What's Changed

• fixes #497 and #524 by @ArtPoon in #525
• Minor: Bug fixes by @GopiGugan in #529

Full Changelog: v3.1...v3.2

• Now writing feature vectors extracted from genomes to a local database (#485)
• Cluster data written to database at completion of analysis
• Only clusters with new data will be rebuilt (#493)
• Bug fixes (#512, #515, #518, #522)

• use MongoDB on front-end server to store cluster information (#433)
• split lineages into XBB and main trees, as well as a subset of other recombinants (#489)
• added regression model to predict the number of unsampled infections per lineage (HUNePi) (#472)
• added walkthrough (interactive user guide for webpage) (#461, #28)
• Cypress test suite (#447)
• user can now download mutation list (#419)
• a lovely assortment of bug fixes

• recombinant lineages are now displayed outside of the time-scaled tree
• bug fixes #416, #417, #421, #424, #428

• added UI to filter time-scaled tree by collection dates, #332
• updated installation instructions for dev environment (using Node.js)
• bug fixes, #410, #411

Major version number change because this release is not backwards compatible.

• added ProblematicSites_SARS-CoV2 and pango-designation as submodules (#334)
• modified by_lineage data structure in batch.py to reduce memory consumption (#387)
• added vertical scroll bar for time-scaled tree
• added front-end diagram documentation (#342, #355)
• mutation table (#381)
• using asynchronous, promise-based transactions (Node.js) to reduce page load time (#401)
• rooting on reference genome as outgroup (#396)

Front-end bug fixes and feature enhancements

• moved horizontal scroll bar for beadplots to top (#347)
• fixed date issue to support multiple browsers (#348)
• click on vertical edge to "lock-in" parent and child variants (#342)
• make beadplot scrollable (i.e., two-finger swipe) (#347)
• fixed edge filtering for large lineages (#349)

• added front-end unit tests (#259)
• bug fixes (#309, #312, #324, #325)
• time-tree tooltip now shows original and displayed number of variants per lineage (#264)
• incorporating Pango lineage designation file (#313)

• language translations; French, Spanish, Chinese (#270)
• computing performance improvements (#295, #296, #304)
• UI enhancements for beadplots (#268, #269, #263, #287)
• added mutation annotations to lineage tooltips (#177)
• changed time-scaled tree reconstruction to earliest samples (#281, #283)
• front-end unit testing (#259)
• SVG export of beadplot adds time axis (#301)
• download lineage statistics as CSV (#292)
• started backend documentation with Mermaid.js (#192)
• bug fixes (#245, #276, #294, #299)

Theme of 0.5 is accessibility (internationalization and UI)

• enhanced user interface
  • event binding to vertical edges #209 and sample table
  • arrow keys to navigate beads #237
  • highlighted bead in foreground #221
• filtering vertical edges with slider UI #255
• starting to build internationalization (language) support #233