Auspice 2.63.1

• Fixed a bug where datasets without the (optional!) display_defaults would crash, which included newick files dragged onto auspice.us. (#1986)

Auspice 2.63.0

• Streamtrees are a new visualisation option for displaying phylogenetic trees. They require datasets with labels on internal nodes which we essentially use to partition the nodes of the tree and render each partition as a streamgraph. Such visualisations are useful for conveying relationships between parts of the tree as well as improving performance for very large trees. See the added documentation for more details. (#1902)

• Label URL queries (available when zoomed into a node which has an branch label) are now added in more cases and, when loading the page, we now remove the query if it is not valid. (#1952)

• Datasets can define display_defaults.label to specify the starting zoom level of a tree, similarly to the ?label=... URL query. (#1952)

• The tree's "Reset Layout" button has been renamed "Zoom to Root". (#1952)

• Removed the experimental markers from "Focus on selected" and "Explode Tree By" options. These seem to be working well. (#1954)

• Toggling "Focus on selected" now updates the URL parameter focus=selected. URLs with this parameter can be shared to enable focus on initial page load. (#1955)

• Added Chinese language support. (#1959)

• Added flexibility to the way the "Built with …" sentence can be translated. (#1964)

• Dropped support for Node.JS versions 16 & 18 and their corresponding NPM versions (7 & 8). (#1975)

Auspice 2.62.0

• Added a new color tree by measurements feature.
  Clicking on a group in the measurements panel will add a new coloring to the tree,
  where the colors represent an average of the measurement values for the matching
  test strain within the selected measurements group.
  For full details, please see #1924.
• Dataset authors can display a warning banner at the top of the page by setting .meta.warning in the main dataset JSON.
  The warning can be plain text or markdown format.
  This can be incorporated into Nextstrain workflows using augur export v2 --warning, available as of Augur version 27.2.0.
  (#1927)
• Bugfix: Clicking on the icons for FULL and GRID layout now changes the layout, just like clicking on the text (#1911)
• The 1Password browser extension, since roughly late November 2024, has interfered with Auspice views, notably when rendering many visual elements which is often the case with a large number of samples and/or genome size. The 1Password developer team is continuing to investigate the issue. In the meantime, we have applied a workaround to mitigate the effects of the issue on Auspice. (#1919)

Internal changes.

• Added a "Cite this repository" button on the GitHub repo.
  (#1921)
• Kept dependencies up to date.
  (#1443,
  #1923)
• Improved TypeScript usage.
  (#1910,
  #1913,
  #1914,
  #1915)
• Improved GitHub Actions usage.
  (#1916,
  #1920,
  #1929)

Auspice 2.61.2

• Bugfix: Fix errors where the tree wouldn't correctly update certain properties (#1907)
• Bugfix: Fix incorrect parsing of root-node dates of 0-99 CE (#1909)
• Bugfix: Fix an out-of-sync bug in the Entropy panel where the tooltip text would remain "Shannon entropy" and not update to "Num changes observed" (the value was correct). (#1906)

Auspice 2.61.1

• Bugfix: Restore shift-click behaviour for branches on the tree (#1901)

Auspice 2.61.0

• Error boundaries added for all panels (tree, map etc) so that in the case of uncaught errors we'll now show an error message rather than crashing Auspice. Hopefully these are never observed in production! (#1897)
• Bugfix: Auspice would crash in some situations when the entropy panel was scrolled back into view (bug introduced in v2.60.0). (#1898)

Internal / development changes

• Convert the tree component (and related tree-parsing functions) to TypeScript (#1864)

Auspice 2.60.0

• Performance improvement: We no longer attempt to animate actions on trees with over 4000 tips which results in more responsive interactions. (#1880)
• Performance improvement: We no longer recompute the entropy data (which can be expensive) when the entropy panel is toggled off or off-screen. (#1879)
• Bugfix: narrative slide changes which removed a filter would not work as expected in some cases (#1883)

Internal / development changes

• Refactor how the measurement-sidecar JSON is loaded (#1881)
• Move jest config to TypeScript (#1885)
• Move jest-puppeteer with Playright (#1884)
• Verbose logging during CI (#1876)

Auspice 2.59.1

• Moved the "Focus on Selected" toggle next to the "Show confidence intervals" toggle.
  (#1875)

Auspice 2.59.0

• Added an experimental "Focus on Selected" toggle in the sidebar.
  When focusing on selected nodes, nodes that do not match the filter will occupy less vertical space on the tree.
  Only applicable to rectangular and radial layouts.
  (#1373)

Auspice 2.58.0

• Fix bug where drag-and-drop metadata columns were no longer included as tip labels (#1845)
• Fixed a bug where internal node names were sometimes omitted from the branch info modal (arrived at via shift-clicking on a branch).
  They are now always displayed irrespective of the selected tip label.
  (#1849)
• Added URL params for measurements panel controls: m_collection, m_display, m_groupBy, m_overallMean, m_threshold, and mf_*.
  See docs for more details. (#1848)