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AllenCell / napari-allencell-segmenter

A plugin that enables image segmentation provided by Allen Institute for Cell Science
BSD 3-Clause "New" or "Revised" License
16 stars 6 forks source link

documentation/categories-for-napari-hub #131

Closed neuromusic closed 2 years ago

neuromusic commented 2 years ago

Pull request recommendations:

Thanks for contributing!

Add categories and preview page workflow for the napari hub

Hello!

I’m Justin Kiggins, the Product Manager at CZI leading our work on the napari hub.

I’m reaching out with this pull request to ask for your help preparing your plugin for a new “Filter by Category” feature we’ll be launching for the napari hub near the end of January.

This PR does 2 things:

  1. adds our proposed labels to .napari/config.yml to help users find your plugin
  2. adds an Action to your repository in .github/workflows/plugin_preview.yml to help you preview changes to your plugin’s napari hub page

What is the “Filter by Category” feature?

We will let users filter plugins on the napari hub by Category, based on your own annotations of your plugin selected fro terms in the EDAM Bioimaging ontology. You are able to specify, in your .napari/config.yml file, any number of EDAM labels at whatever depth of the taxonomy is most appropriate. You can see a mockup of this feature below

prototype of filter dialog letting napari hub users filter plugins based on workflow step

We currently support viewing category metadata on the individual plugin pages, but before we let users filter by category, we want to get categories populated for as many plugins as possible.

For more information, see A plugin developer’s guide to categories on the napari hub.

Can you make adding category labels to my plugin easier?

Totally. We know that learning about the EDAM Bioimaging ontology and adding relevant categories is a lot of work. So we took a first pass for you!

To help you get started, our team has reviewed your plugin’s description and metadata and identified category labels that we feel would be a good fit based on the information you’ve provided so far. These were proposed initially by our Biocuration Team who are experts in annotating scholarly literature with biological concepts, then reviewed by my colleague, @chili-chiu, an Application Scientist on our team.We did our best to select relevant labels, but we might be wrong! Please review and edit these categories to best fit your plugin… and let us know how we did! We’re exploring ways that we might be able to automate suggestions in the future for new plugin developers. We’ll be launching the “Filter by Category” feature on Jan 27, 2022, so if you’d like to take advantage of this new feature, please merge this PR by then!

Can you let me preview the changes before I merge this PR?

Yeah, we can do that… not just for categories, but for all of your metadata!

To make it easier for you to update and maintain your plugin’s metadata, and see immediately how changes to links or your description will affect your napari hub listing, we’ve launched a new service that lets you preview your plugin’s page directly from PRs onto your plugin repository (like this one) and see what metadata you might be missing.

Prototype of the napari hub Preview Page feature, which highlights missing metadata from your Github repository

This service has two parts:

To use the new Preview Page feature, you simply need to install the Github App by clicking here and configuring it for this repository. Once you do that, make any update to this PR and you will get a comment from the @napari-hub-bot below with a link to your preview page!

For more information, see Setting Up Plugin Page Previews

We hope that these new features are useful to you! Happy to answer any questions here or on our Discussions page.

chili-chiu commented 2 years ago

Just want to follow up on this PR- we’re planning to launch the filter-by category feature on Jan 27. If you want your plugin to be filterable by category when we launch, please review and merge this PR by then. Many plugins have already added categories, for example: https://www.napari-hub.org/plugins/napari-segment-blobs-and-things-with-membranes

If you don’t want categories, feel free to close this PR.

codecov[bot] commented 2 years ago

Codecov Report

Merging #131 (d925db3) into main (d112c15) will not change coverage. The diff coverage is n/a.

Impacted file tree graph

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  Coverage   84.70%   84.70%           
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  Files          34       34           
  Lines        1432     1432           
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  Hits         1213     1213           
  Misses        219      219

Continue to review full report at Codecov.

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schoinh commented 2 years ago

Just want to follow up on this PR- we’re planning to launch the filter-by category feature on Jan 27. If you want your plugin to be filterable by category when we launch, please review and merge this PR by then.

Thanks @chili-chiu . Do we also have to publish a new version of the plugin with this change merged in, or is merging this PR into the main branch sufficient?

chili-chiu commented 2 years ago

Currently you will have to publish it in order to have the new category shown on napari hub. We are exploring possible workflows that allow the update without publishing (some potential options: (1) add commands for the napari hub bot to update/sync metadata (2) include it in the preview page as part of github action).

If you have any preferences/thoughts please let us know, thanks!

neuromusic commented 2 years ago

Also...

  1. We are planning to refresh all of the metadata along with the Jan 27 launch so your categories will go live then, even if you don't cut a new release
  2. We can always manually trigger a refresh of the Github metadata... just file an issue at https://github.com/chanzuckerberg/napari-hub/issues requesting the refresh for your plugin