diff --git a/README.md b/README.md index b507eca..13394d0 100644 --- a/README.md +++ b/README.md @@ -1,20 +1,35 @@ # napari-cryoet-data-portal -[![tests](https://github.com/chanzuckerberg/napari-cryoet-data-portal/workflows/tests/badge.svg)](https://github.com/chanzuckerberg/napari-cryoet-data-portal/actions) -[![codecov](https://codecov.io/gh/chanzuckerberg/napari-cryoet-data-portal/branch/main/graph/badge.svg)](https://codecov.io/gh/chanzuckerberg/napari-cryoet-data-portal) +[![MIT License](https://img.shields.io/pypi/l/napari-cryoet-data-portal.svg?color=green)](https://github.com/chanzuckerberg/napari-cryoet-data-portal/raw/main/LICENSE) +[![Python package index](https://img.shields.io/pypi/v/napari-cryoet-data-portal.svg?color=green)](https://pypi.org/project/napari-cryoet-data-portal) +[![Supported Python versions](https://img.shields.io/pypi/pyversions/napari-cryoet-data-portal.svg?color=green)](https://python.org) +[![Test status](https://github.com/chanzuckerberg/napari-cryoet-data-portal/workflows/tests/badge.svg)](https://github.com/chanzuckerberg/napari-cryoet-data-portal/actions) +[![Code coverage](https://codecov.io/gh/chanzuckerberg/napari-cryoet-data-portal/branch/main/graph/badge.svg)](https://codecov.io/gh/chanzuckerberg/napari-cryoet-data-portal) +[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cryoet-data-portal)](https://napari-hub.org/plugins/napari-cryoet-data-portal) -List and open tomograms from the [CZII CryoET Data Portal] in [napari]. +List and open tomograms from the CZ Imaging Institute's [CryoET Data Portal] in [napari]. -https://github.com/chanzuckerberg/napari-cryoet-data-portal/assets/2608297/6ccbd314-fd2b-40aa-abeb-dd1afe2a61e2 +![Plugin showing tomogram TS_026](https://github.com/andy-sweet/napari-cryoet-data-portal/assets/2608297/f8470b1c-2e91-4730-924c-95dc7c6256bb) ## Installation -You can install the latest development version using [pip]: +You can install the latest stable version using [pip]: + + pip install napari-cryoet-data-portal + +You will also need to install napari separately as a Python package in the same environment. +One way to do that with Qt included is to run: - pip install git+https://github.com/chanzuckerberg/napari-cryoet-data-portal.git + pip install "napari[all]" + +but more generally you should follow the [latest napari installation instructions]. ## Usage +See the following video for a demonstration of basic usage of the plugin. + +https://github.com/chanzuckerberg/napari-cryoet-data-portal/assets/2608297/6ccbd314-fd2b-40aa-abeb-dd1afe2a61e2 + Click the *Connect* button to establish a connection to the data portal. ![Connect button and editable URI to the portal](https://github.com/chanzuckerberg/napari-cryoet-data-portal/assets/2608297/1bc5ecba-daf6-4a14-83a5-332ea5625604) @@ -53,6 +68,10 @@ These operations can also be cancelled by clicking the *Cancel* button. This is still in early development, but contributions and ideas are welcome! Don't hesitate to [open an issue] or [open a pull request] to help improve this plugin. +To setup a development environment, fork this repository, clone your fork, change into its top level directory and run: + + pip install -e ".[testing]" + This project adheres to the [Contributor Covenant code of conduct]. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com. @@ -72,7 +91,7 @@ This plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-na [napari]: https://github.com/napari/napari [@napari]: https://github.com/napari -[CZII CryoET Data Portal]: https://chanzuckerberg.github.io/cryoet-data-portal +[CryoET Data Portal]: https://chanzuckerberg.github.io/cryoet-data-portal [pip]: https://pypi.org/project/pip/ [Cookiecutter]: https://github.com/audreyr/cookiecutter [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin @@ -82,3 +101,4 @@ This plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-na [Contributor Covenant code of conduct]: https://github.com/chanzuckerberg/.github/tree/master/CODE_OF_CONDUCT.md [open an issue]: https://github.com/chanzuckerberg/napari-cryoet-data-portal/issues [open a pull request]: https://github.com/chanzuckerberg/napari-cryoet-data-portal/pulls +[latest napari installation instructions]: https://napari.org/stable/tutorials/fundamentals/installation.html#install-as-python-package-recommended