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** [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/cpp-lln-lab/CPP_BIDS/master?filepath=notebooks%2Fbasic_usage.ipynb) +**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) @@ -17,34 +23,34 @@ [![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#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-