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# cookiecutter-napari-plugin
# ⚠️ **OUTDATED DO NOT USE** ⚠️

[Cookiecutter] template for authoring ([npe2]-based) [napari] plugins.
## cookiecutter-napari-plugin

**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:

```bash
pip install cookiecutter
cookiecutter https://github.com/napari/cookiecutter-napari-plugin
```

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

```bash
full_name [Napari Developer]: Ramon y Cajal
email [[email protected]]: [email protected]
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 - https://github.com/neuronz52/napari-growth-cone-finder
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](./PROMPTS.md).

```no-highlight
napari-growth-cone-finder/
│
├── .github
│ └── workflows
│ └── test_and_deploy.yml
├── LICENSE
├── MANIFEST.in
├── napari_growth_cone_finder
│ ├── __init__.py
│ ├── _widget.py
│ ├── _reader.py
│ ├── napari.yaml
│   └── _tests
│   ├── __init__.py
│   ├── test_widget.py
│   └── test_reader.py
├── pyproject.toml
├── README.md
├── 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](#automatic-deployment-and-version-management))

```bash
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:

```bash
# here, continuing with the example above...
# but replace with your own username and repo name

git remote add origin https://github.com/neuronz52/napari-growth-cone-finder.git
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!

Currently, the timeout for these runs is set to 30 minutes to save resources. You can modify the settings if necessary. Here you can find information on [GitHub workflows](https://docs.github.com/en/actions/learn-github-actions) and the [timeout parameter](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idtimeout-minutes).

When the tests are done, test coverage will be viewable at
[codecov.io](https://codecov.io/) (assuming your repository is public):
`https://codecov.io/gh/<your-github-username>/<your-package-name>`

You will need to enable the [codecov](https://github.com/apps/codecov) github app
for this to work. See [here](https://github.com/apps/codecov/installations/new)
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](https://pypi.org/help/#apitoken), and then add it to your github
repository:

1. If you don't already have one, [create an
account](https://pypi.org/account/register/) at [PyPI]
2. Verify your email address with PyPI, (if you haven't already)
3. Generate an [API token](https://pypi.org/help/#apitoken) at PyPi: In your
[account settings](https://pypi.org/manage/account/) go to the API tokens
section and select "Add API token". Make sure to copy it somewhere safe!
4. [Create a new encrypted
secret](https://help.github.com/en/actions/configuring-and-managing-workflows/creating-and-storing-encrypted-secrets#creating-encrypted-secrets)"
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](https://github.com/pypa/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.

```bash
# the tag will be used as the version string for your package
# make it meaningful: https://semver.org/
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:

`https://pypi.org/project/<your-package-name>/`

and available for pip install with:

```bash
# 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](https://docs.pytest.org/en/7.1.x/).
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):

```bash
pip install -e ".[testing]"
pytest
```

### 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]

### Pre-commit

This template includes a default yaml configuration for [pre-commit](https://pre-commit.com/).
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:

```bash
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](https://pre-commit.ci/) on your repository.

## Dependabot

This template also includes a default yaml configuration for [Dependabot](https://docs.github.com/en/code-security/dependabot). This can help you check for security updates to easily update vulnerable dependencies.

You will still need to enable Dependabot in your github settings, [see the instructions at this link](https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/configuring-dependabot-security-updates#managing-dependabot-security-updates-for-your-repositories). Your Dependabot configuration file is located at `.github/dependabot.yml`.

## Features

- Installable [PyPI] package
- [tox] test suite, testing various python versions and platforms.
- `README.md` file that contains useful information about your plugin
- Continuous integration configuration for [github actions] that handles testing
and deployment of tagged releases
- git-tag-based version management with [setuptools_scm]
- Choose from several licenses, including [BSD-3], [MIT], [MPL v2.0], [Apache
v2.0], [GNU GPL v3.0], or [GNU LGPL v3.0]

## Resources

Please consult the [napari plugin
docs](https://napari.org/stable/plugins/index.html) for more information on
how to create a plugin.

Details on why this plugin template is using the `src` layout can be found [here](https://blog.ionelmc.ro/2014/05/25/python-packaging/#the-structure) and [here](https://hynek.me/articles/testing-packaging/)

## Issues

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

## License

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

[napari organization]: https://github.com/napari/
[gitter_badge]: https://badges.gitter.im/Join%20Chat.svg
[gitter]: https://gitter.im/napari/cookiecutter-napari-plugin?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge "Join Chat on Gitter.im"
[travis_badge]: https://travis-ci.org/napari/cookiecutter-napari-plugin.svg?branch=main
[travis]: https://travis-ci.org/napari/cookiecutter-napari-plugin "See Build Status on Travis CI"
[docs_badge]: https://readthedocs.org/projects/cookiecutter-napari-plugin/badge/?version=latest
[documentation]: https://cookiecutter-napari-plugin.readthedocs.io/en/latest/ "Documentation"
[cookiecutter]: https://github.com/audreyr/cookiecutter
[napari]: https://github.com/napari/napari
[npe2]: https://github.com/napari/npe2
[pypi]: https://pypi.org/
[tox]: https://tox.readthedocs.io/en/latest/
[file an issue]: https://github.com/napari/cookiecutter-napari-plugin/issues
[sphinx]: https://www.sphinx-doc.org/en/master/usage/quickstart.html
[mkdocs]: https://www.mkdocs.org/getting-started/
[jupyterbook]: https://jupyterbook.org/en/stable/start/your-first-book.html
[mit]: http://opensource.org/licenses/MIT
[mpl v2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[bsd-3]: http://opensource.org/licenses/BSD-3-Clause
[gnu gpl v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[gnu lgpl v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[apache v2.0]: http://www.apache.org/licenses/LICENSE-2.0
[travis ci]: https://travis-ci.com/
[appveyor]: http://www.appveyor.com/
[pypa code of conduct]: https://www.pypa.io/en/latest/code-of-conduct/
[shortbread]: https://github.com/audreyr/cookiecutter/releases/tag/1.4.0
[osi_certified]: https://opensource.org/trademarks/osi-certified/web/osi-certified-120x100.png
[osi]: https://opensource.org/
[github actions]: https://github.com/features/actions
[new github repository]: https://help.github.com/en/github/getting-started-with-github/create-a-repo
[setuptools_scm]: https://github.com/pypa/setuptools_scm
This repository is archived and no longer maintained. Please see [napari/napari-plugin-template](https://github.com/napari/napari-plugin-template/?tab=readme-ov-file#napari-plugin-template) for an up-to-date template from which to start a napari plugin.