This document describes how to contribute to the napari-imagej source.
If your goal is only to use napari-imagej to call ImageJ ecosystem routines in napari, see this page.
Configuring a Mamba environment for development
napari-imagej requires Java and Python components, and as such we highly recommend contributors use virtual environments to manage their development environment
The first step towards development is installing napari-imagej from source. With Mamba, this is particularly easy.
git clone https://github.com/imagej/napari-imagej cd napari-imagej mamba env create -f dev-environment.yml
This virtual environment must then be activated to work on the napari-imagej source:
mamba activate napari-imagej-dev
napari-imagej uses pytest to automate testing. By installing the developement environment above,
pytest will come installed.
To test napari-imagej, simply run:
napari-imagej uses Read the Docs for user-facing documentation. If you make front-end changes to napari-imagej, please describe your changes with the files in the
doc folder of the napari-imagej source.
Once you’ve made your changes, run the following:
This will build the documentation into HTML files locally, stored in the
doc/_build/html folder. You can then view the documentation locally by loading
doc/_build/html/index.html in the browser of your choice.
Production documentation is available online at https://napari-imagej.readthedocs.io/
black, flake8, and isort are used to lint and standardize the napari-imagej source.
To manually format the source, run (MacOS/Linux):
napari-imagej also includes pre-commit configuration for those who want it. By using pre-commit, staged changes will be formatted before they can be commited to a repository. pre-commit can be set up using:
Building distribution bundles
You can run the following to bundle napari-imagej (MacOS/Linux):