bids-standard / stats-models

BIDS Stats Models Specification

BIDS Stats Models Specification

This repository is intended to be the authoritative reference for the BIDS Stats Models specification. It consists of two parts:

1. bsmschema, a Pydantic description of the BIDS Stats Models files, which can be used as a schema validator or generate JSON schema for independent validation.
2. specification, a JupyterBook website that includes more human readable introductions and explanations, as well as a reference document for bsmschema.

Installing bsmschema

From the Python package index

pip install bsmschema

From source

git clone https://github.com/bids-standard/stats-models.git
pip install stats-models/bsmschema

You may wish to install in editable mode, to ensure that your changes get propagated without reinstalling:

pip install -e stats-models/bsmschema

How to run schema validator

from bsmschema.models import BIDSStatsModel
BIDSStatsModel.parse_file('stats-models/specification/examples/model-example_smdl.json')

Building the documentation locally

1. Install the requirements, including the local copy of bsmschema:

   pip install -r requirements.txt
   

2. Build the schema files to ensure the local validator will work:

   python -m bsmschema specification/schema
   

3. Build the JupyterBook:

   jb build specification
   

4. Serve the built website:

   python -m http.server -d specification/_build/html/
   

Note that this will start a long-running web-server that will occupy your terminal. Ctrl-C quits.