Release v3.5.1

Hi all,
This has a number of small bugfixes and features. Here are a couple highlights

Better dropdown menus

In previous releases, the dropdown submenus would close the instant your mouse left their boundaries, but now, they stay open until you select a menu item or click away

Ability to customize root configuration

We added the ability for plugins to add new entries to the root configuration. This now makes it possible to add easy-to-access configuration for your plugin. Example:

export default class MsaViewPlugin extends Plugin {
  name = 'MyPlugin'

  install(pluginManager: PluginManager) {}

  configure(pluginManager: PluginManager) {}

  rootConfigurationSchema(pluginManager: PluginManager) {
    return {
      mything: ConfigurationSchema('MyConfig', {
        greetings: {
          type: 'string',
          defaultValue: 'hello world',
        },
      }),
    }
  }
}

A user could then customize their greeting in a new way like

{
  "assemblies": [...],
  "tracks": [...],
  "plugins": [...],
  "mything": {
    "greetings": "hello jbrowsers"
  }
}

This can then be used in your code by readConfObject(session.jbrowse, ['mything','greetings'])

Here is an example used by the MSA view plugin https://github.com/GMOD/jbrowse-plugin-msaview/blob/7027f01abe2b4253fd2a250021d2b13a1b4f2fce/src/index.ts#L37-L59

We anticipate that this will enable new and easier plugin customizations

More small updates

• Fixed @jbrowse/img complaining about loading CSS files
• Updated embedded website tutorial https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/
• Added the React compiler

See the release notes below for more info

3.5.1 (2025-06-05)

🚀 Enhancement

• Other
  • #5064 Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) (@cmdcolin)
  • #5059 Canonicalize refNames in search results (@cmdcolin)
  • #5056 Use assembly displayName on synteny header and ruler (@garrettjstevens)
  • #5050 Use standard sessionId for linear synteny view to reduce data re-fetching (@cmdcolin)
• app-core, core, embedded-core
  • #5063 Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave (@cmdcolin)
• core
  • #5049 Add react compiler (@cmdcolin)
• app-core, core
  • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

🐛 Bug Fix

• Other
  • #5062 Fix useSWR usage from plugins (@cmdcolin)
  • #5053 Fix @jbrowse/img using a no-op css import (@cmdcolin)
  • #5051 Fix race condition with text search using useEffect cleanup (@cmdcolin)
• core
  • #5058 Improve speed of navigation for fragmented assemblies (@cmdcolin)

📝 Documentation

• #5047 Reduce the embedded website tutorial (@cmdcolin)

🏠 Internal

• Other
  • #5057 Reduce S3 uploads per-branch (@cmdcolin)
  • #5054 Add ability to make commits to update docs only and avoid running CI (@cmdcolin)
• core
  • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.94s.
  Done in 0.59s.