Auspice 2.67.0

• Mutations in a node-info modal (via tip click or shift+branch click) are now clickable. Clicking on a mutation will colour the tree by the genotypes at that position. Shift+clicking will append that position to the current genotype colouring (if possible), or remove it if it's already part of it. Command clicking (with or without shift) will behave similarly but filter the tree via the specific mutated state instead of changing the colouring. (#2018)
• Shift-clicking bars in the entropy panel will now add the position to the existing color-by (as long as the gene is the same), or remove it if it was already part of the color-by. (#2019)
• Added support for Node.js version 24 and its corresponding NPM version (11). (#2012)

Auspice 2.66.0

• Fixed a bug that prevented drag-and-drop metadata files from being parsed that was introduced in version 2.64.0 (#2007)
• Added SVG-download support for the measurements panel. (#2005)

Auspice 2.65.0

• "show all branch labels" toggle has been updated to only show labels for visible branches, i.e. branches of selected tips after applying filters (#2004)

Auspice 2.64.0

• Link-outs are explicitly disabled for v1 datasets because the nextstrain.org API does not support the v1 -> v2 conversion. (#2002)
• Added a treeZoom=selected query to load trees at the same zoom level after the "zoom to selected" button has been pressed, where applicable. See the view settings docs for more details. (#1321)
• Downloaded metadata and acknowledgments TSVs will now use extra columns to export associated URLs. (#2003)

internal changes

• The JS bundles created when Auspice (client) is built have been changed in various ways (#1992):
  • Polyfills have been updated and we now only add a subset of polyfills to match our 95% browser target used for JS syntax.
  • Bundles are now available using Brotli compression (in addition to gzip) and the Auspice server is updated to support them.
  • Duplicated code has been reduced in the bundles, and the bundle layout has changed.
  • The map component is separated into a new bundle which should improve load times on datasets which don't use it.
• Loading spinners have been improved in various ways. (#1991)
• Logos available in the bundle are used rather than a fetch to an external domain. (#1996)
• Added unit tests for createStateFromQueryOrJSONs. (#1988)

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)