Auspice v3

[jameshadfield]

It's been a while since we had a major Auspice version release. Work on vector map tiles will necessitate a v3 release. There's a few other breaking changes I'd like to get over the line while we're here:

Proposed changes (which don't yet have PRs up)

• Changes to the extensions API
  • Drop the navbarComponent customisation? (I don't even remember what this is!) NavBar is the part at the top of the sidebar; nextstrain.org customises it

• Webpack / nodejs version updates? Spend a little time re-examining how we import auspice code from projects.

  • nodejs v24 is now the minimum (see changelog below)
  • React v18 doesn't seem worth it for us at the moment Upgrade to React 18 #1659, and could be a minor bump anyway

• PR Use preset colours for (single) AA / NUC genotypes #739 - Use preset colours for (single) AA / NUC genotypes. (We discussed this recently, but I can't remember where)

• Simplify app when viewing tangletrees #1939

Changes which became v2 releases instead

• Editable dataset #2046 (Editable dataset UI) is soon to be merged & was released in 2.73

• Remove hardcoded footer descriptions #980 - merged & released as part of 2.72.0

• Offline Page "Refresh" auspice.us#62 - Add option to enable service worker #2062 is merged into master & was released in 2.73

v3 changelog entry (edit as needed)

This reflects the various PRs that are merged / are open to merge into the v3 branch

• Frontend (client) changes:

  • Map tiles are now vector images which are rendered client-side. This should result in quicker loading times and sharper looking maps. PR 2060

• CLI changes:

  • Directories to search for datasets and narratives should now be specified as positional arguments for auspice view and auspice develop. Example: auspice view datasets. The previous --datasetDir <path> --narrativeDir <path> are still valid, but are deprecated and will be eventually removed. PR 1967
  • Auspice no longer provisions a set of default dataset JSONs, instead you should point it at directories with existing datasets. PR 2067
  • The docs around server APIs and server-exported code has been improved. PR 2066

• Development changes:

  • Node v24 is now the minimum version to run the Auspice CLI / server. Version 26 is also supported. PR 2066
  • The Auspice package is now declared as using ES Modules (import syntax, not require). Most customisations, and all the frontend code, already used this approach however if you have custom server handlers in CJS which you use with auspice {view,develop} these may need updating. PR 2066
  • The server / cli code is now written mostly in TypeScript. PR 2066
  • We no longer use Heroku for Auspice-specific review apps, instead leveraging nextstrain.org and auspice.us review apps for testing purposes. PR 2067

• Client customisation (extension) changes:

  • The map-tile extension API has changed, related to our shift to vector map tiles. See updated API docs. PR 2060
  • Support for Google Analytics has now been removed entirely. This funcionality was deprecated as of version 2.44.0. PR 2082

Progress

• Auspice v3 #2093
• Auspice v3 docker-base#291
• Update auspice to v3.0.0 bioconda/bioconda-recipes#68748
• Auspice v3 nextstrain.org#1372
• Auspice v3 auspice.us#161

[joverlee521]

Other issues that I think could be considered "breaking":

• Remove hardcoded footer descriptions #980
• Simplify app when viewing tangletrees #1939
• revisit changes needed for Offline Page "Refresh" auspice.us#62