ChRIS Plugin Template

This is a minimal template repository for ChRIS plugin applications in Python.

About ChRIS Plugins

A ChRIS plugin is a scientific data-processing software which can run anywhere all-the-same: in the cloud via a web app, or on your own laptop from the terminal. They are easy to build and easy to understand: most simply, a ChRIS plugin is a command-line program which processes data from an input directory and creates data to an output directory with the usage commandname [options...] inputdir/ outputdir/.

For more information, visit our website https://chrisproject.org

How to Use This Template

Go to https://github.com/FNNDSC/python-chrisapp-template and click "Use this template". The newly created repository is ready to use right away.

A script bootstrap.sh is provided to help fill in and rename values for your new project. It is optional to use.

1. Edit the variables in bootstrap.sh
2. Run ./bootstrap.sh
3. Follow the instructions it will print out

Example Plugins

Here are some good, complete examples of ChRIS plugins created from this template.

• https://github.com/FNNDSC/pl-dcm2niix (basic command wrapper example)
• https://github.com/FNNDSC/pl-adapt_object_mesh (parallelizes a command)
• https://github.com/FNNDSC/pl-mri-preview (uses NiBabel)
• https://github.com/FNNDSC/pl-pyvista-volume (example using Python package project structure and pytest)
• https://github.com/FNNDSC/pl-fetal-cp-surface-extract (has a good README.md)

What's Inside

Path	Purpose
app.py	Main script: start editing here!
tests/	Unit tests
setup.py	Python project metadata and installation script
requirements.txt	List of Python dependencies
Dockerfile	Container image build recipe
.github/workflows/ci.yml	"continuous integration" using Github Actions: automatic testing, building, and uploads to https://chrisstore.co

Contributing

The source code for the main branch of this repository is on the src branch, which has an additional file .github/workflows/src.yml When tests pass, changes are automatically merged into main. Developers should commit to or make pull requests targeting src. Do not push directly to main.

This is a workaround in order to do automatic testing of this template without including the .github/workflows/src.yml file in the template itself.