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* Add container example and more docs

* Fix annotation for qwidget

* Fix some tests

* Fix import

* Update precommit stuff

* Add container test

* Sort imports

* Document the test

* Threshold on checkbox changed

* Fix test

* Rename some functions and cast images as float before thresholding

* Add a bit more detail to the docstring

* Try to fix precommit

* Remove whitespace...

* Add float to autogenerate test

* Remove unused import

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Cookiecutter template for authoring (npe2-based) napari plugins.

NOTE: This repo is not meant to be cloned/forked directly! Please read "Getting Started" below

Getting Started

Create your plugin package

Install Cookiecutter and generate a new napari plugin project:

pip install cookiecutter

Cookiecutter prompts you for information regarding your plugin (A new folder will be created in your current working directory):

full_name [Napari Developer]: Ramon y Cajal
email []:
github_username_or_organization [githubuser]: neuronz52
# NOTE: for packages whose primary purpose is to be a napari plugin, we
# recommend using the 'napari-' prefix in the package name.
# If your package provides functionality outside of napari, you may
# choose to leave napari out of the name.
plugin_name [napari-foobar]: napari-growth-cone-finder
Select github_repository_url:
1 -
2 - provide later
Choose from 1, 2 [1]:
module_name [growth_cone_finder]: napari_growth_cone_finder
display_name [napari FooBar]: Growth Cone Finder
short_description [A simple plugin to use with napari]:
# you can select from various plugin template examples
include_reader_plugin [y]:
include_writer_plugin [y]:
include_sample_data_plugin [y]:
include_dock_widget_plugin [y]:
use_git_tags_for_versioning [n]:
Select license:
1 - BSD-3
2 - MIT
3 - Mozilla Public License 2.0
4 - Apache Software License 2.0
5 - GNU LGPL v3.0
6 - GNU GPL v3.0
Choose from 1, 2, 3, 4, 5, 6 (1, 2, 3, 4, 5, 6) [1]:

You just created a minimal napari plugin, complete with tests and ready for automatic deployment!

For more detailed information on each prompt see the prompts reference.

├── .github
│   └── workflows
│      └── test_and_deploy.yml
├── napari_growth_cone_finder
│   ├──
│   ├──
│   ├──
│   ├── napari.yaml
│   └── _tests
│       ├──
│       ├──
│       └──
├── pyproject.toml
├── setup.cfg
└── tox.ini

Initialize a git repository in your package

NOTE: This is important not only for version management, but also if you want to pip install your package locally for testing with pip install -e .. (because the version of your package is managed using git tags, see below)

cd napari-growth-cone-finder
git init
git add .
git commit -m 'initial commit'

Upload it to github

  1. Create a new github repository

  2. Add your newly created github repo as a remote and push:

    # here, continuing with the example above...
    # but replace with your own username and repo name
    git remote add origin
    git push -u origin main

Monitor testing and coverage

The repository should already be setup to run your tests each time you push an update (configuration is in .github/workflows/test_and_deploy.yml). You can monitor them in the "Actions" tab of your github repository. If you're following along, go have a look... they should be running right now!

When the tests are done, test coverage will be viewable at (assuming your repository is public):<your-github-username>/<your-package-name>

You will need to enable the codecov github app for this to work. See here to install the codecov github app and give it access to your napari plugin repository.

Set up automatic deployments

Your new package is also nearly ready to automatically deploy to PyPI (whenever you create a tagged release), so that your users can simply pip install your package. You just need to create an API token to authenticate with PyPi, and then add it to your github repository:

  1. If you don't already have one, create an account at PyPI
  2. Verify your email address with PyPI, (if you haven't already)
  3. Generate an API token at PyPi: In your account settings go to the API tokens section and select "Add API token". Make sure to copy it somewhere safe!
  4. Create a new encrypted secret" in your github repository with the name "TWINE_API_KEY", and paste in your API token.

You are now setup for automatic deployment!

Automatic deployment and version management

Each time you want to deploy a new version, you just need to create a tagged commit, and push it to your main branch on github. Your package is set up to use setuptools_scm for version management, meaning you don't need to hard-code your version anywhere in your package. It will be inferred from the tag each time you release.

# the tag will be used as the version string for your package
# make it meaningful:
git tag -a v0.1.0 -m "v0.1.0"

# make sure to use follow-tags so that the tag also gets pushed to github
git push --follow-tags

Note: as of git 2.4.1, you can set follow-tags as default with git config --global push.followTags true

Monitor the "actions" tab on your github repo for progress... and when the "deploy" step is finished, your new version should be visible on pypi:<your-package-name>/

and available for pip install with:

# for example
pip install napari-growth-cone-finder

Running tests locally

Tests are automatically setup to run on github when you push to your repository.

You can run your tests locally with pytest. You'll need to make sure that your package is installed in your environment, along with testing requirements (specified in the setup.cfg extras_require section):

pip install -e ".[testing]"

Create your documentation

Documentation generation is not included in this template. We recommend following the getting started guides for one of the following documentation generation tools:

  1. Sphinx
  2. MkDocs
  3. JupyterBook


This template includes a default yaml configuration for pre-commit. Among other things, it includes checks for best practices in napari plugins. You may edit the config at .pre-commit-config.yaml

To use it run:

pip install pre-commit
pre-commit install

You can also have these checks run automatically for you when you push to github by installing pre-commit ci on your repository.



Please consult the napari plugin docs for more information on how to create a plugin.

Details on why this plugin template is using the src layout can be found here and here


If you encounter any problems with this cookiecutter template, please file an issue along with a detailed description.


Distributed under the terms of the BSD-3 license, cookiecutter-napari-plugin is free and open source software.