Release v2.6.1

Hello all,
This ended up being a big release with a lot of new stuff!

Features

• Created the @jbrowse/react-app NPM package which effectively makes the jbrowse-web package NPM-installable. This is still new so let us know what you think. See the docs at https://jbrowse.org/storybook/app/main and example usages at https://jbrowse.org/jb2/docs/embedded_components/ (this is pretty new, there may be more updates or changes to come with this package!)
• Improved code sharing across web, desktop, and embedded products (this was a large refactor, if you see any bugs let us know!)
• Improved display of inversions in the read cloud display (see screenshot)
• Fixed persistent issue with jbrowse create CLI creating corrupted output (update your local install with npm install -g @jbrowse/cli)

Figure showing split long reads alignments on the read cloud display spanning an inversion showing forward (red) to reverse (blue) and back to forward again.

🚀 Enhancement

• Other
  • #3743 Create mixin for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay (@cmdcolin)
  • #3711 Allow synteny data adapters to open files larger than 512Mb (@cmdcolin)
  • #3639 Add button to bookmark in jbrowse-web share dialog (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3700 Render alignment track arcs instantly after bpPerPx change (@cmdcolin)
  • #3695 Reduce re-drawing on alignments track paired read arcs/cloud display types (@cmdcolin)
• core
  • #3725 Filter tracks that match all view.assemblyNames in multi-assembly track selector modes (@cmdcolin)
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
  • #3653 Evaluate extension point on track config pre-process snapshot (@cmdcolin)
  • #3706 Miscellaneous alignments arc/cloud fixes (@cmdcolin)
  • #3698 Add column resizers to the variant ANN/CSQ panels (@cmdcolin)
• app-core, product-core, web-core
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
• __mocks__
  • #3707 Improved read cloud display for long reads with inversions (@cmdcolin)

🐛 Bug Fix

• core
  • #3749 Avoid re-prompting a user login when refresh token is processed (@cmdcolin)
  • #3572 Add OAuth and HTTP BasicAuth servers for local testing, fix some OAuth flows (@garrettjstevens)
  • #3708 Add removable-media to jbrowse desktop snap (@cmdcolin)
  • #3687 Take into account ML tag when showing MM tag on alignments, misc refactoring (@cmdcolin)
• Other
  • #3747 Fix blank lines in GFF crashing text-index (@cmdcolin)
  • #3739 Fix specifying the assemblyNames config slot on add-connection CLI (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3667 Fix horizontal flip functionality for Hi-C display (@studentshivang)
  • #3703 Fix rendering error in alignments tracks when filtering by tag in CRAM file (@Lilas-w)
  • #3694 Fix ability to filter certain fields in BAM/CRAM files (@cmdcolin)
  • #3691 Fix breakpoint split view alignment connections not pointing at right position in v2.5.0 (@cmdcolin)
  • #3686 Fix jbrowse create/jbrowse upgrade CLI intermittent failures (@cmdcolin)
• product-core, web-core
  • #3738 Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config (@cmdcolin)
• app-core, core, embedded-core
  • #3731 Fix view menu going off screen in some cases (@cmdcolin)
• app-core
  • #3713 Fix centering of the ImportForm on SV inspector (@cmdcolin)

📝 Documentation

• Other
  • #3752 Add storybook example for fetching features currently in view (@cmdcolin)
  • #3732 Add JBrowse R shiny app demo (@carolinebridge-oicr)
  • #3693 Remove package table from release blogposts (@cmdcolin)
• core, embedded-core, product-core
  • #3704 Organize autogenerated docs into categories (@cmdcolin)

🏠 Internal

• app-core, core, product-core, text-indexing
  • #3740 Bump electron, proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed array to object (@cmdcolin)
• core
  • #3741 Distinguish between SessionWithConnections and SessionWithConnectionEditing (@cmdcolin)
• Other
  • #3734 PileupRenderer refactor (@cmdcolin)
• app-core, core, product-core, web-core
  • #3717 More modularizing of shared app code (@cmdcolin)
• product-core
  • #3709 Silence console warn in CopyAndDelete test (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing
  • #3701 Create app-core and embedded-core packages (@cmdcolin)
• core, product-core
  • #3661 Create packages/product-core containing shared code between the various products (@rbuels)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• Shivang Dwivedi (@studentshivang)
• @Lilas-w Done in 2.84s.