Release v2.2.0

[cmdcolin]

This release includes several important improvements including

• Lazily loading assembly refNames: previously when you had multiple assemblies
  in your config, it would load all their refNames at browser startup. Now, it
  only fetches refNames when you request to use an assembly.
• Simplified "synteny track selector" on the dotplot and synteny import forms
• Improved documentation! The entire jbrowse 2 documentation has been
  overhauled, and the monolithic user guide, config guide, and developer guide
  pages have been split into smaller pages. We also now auto-generate
  documentation on our config and state tree models, and have a search bar
• Improved speed on alignments tracks: a small optimization was made for
  alignments tracks that can improve performance on alignments tracks by 30% or
  so especially on short reads

Figure showing improved speed on short read alignments of the refactor (this
release) vs main (which was v2.1.7)

Note that the changes to allow lazy loading assemblies may have somewhat
changed the "contract", so if your code is using the assemblyManager directly
in any places, please be aware of this change. Proper usage of the
assemblyManager API uses either

1. use assemblyManager.get(assemblyName) which can return undefined initially,
   but then this initiates the lazy load and can be caught by reactivity of
   wrapping your components in observers
2. use assemblyManager.waitForAssembly(assemblyName) function, which is
   asynchronous but returns a promise. this avoids the initial return undefined
   behavior
3. avoid directly accessing e.g. assemblyManager.assemblies

🚀 Enhancement

• Other
  • #3296 Add option to use OAuth "state" param in internet accounts (@garrettjstevens)
  • #3285 Use typescript version of @gmod/cram (@cmdcolin)
• core
  • #3299 Add ability to open a synteny track directly from the dotplot/linear synteny view import forms (@cmdcolin)
  • #3287 Lazy-load assemblies on demand instead of all at app startup (@cmdcolin)
  • #3279 Remove unnecessary expanded region query and small refactors (@cmdcolin)

🐛 Bug Fix

• core
  • #3309 Fix animated "Loading..." message keyframes (@cmdcolin)
  • #3306 Fix the RefNameAutocomplete displaying a stale value for chromosome names (@cmdcolin)
  • #3302 Improve rubberband zooming across elided regions (@cmdcolin)
• Other
  • #3293 Fix CRAM plotting for data files that encode insertions in uncommon way (@cmdcolin)

📝 Documentation

• core, text-indexing
  • #3278 Auto-generate docs (@cmdcolin)

🏠 Internal

• #3310 Remove CacheProvider emotion cache (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)

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This discussion was created from the release Release v2.2.0.