diff --git a/.travis.yml b/.travis.yml
index 338ab7c2..d5cfa910 100644
--- a/.travis.yml
+++ b/.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 bids-validator
+ - sudo npm install -g bids-validator@1.5.4
install:
# make octave file the JSONio submodule
@@ -56,4 +56,7 @@ jobs:
before_script:
- npm install `cat npm-requirements.txt`
script:
- - remark . --frail
+ - remark README.md --frail
+ - remark ./notebooks/ --frail
+ - remark ./tests/ --frail
+ - remark ./docs/ --frail
diff --git a/README.md b/README.md
index a54cff20..5280ce92 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,13 @@
+
+
**Try it**
[](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb)
+**Cite it**
+
+[](https://doi.org/10.5281/zenodo.4007674)
+
**Unit tests and coverage**
[](https://github.com/cpp-lln-lab/CPP_BIDS/actions)
@@ -17,34 +23,34 @@
[](#contributors-)
----
+* * *
# CPP_BIDS
-
+
-- 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)
+- [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-)
-
-
+
+
+
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. Output format
+## Output format
-### 1.1. 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`).
@@ -63,31 +69,33 @@ 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. Documentation
+## Documentation
- [Installation](./docs/installation.md)
- [How to use it: jupyter notebooks](./notebooks)
-- [Functions description](./docs/functions_description.md)
+- [Functions description](./docs/functions-description.md)
-## 3. Contributing
+## Contributing
Feel free to open issues to report a bug and ask for improvements.
-### 3.1. 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. BIDS naming convention
+### BIDS naming convention
Here are the naming templates used.
@@ -137,18 +145,21 @@ future BEP format in a dedicated eyetracker folder
`[_recording-