Contributing¶

Reporting Issues¶

Please open an issue on GitHub to report bugs or request features. Include:

The command you ran
Relevant log output (logs/preprocessing_log_*.txt or logs/dce_log_*.txt)
Your environment (Docker tag or local install details)

Branch Strategy¶

Branch	Purpose
`main`	Stable releases — Docker images tagged with `-main` are built from this branch
`dev`	Active development — new features and fixes land here first
Feature branches	Short-lived branches for individual features or fixes, branched from `dev`

To contribute:

Fork the repository
Create a feature branch from dev
Make your changes and push to your fork
Open a pull request targeting dev

Development Setup¶

Local environment¶

# Clone the repository
git clone https://github.com/petmri/DCEPrep.git
cd DCEPrep
git checkout dev

# Set up Python environment
python3 -m venv tf
source tf/bin/activate
pip install -r venv_requirements.txt

You will also need FSL, ANTs, FreeSurfer, and MATLAB installed locally (see Installation).

Running with Docker¶

For testing without a full local install, use the dev Docker image:

docker pull lsaca05/dce:R2023a-dev

CI/CD¶

The GitHub Actions workflow automatically clones the petmri/ROCKETSHIP dev branch and builds the Docker image. Check .github/workflows/ for the current CI configuration.

Building Docs Locally¶

pip install mkdocs-material mkdocs-minify-plugin
mkdocs serve

Then open http://127.0.0.1:8000 in a browser.