coverage*
 
+*filteredBy*
+
 tests/*.nii*
 tests/*.json*
 tests/*.tsv*

.prettierrc

@@ -0,0 +1,13 @@
+{
+  "parser": "markdown",
+  "proseWrap": "always",
+  "tabWidth": 2,
+  "overrides": [
+    {
+      "files": "*.md",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}

.remarkrc

@@ -0,0 +1,11 @@
+{
+  "plugins": [
+    "preset-lint-consistent",
+    "preset-lint-markdown-style-guide",
+    "preset-lint-recommended",
+    ["lint-no-duplicate-headings", false],
+    ["lint-list-item-indent", "tab-size"],
+    ["lint-maximum-line-length", true],
+    ["lint-maximum-heading-length", false]
+  ]
+}

.travis.yml

@@ -6,12 +6,19 @@
 dist: bionic
 
 # Language and version
-language: python
-python:
-  - "3.6" # current default Python on Travis CI
+language: node_js
+node_js:
+  - "10"
 
 cache:
   apt: true # only works with Pro version
+  directories:
+  - node_modules # NPM packages for the remark markdown linter
+
+branches:
+  only:  # only run the CI for those branches 
+  - master
+  - dev
 
 env:
   global: # Define environment variables for bash
@@ -26,9 +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 bids-validator
-  # Install miss_hit linter
-  - pip3 install miss_hit
+  - sudo npm install -g bids-validator@1.5.4
 
 install:
   # make octave file the JSONio submodule
@@ -43,9 +48,15 @@ before_script:
 
 jobs:
   include:
+
     - name: "BIDS validator: create and check dataset"
       script: octave $OCTFLAGS --eval "test_makeRawDataset" && bids-validator `pwd`/output/raw/ --ignoreNiftiHeaders
-    - name: "miss_hit: checking code quality"
-      script: mh_metric . --ci
-    - name: "miss_hit: checking code style"
-      script: mh_style .
+
+    - 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

README.md

@@ -1,11 +1,13 @@
+<!-- lint disable -->
+
 **Try it**
 
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb)
 
 **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)
-![](https://github.com/cpp-lln-lab/CPP_BIDS/workflows/CI/badge.svg) 
+![](https://github.com/cpp-lln-lab/CPP_BIDS/workflows/CI/badge.svg)
 
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS/branch/master/graph/badge.svg)](https://codecov.io/gh/cpp-lln-lab/CPP_BIDS)
 
@@ -15,64 +17,81 @@
 
 **Contributors**
 
-[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-) 
+[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)
+
+* * *
 
----
-
 # CPP_BIDS
 
-<!-- vscode-markdown-toc -->
-* 1. [Output format](#Outputformat)
-	* 1.1. [Modality agnostic aspect](#Modalityagnosticaspect)
-* 2. [Documentation](#Documentation)
-* 3. [Contributing](#Contributing)
-	* 3.1. [Guidestyle](#Guidestyle)
-	* 3.2. [BIDS naming convention](#BIDSnamingconvention)
-	* 3.3. [Contributors ✨](#Contributors)
+<!-- TOC -->
+
+-   [CPP_BIDS](#cpp_bids)
+-   [Output format](#output-format)
+    -   [Modality agnostic aspect](#modality-agnostic-aspect)
+-   [Documentation](#documentation)
+-   [Contributing](#contributing)
+    -   [Guidestyle](#guidestyle)
+    -   [BIDS naming convention](#bids-naming-convention)
+    -   [Change log](#change-log)
+    -   [Contributors ✨](#contributors-)
+
+<!-- /TOC -->
 
-<!-- vscode-markdown-toc-config
-	numbering=true
-	autoSave=true
-	/vscode-markdown-toc-config -->
-<!-- /vscode-markdown-toc -->
+<!-- lint enable -->
 
-A set of function for matlab and octave to create [BIDS-compatible](https://bids-specification.readthedocs.io/en/stable/) folder structure and filenames for the output of behavioral, EEG, fMRI, eyetracking studies.
+A set of function for matlab and octave to create
+[BIDS-compatible](https://bids-specification.readthedocs.io/en/stable/) folder
+structure and filenames for the output of behavioral, EEG, fMRI, eyetracking
+studies.
 
-##  1. <a name='Outputformat'></a>Output format
+## Output format
 
-###  1.1. <a name='Modalityagnosticaspect'></a>Modality agnostic aspect
+### 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`).
+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`).
+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.
+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
 ```
 
-##  2. <a name='Documentation'></a>Documentation
+## Documentation
 
-- [Installation](./docs/installation.md)
-- [How to use it: jupyter notebooks](./notebooks)
-- [Functions description](./docs/functions_description.md)
+-   [Installation](./docs/installation.md)
+-   [How to use it: jupyter notebooks](./notebooks)
+-   [Functions description](./docs/functions-description.md)
 
-##  3. <a name='Contributing'></a>Contributing
+## Contributing
 
 Feel free to open issues to report a bug and ask for improvements.
 
-###  3.1. <a name='Guidestyle'></a>Guidestyle
+### Guidestyle
 
 -   We use camelCase.
--   We keep the McCabe complexity as reported by the [check_my_code function](https://github.com/Remi-Gau/check_my_code) below 15.
--   We use the [MISS_HIT linter](https://florianschanda.github.io/miss_hit/style_checker.html) to automatically fix some linting issues.
 
-###  3.2. <a name='BIDSnamingconvention'></a>BIDS naming convention
+-   We keep the McCabe complexity as reported by the
+    [check_my_code function](https://github.com/Remi-Gau/check_my_code)
+    below 15.
+
+-   We use the
+    [MISS_HIT linter](https://florianschanda.github.io/miss_hit/style_checker.html)
+    to automatically fix some linting issues.
+
+### BIDS naming convention
 
 Here are the naming templates used.
 
@@ -104,16 +123,13 @@ The format used by the MATLAB toolbox EEGLAB (Each recording consisting of a .se
 
 Biosemi data format (Each recording consisting of a .bdf file) -->
 
-
-
 -   MEG
 
 ???
 
 -   Eyetracker
 
-current format
-`<matches>_recording-eyetracking_physio.tsv.gz`
+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>`
@@ -125,17 +141,21 @@ future BEP format in a dedicated eyetracker folder
 `<matches>[_recording-<label>]_stim.tsv.gz`
 `<matches>[_recording-<label>]_stim.json`
 
-### change log
+### Change log
 
  <!-- 93b4c584bf22883a3c4f8b9031b70e381deef272 -->
 
-###  3.3. <a name='Contributors'></a>Contributors ✨
+### Contributors ✨
 
-Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):
+Thanks goes to these wonderful people
+([emoji key](https://allcontributors.org/docs/en/emoji-key)):
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+
 <!-- prettier-ignore-start -->
+
 <!-- markdownlint-disable -->
+
 <table>
   <tr>
     <td align="center"><a href="https://github.com/CerenB"><img src="https://avatars1.githubusercontent.com/u/10451654?v=4" width="100px;" alt=""/><br /><sub><b>CerenB</b></sub></a><br /><a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Code">💻</a> <a href="#design-CerenB" title="Design">🎨</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/commits?author=CerenB" title="Documentation">📖</a> <a href="#userTesting-CerenB" title="User Testing">📓</a> <a href="#ideas-CerenB" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/cpp-lln-lab/CPP_BIDS/issues?q=author%3ACerenB" title="Bug reports">🐛</a></td>
@@ -145,7 +165,11 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 </table>
 
 <!-- markdownlint-enable -->
+
 <!-- prettier-ignore-end -->
+
 <!-- ALL-CONTRIBUTORS-LIST:END -->
 
-This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!
+This project follows the
+[all-contributors](https://github.com/all-contributors/all-contributors)
+specification. Contributions of any kind welcome!