Web app for visualizing pathogen evolution

version 1.12.0 - 2018/02/14

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

version 1.11.0 - 2018/02/05

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)

version 1.10.0 - 2018/02/05

Features

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

Internals

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

version 1.9.0 - 2018/01/30

Animation

  • Animations can now loop! This is selected via a toggle in the sidebar.
  • While animating, the URL displays information which defines the animation (bounds, looping, cumulative, speed). This allows the animation to start automatically by linking to this URL.
  • The code for the animation (i.e. the setInterval code) has been moved out of Map and into a separate AnimationController component.
  • Animation is stopped & started by examining redux state, rather than with imperative controls.

misc

  • The narrative machinery has been moved forward, but this functionality is still disabled and not present in production code.
  • The (rather expensive) calendarToNumeric calculations have become part of state.controls so that components no longer have to calculate them from the string form.

version 1.8.0 - 2018/01/18

entropy calculated via tree

  • The entropy panel data is now computed within auspice by examining mutations throughout the tree, and is throttled to improve speed under load.
  • Both entropy and number of mutations are available via a toggle similar to AA/NT
  • This results in entropy.JSON no longer being fetched.
  • The entropy data is stored in redux state rather than the react component
  • The D3 code has been reorganised
  • Note that the entropy values are slightly different to those exported by augur in some situations - see https://github.com/nextstrain/auspice/pull/478#issuecomment-358496901

genotype calculated via tree

  • This results in sequences.JSON no longer being fetched.
  • Augur was updated to export annotations which are needed for entropy gene display.

middleware / react router

  • All changes to the URL are now performed via middleware rather than side-effects within the action definition.
  • React router has been removed
  • Browser back/forward is detected via window.addEventListener('popstate', this.onURLChanged) which also fires on initial page load.
  • Pages are selected via the <PageSelect> component.

other

  • The number of proteins displayed while hovering over a branch has been limited to 7 (issue #484)
  • The presence of author data is checked before display (issue #488)
  • This changelog has been created and a step in the releaseNewVersion script added to prepend the version number upon release.

version 1.7.2 - 2018/1/4

Narrative / situational report

  • Functionality has been added, but is currently disabled via a flag in globals.js.
  • This is currently rendered in a right-hand sidebar. This feature is not yet complete.

URL queries

  • The following state has been added to the URL query:
    • filters, e.g. f_authors=Tong_et_al,Capobianchi_et_al&f_division=kerouane
    • genotype URLs (these were previously set as the URL but not parsed)
    • panel layout (grid/full)
  • A number of bugs regarding URL query state parsing (esp with genotype colorBys) have been fixed.

version 1.7.1 - 2017/10/31

  • Added mumps acknowledgment

version 1.7.0 - 2017/10/17

version - 2018/01/18