v1.24.0

• Tree grid improvements - PR 610
  • Allow negative (i.e. BCE) dates
  • Display y-dates and horizontal lines in the clock layout view
  • Improved spacing between grid points
• SVG elements in the DOM are now in named groups which improves debugging and prevents incorrect-layering bugs. PR 612
• Fixed a bug where the available datasets (dropdowns in sidebar) contained invalid values PR 614
• Community sourced datasets (nextstrain.org/community/...) display a link to the github repo in the sidebar PR 615
• Since v1.22.3 changing datasets preserved the URL queries (e.g. ?l=radial).
  A number of bugs relating to this have been fixed, where these queries were no longer valid for the new dataset.
  This also fixed potential issues related to loading datasets where the URL queries were invalid.
  PR 613

v1.17.0

Narrative

• Now exposed via a "hidden" URL query. E.g. flu/h3n2/3y?n=1
• Frequencies added to narrative
• block in focus is part of the URL query, and can be reloaded via the URL

Second Tree / Tanglegram

• Second tree can be loaded via a URL (e.g. ?tt=na). Sidebar dropdown currently disabled.
• In this mode, trees are forced to be rectangular, and the map & frequencies are not displayed.
• Tanglegram exists, but no untangling (yet)
• Bugs still exist (which is why the sidebar has been disabled)

Internals

• All JSONs (incl. frequencies, narrative) are loaded within a single Promise & dispatch
• phylotree.change() only ever called once, and always in componentDidUpdate (fixes bugs where it fired in both CWRP and CDU)
• old & deprecated code removed

v1.16.2

• Add redirect of www.nextstrain.org to nextstrain.org via express middleware

v1.16.0

Browser support

• Now works on Internet Explorer 11 (tested on windows 7)
• Grid layout issue fixed for Firefox on linux/windows
• Embedding Nextstrain in an iFrame works - see /scripts/gisaid_iframe.html

v1.15.0

• Multiple genotypes (for the same amino acid) by typing in multiple comma separated AA/nuc positions.
  PR 523.

v1.14.0

Features

• Strain search (using awesomplete).
  This highlights the path to a single tip and increases the tip radius.
  Strain is stored in the URL query (s=...) and can be restored via URL.
  Selected strain also appears in the info panel (top of screen).
• Amino acid branch labels (for every tree) as well as clade labels if specified by the clade_annotation attribute.
  AA labels are shown where the descendent visible tips account for more than 5% of the total visible tips (same as nextflu).
  Clade labels are always displayed.
• Default geneotype gene is now HA1 if available (previously nucleotide).
• ColorBy ordering (sidebar dropdown) is now ordered (via an array in globals.js)

Internals

• The JSON processing on initial load has been shifted from the reducers to a single action - fewer dispatches, fewer potential bugs, faster code.
• Frequencies are initialised in a single action (previously 2).
• tip-frequencies are now downloaded via get_data.sh
• Frequency actions are not dispatched unless the frequency panel is loaded.

v1.13.0

Features

• Frequencies are now displayed via a stream graph panel - see PR 497.
  These require the fetching of a separate tip-frequencies JSON, and must be specified in the panels array of the meta.JSON.
• "Panels To Display" toggles in the sidebar allow customisation of the display, and this is reflected in the URL.
• The + - buttons in the tree have been replaced by a "reset tree" button.
  This resets the bounds to the entire tree & completely re-renders the tree (filters are maintained).
  Pan behaviour is unchanged.

Internals

• React-PhyloTree interface is completely rewritten to use phylotree.change() - see PR 501 for the API.
  The new interface is both easier to understand and quicker.
• changePageQuery (used for changing narrative blocks) is now a single action
• Ongoing narrative work (still disabled).
• React sidebar has been removed (no UI changes).

v1.12.0

Features

• Vaccine strains are shown at their use date (in temporal trees), with dotted lines connecting them to their tips (representing collection date) (PR 498)

Internals

• updateGeometryFade uses counters to know when transitions are finished rather than setTimeout

v.1.11.0

Features

• Vaccine strains are now displayed if they are specified in metaJSON.vaccine_choices (PR 490)

Internals

• Tree components and PhyloTree have been reorganized (in src/components/tree) and the syntax improved (PR 493)
• Upgraded to React 16, as well as upgrading redux & react-svg-pan-zoom (PR 494)

v1.10.0

Features

• Local Branching Index (LBI) coloring can be calculated in auspice (code identical to nextflu) if specified in color_options (meta JSON) #491

Internals

• get_data.sh script updated to no longer download sequences & entropy JSONs
• action logging middleware available for debugging / development