auspice/CHANGELOG.md

Web app for visualizing pathogen evolution

# Changelog

## version 2.69.0 - 2026/04/14


* Allow protein-only datasets, i.e. a dataset whose genome annotation is missing a nuc block but with CDSs defined. This work is in tandem with [this Augur PR](https://github.com/nextstrain/augur/pull/1958). ([Auspice PR #2040](https://github.com/nextstrain/auspice/pull/2040))

## version 2.68.0 - 2026/01/20

#### Major changes

* The "Focus on selected" toggle now zoooms horizontally as well as vertically. This helps to explore clades which only existed for a small proportion of the entire tree's temporal / divergence range. ([#1993](https://github.com/nextstrain/auspice/pull/1993))

* When multiple trees are displayed ("tangletrees") the tree-buttons (zoom out, zoom to selected, zoom to root) are now present for each tree and only change their respective tree. ([#2026](https://github.com/nextstrain/auspice/pull/2026))

* We now have a completely new dataset selector, replacing the dropdowns in the sidebar. This is activated by clicking on the dataset name in the sidebar, and allows you to select a new dataset based on the available datasets. This fixes a slew of bugs and should make it much clearer to navigate between datasets. ([#2030](https://github.com/nextstrain/auspice/pull/2030))

#### Minor changes

* Downloaded TSV will include associated URL regardless of value type ([#2024](https://github.com/nextstrain/auspice/pull/2024))
* Tip info modal displays link for traits that have a URL regardless of value type ([#2024](https://github.com/nextstrain/auspice/pull/2024))

## version 2.67.0 - 2025/11/03

* 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](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/pull/2019))
* Added support for Node.js version 24 and its corresponding NPM version (11). ([#2012](https://github.com/nextstrain/auspice/pull/2012))

## version 2.66.0 - 2025/09/05

* Fixed a bug that prevented drag-and-drop metadata files from being parsed that was introduced in version 2.64.0 ([#2007](https://github.com/nextstrain/auspice/pull/2007))
* Added SVG-download support for the measurements panel. ([#2005](https://github.com/nextstrain/auspice/pull/2005))

## version 2.65.0 - 2025/09/02

* "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](https://github.com/nextstrain/auspice/pull/2004))

## version 2.64.0 - 2025/08/15

* Link-outs are explicitly disabled for v1 datasets because the nextstrain.org API does not support the v1 -> v2 conversion. ([#2002](https://github.com/nextstrain/auspice/pull/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](https://docs.nextstrain.org/projects/auspice/en/latest/advanced-functionality/view-settings.html) for more details. ([#1321](https://github.com/nextstrain/auspice/pull/1321))
* Downloaded metadata and acknowledgments TSVs will now use extra columns to export associated URLs. ([#2003](https://github.com/nextstrain/auspice/pull/2003))

**internal changes**

* The JS bundles created when Auspice (client) is built have been changed in various ways ([#1992](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/pull/1991))
* Logos available in the bundle are used rather than a fetch to an external domain. ([#1996](https://github.com/nextstrain/auspice/pull/1996))
* Added unit tests for `createStateFromQueryOrJSONs`. ([#1988](https://github.com/nextstrain/auspice/pull/1988))

## version 2.63.1 - 2025/06/04

* Fixed a bug where datasets without the (optional!) `display_defaults` would crash, which included newick files dragged onto auspice.us. ([#1986](https://github.com/nextstrain/auspice/pull/1986))

## version 2.63.0 - 2025/06/02

* **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](https://docs.nextstrain.org/projects/auspice/en/latest/advanced-functionality/streamtrees.html) for more details. ([#1902](https://github.com/nextstrain/auspice/issues/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](https://github.com/nextstrain/auspice/pull/1952))
* Datasets can define `display_defaults.label` to specify the starting zoom level of a tree, similarly to the `?label=...` URL query. ([#1952](https://github.com/nextstrain/auspice/pull/1952))
* The tree's "Reset Layout" button has been renamed "Zoom to Root". ([#1952](https://github.com/nextstrain/auspice/pull/1952))
* Removed the experimental markers from "Focus on selected" and "Explode Tree By" options. These seem to be working well. ([#1954](https://github.com/nextstrain/auspice/issues/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](https://github.com/nextstrain/auspice/issues/1955))
* Added Chinese language support. ([#1959](https://github.com/nextstrain/auspice/pull/1959))
* Added flexibility to the way the "Built with …" sentence can be translated. ([#1964](https://github.com/nextstrain/auspice/pull/1964))
* Dropped support for Node.JS versions 16 & 18 and their corresponding NPM versions (7 & 8). ([#1975](https://github.com/nextstrain/auspice/pull/1975))

## version 2.62.0 - 2025/01/21

* 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](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/issues/1927))
* Bugfix: Clicking on the icons for FULL and GRID layout now changes the layout, just like clicking on the text ([#1911](https://github.com/nextstrain/auspice/issues/1911))
* The [1Password browser extension](https://support.1password.com/getting-started-browser/), 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](https://github.com/nextstrain/auspice/issues/1919))

_Internal changes._

* Added a "Cite this repository" button on the GitHub repo.
  ([#1921](https://github.com/nextstrain/auspice/pull/1921))
* Kept dependencies up to date.
  ([#1443](https://github.com/nextstrain/auspice/pull/1443),
   [#1923](https://github.com/nextstrain/auspice/pull/1923))
* Improved TypeScript usage.
  ([#1910](https://github.com/nextstrain/auspice/pull/1910),
   [#1913](https://github.com/nextstrain/auspice/pull/1913),
   [#1914](https://github.com/nextstrain/auspice/pull/1914),
   [#1915](https://github.com/nextstrain/auspice/pull/1915))
* Improved GitHub Actions usage.
  ([#1916](https://github.com/nextstrain/auspice/pull/1916),
   [#1920](https://github.com/nextstrain/auspice/pull/1920),
   [#1929](https://github.com/nextstrain/auspice/pull/1929))

## version 2.61.2 - 2024/11/19



* Bugfix: Fix errors where the tree wouldn't correctly update certain properties ([#1907](https://github.com/nextstrain/auspice/pull/1907))
* Bugfix: Fix incorrect parsing of root-node dates of 0-99 CE ([#1909](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/pull/1906))


## version 2.61.1 - 2024/11/14

* Bugfix: Restore shift-click behaviour for branches on the tree ([#1901](https://github.com/nextstrain/auspice/pull/1901))

## version 2.61.0 - 2024/11/14


* 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](https://github.com/nextstrain/auspice/pull/1897))
* Bugfix: Auspice would crash in some situations when the entropy panel was scrolled back into view (bug introduced in v2.60.0). ([#1898](https://github.com/nextstrain/auspice/pull/1898))

#### Internal / development changes
* Convert the tree component (and related tree-parsing functions) to TypeScript ([#1864](https://github.com/nextstrain/auspice/pull/1864))

## version 2.60.0 - 2024/11/07

> _Note: this release contains a few rather large bugs and we suggest you upgrade to 2.61.2 or later_

* Performance improvement: We no longer attempt to animate actions on trees with over 4000 tips which results in more responsive interactions. ([#1880](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/pull/1879))
* Bugfix: narrative slide changes which removed a filter would not work as expected in some cases ([#1883](https://github.com/nextstrain/auspice/pull/1883))

#### Internal / development changes
* Refactor how the measurement-sidecar JSON is loaded ([#1881](https://github.com/nextstrain/auspice/pull/1881))
* Move jest config to TypeScript  ([#1885](https://github.com/nextstrain/auspice/pull/1885))
* Move jest-puppeteer with Playright  ([#1884](https://github.com/nextstrain/auspice/pull/1884))
* Verbose logging during CI ([#1876](https://github.com/nextstrain/auspice/pull/1876))


## version 2.59.1 - 2024/10/23


* Moved the "Focus on Selected" toggle next to the "Show confidence intervals" toggle.
  ([#1875](https://github.com/nextstrain/auspice/pull/1875))

## version 2.59.0 - 2024/10/22


* 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](https://github.com/nextstrain/auspice/pull/1373))

## version 2.58.0 - 2024/09/12


* Fix bug where drag-and-drop metadata columns were no longer included as tip labels ([#1845](https://github.com/nextstrain/auspice/pull/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](https://github.com/nextstrain/auspice/pull/1849))
* Added URL params for measurements panel controls: m_collection, m_display, m_groupBy, m_overallMean, m_threshold, and mf_*.
  See [docs](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/view-settings.html#measurements-panel-url-query-options) for more details. ([#1848](https://github.com/nextstrain/auspice/pull/1848))

## version 2.57.0 - 2024/08/30


* Remove hardcoded color scale for LBI ([#1842](https://github.com/nextstrain/auspice/pull/1842))
* Any `node_attr` in the tree can be used as a tip label, as well as the special-cases of strain-name and "none".
  Previously we only allowed valid colorings.
  ([#1668](https://github.com/nextstrain/auspice/pull/1668))
* The specified tip label is surfaced more prominently within the the on-hover info boxes & on-click modals.
  ([#1668](https://github.com/nextstrain/auspice/pull/1668))
* Temporal colour scales can now use YYYY-MM-DD values (previously only numeric dates were allowed).
  Ambiguous (YYYY-MM-XX, YYYY-XX-XX) dates are allowed and the midpoint of the range will be used to choose the colour.
  ([#1832](https://github.com/nextstrain/auspice/pull/1832), [#1836](https://github.com/nextstrain/auspice/pull/1836))
* Parsing and error handling for URL query-encoded dates (`dmin`, `dmax`, `animate`) has been improved.
  ([#1832](https://github.com/nextstrain/auspice/pull/1832))
* Div-only trees (i.e. no timetree) now hide the date / animation sections in the sidebar.
  ([#1834](https://github.com/nextstrain/auspice/pull/1834))
* Improvements to how we use React within the measurements panel (should not result in any user-facing changes).
  ([#1838](https://github.com/nextstrain/auspice/pull/1838))

## version 2.56.1 - 2024/08/22


* Fix bug where app crashed if measurements JSON did not define thresholds ([#1802](https://github.com/nextstrain/auspice/pull/1802))
* Fix bug where measurements display did not honor the default `measurements_display` ([#1802](https://github.com/nextstrain/auspice/pull/1802))
* Only display download-JSON button if the dataset name can be parsed from pathname ([#1804](https://github.com/nextstrain/auspice/pull/1804))
* Fix bug where measurements panel did not display means for measurements that had an "undefined" coloring ([#1827](https://github.com/nextstrain/auspice/pull/1827))
* Measurement panel's x-axis min/max values are now limited by visible measurements ([#1827](https://github.com/nextstrain/auspice/pull/1827))

## version 2.56.0 - 2024/07/01


* We now use the reported confidence / entropy values to change the saturation of tips (circles) on the tree, which matches the behaviour seen for branches. If there is no (or very little) uncertainty in these nodes then the tips will appear the same as seen in previous versions of Auspice. ([#1796](https://github.com/nextstrain/auspice/pull/1796))
* We no longer show the "second tree" sidebar dropdown when there are no available options. The possible options are defined by [the charon/getAvailable API](https://docs.nextstrain.org/projects/auspice/en/stable/server/api.html) response and as such vary depending on the server in use. ([#1795](https://github.com/nextstrain/auspice/pull/1795))


## version 2.55.1 - 2024/06/25


* Small bugfix to the filter badge improvements introduced in v2.55.0 where we incorrectly showed the 2-tree display when viewing a single tree. ([#1794](https://github.com/nextstrain/auspice/pull/1794))

## version 2.55.0 - 2024/06/17


* A number of improvements when viewing multiple trees (tangletrees) ([#1788](https://github.com/nextstrain/auspice/pull/1788))
  * Attributes only present on the RHS tree are now available as filter options, as well as genotypes and node names unique to the RHS tree.
  * Filter badges (shown in the header) now indicate how many matches are present in both trees (formerly only the LHS tree was considered)
  * Branch labels unique to the RHS tree are now available
* remove missing warning when dataset JSON has no `.meta.geo_resolutions` field ([#1791](https://github.com/nextstrain/auspice/pull/1791))
* Add support for Node.js version 22. ([#1779](https://github.com/nextstrain/auspice/pull/1779))

## version 2.54.3 - 2024/06/12


* Minor improvement to the [onlyPanels](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/view-settings.html#url-query-options) view - we now also hide the panel name and top-border. ([#1790](https://github.com/nextstrain/auspice/pull/1790))

## version 2.54.2 - 2024/06/12

* Tangletrees can now be coloured by genotype (previously such a colouring would only work for the LHS tree). This requires the genome annotation (in the dataset JSON) to be identical across both datasets. This can be especially useful when comparing trees generated from the same sequences or a similar set of sequences in order to understand the differences in tree structure. ([#1785](https://github.com/nextstrain/auspice/pull/1783))
* Bugfix: The legend entries shown for a tangletree may not have shown values only observed in the RHS tree when the dataset was first loaded. ([#1785](https://github.com/nextstrain/auspice/pull/1783))
* Bugfix: Multiple trees ("tanglegrams") now render correctly in Safari. ([#1786](https://github.com/nextstrain/auspice/pull/1786))
* Bugfix: The [onlyPanels](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/view-settings.html#url-query-options) URL query now hides all parts of the footer, as intended. ([#1787](https://github.com/nextstrain/auspice/pull/1787))

## version 2.54.1 - 2024/06/10

* Fixed a big bug where clicking on tips (and shift-clicking on branches) on the RHS tree in a tanglegram would bring up a modal detailing a node in the LHS tree. ([#1783](https://github.com/nextstrain/auspice/pull/1783))
* Fixed a small bug where branch labels prevented you from hovering on the branch itself, a situation that was more common in tangletrees. ([#1783](https://github.com/nextstrain/auspice/pull/1783))


## version 2.54.0 - 2024/06/06

* Add a link-out to use datasets in Nextclade (this functionality is only enabled when running within the larger nextstrain.org ecosystem.)
This builds on functionality introduced in [Nextclade 3.7.0](https://github.com/nextstrain/nextclade/releases/tag/3.7.0) allowing an Auspice dataset to be used as a nextclade dataset so that users can then add new sequences (via drag-and-drop) and see them placed on the tree. ([#1776](https://github.com/nextstrain/auspice/pull/1776))

## version 2.53.0 - 2024/04/29

* Add a download-JSON button within the downloads modal. This is disabled for GISAID sourced data. ([#1764](https://github.com/nextstrain/auspice/pull/1764))
* Add link-outs to load the current dataset in external platforms MicrobeTrace and Taxonium. Note this functionality only works when Auspice is running within the larger nextstrain.org server. ([#1763](https://github.com/nextstrain/auspice/pull/1763))

_Internal changes._

* Use Nextstrain CLI to create PRs on other repos. ([#1765](https://github.com/nextstrain/auspice/pull/1765))
* Create PRs on projects which depend on Auspice by adding a label ([#1767](https://github.com/nextstrain/auspice/pull/1767) and [#1768](https://github.com/nextstrain/auspice/pull/1768))


## version 2.52.1 - 2024/02/21

* Bugfix: Restore the intended behaviour when hovering or clicking on terminal branches. ([#1753](https://github.com/nextstrain/auspice/pull/1753))

## version 2.52.0 - 2024/02/09

* Sidebar filtering now contains all non-continuous metadata defined across the tree (i.e. all data within `node.node_attrs`). The traits listed in `meta.filters` are now only used to determine which filters to list in the footer of the page. ([#1743](https://github.com/nextstrain/auspice/pull/1743))
* The interaction between strain-selected modals and the corresponding strain-filter has been improved. We now preserve the strain filter state present before the node was clicked. ([#1749](https://github.com/nextstrain/auspice/issues/1749))
* Added a link to this changelog from the Auspice view. ([#1727](https://github.com/nextstrain/auspice/pull/1727))
* Updated "contact us"-type links to point to nextstrain.org/contact. ([#1734](https://github.com/nextstrain/auspice/issues/1734))
* Bugfix: When showing the strain-selected modal, disabling the corresponding filter now clears the modal. ([#1749](https://github.com/nextstrain/auspice/issues/1749))

_Internal changes which should not result in any different behaviour while using Auspice._

* Updates to GitHub actions. ([#1739](https://github.com/nextstrain/auspice/issues/1739), [#1741](https://github.com/nextstrain/auspice/issues/1741))
* Updates to documentation setup. ([#1730](https://github.com/nextstrain/auspice/issues/1730))
* Updates to PR template. ([#1728](https://github.com/nextstrain/auspice/issues/1728))
* Updated and then reverted Webpack configuration ([#1733](https://github.com/nextstrain/auspice/issues/1733), [#1738](https://github.com/nextstrain/auspice/issues/1738))

## version 2.51.0 - 2023/11/16


* Redesigned the panel sections in the sidebar. ([#1704](https://github.com/nextstrain/auspice/pull/1704))
    * Moved panel visibility toggles to the header.
    * Added the ability to show/hide panel options.
* customisation: Renamed `sidebarTheme.unselectedBackground` to a more generic name, `sidebarTheme.alternateBackground`, while keeping backwards compatibility. ([#1704](https://github.com/nextstrain/auspice/pull/1704/commits/1ad4376bb3be9787181110d47fe8c5f26a207896))
* Fixed a bug that prevented the narratives debugger (`/edit/narratives`) from working. ([#1725](https://github.com/nextstrain/auspice/issues/1725))

## version 2.50.0 - 2023/10/30


* Fixed a bug that showed SVG-related errors in the development browser console when viewing a tree in the rectangular layout. ([#1714](https://github.com/nextstrain/auspice/pull/1714))
* Added "Data updated" date under the dataset title, in addition to the existing mention in the footer. ([#1715](https://github.com/nextstrain/auspice/pull/1715))
* Updated docs on customizing the sidebar style with `sidebarTheme`. ([#1718](https://github.com/nextstrain/auspice/pull/1718))

_Internal changes which should not result in any different behaviour while using Auspice._

* Updated Redux usage. ([#1710](https://github.com/nextstrain/auspice/pull/1710), [#1712](https://github.com/nextstrain/auspice/pull/1712))

## version 2.49.0 - 2023/09/28



* Allow the tip label key to be defined in the JSON via `display_defaults.tip_label`, in addition to being settable via a URL query.
See [the docs](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/view-settings.html) or [PR #1668](https://github.com/nextstrain/auspice/pull/1668) for more.
* Tree-specific options in the sidebar are now hidden when the tree panel is not displayed. ([#1698](https://github.com/nextstrain/auspice/pull/1698))
* Fixed a bug where the radial trees would have their inner grid circles offset. ([#1693](https://github.com/nextstrain/auspice/pull/1693))
* Fixed a bug where SVG export of the entropy panel was invalid. ([#1694](https://github.com/nextstrain/auspice/pull/1694))

_Internal changes which should not result in any different behaviour while using Auspice._

* Read the Docs build config updated. ([#1700](https://github.com/nextstrain/auspice/pull/1700))
* CI improvements. ([#1702](https://github.com/nextstrain/auspice/pull/1702))

## version 2.48.0 - 2023/08/31

* Root sequence data may be inlined in the main dataset JSON
([Auspice PR #1688](https://github.com/nextstrain/auspice/pull/1688) and [Augur PR #1295](https://github.com/nextstrain/augur/pull/1295)).
* Bugfix: Fixes a crash when a dataset without the entropy panel attempted to change colorings. ([#1691](https://github.com/nextstrain/auspice/pull/1691))

## version 2.47.0 - 2023/08/21

* Entropy panel now supports more complex genome architectures and has improved styling.
The JSON schema has been extended to allow segmented CDSs, which allows us to represent CDSs such as those which
wrap the origin (common in HepB), and those with ribosomal slippage (nCoV, EBOV). The visual representation of CDSs
now better conveys overlapping CDSs, both in the lower "nav" axis where CDSs are stacked on top of each other and
in the upper "main" axis where we now view the translations for each CDS individually.
A number of small genotype-related bugs have also been fixed and the internal representation of the genome streamlined.
For full details please see [#1684](https://github.com/nextstrain/auspice/pull/1684), and the schema changes are
detailed in [augur PR #1281](https://github.com/nextstrain/augur/pull/1281).
* Fixed a bug where metadata TSV download was sometimes empty or incomplete, described in [issue #1411](https://github.com/nextstrain/auspice/issues/1411).
([PR #1681](https://github.com/nextstrain/auspice/pull/1681))
* Remove support for Node.js version 14. ([#1674](https://github.com/nextstrain/auspice/pull/1674))
* Add support for Node.js version 20. ([#1673](https://github.com/nextstrain/auspice/pull/1673))

## version 2.46.1 - 2023/06/12


* Fix a number of bugs related to continuous traits:
    * Negative (string) values are now correctly interpreted. See [issue #1626](https://github.com/nextstrain/auspice/issues/1626) and [PR #1655](https://github.com/nextstrain/auspice/pull/1655) for more.
    * Fix legend matching bounds (used when hovering over legend items). See [PR #1657](https://github.com/nextstrain/auspice/pull/1657) for more.
* Dependencies updated. See [PR #1669](https://github.com/nextstrain/auspice/pull/1669) for more.

## version 2.46.0 - 2023/05/15
* Fixed a bug where narratives with multiple datasets that had measurements panels would error when switching datasets. ([#1603](https://github.com/nextstrain/auspice/issues/1603))

_There have been a number of internal changes with this release, most of which should not result in any different behavior while using Auspice._

* Add basic TypeScript support ([#1450](https://github.com/nextstrain/auspice/pull/1450))
* Minor dev docs updates ([#1660](https://github.com/nextstrain/auspice/pull/1660))
* Overhaul of ESLint rules ([#1665](https://github.com/nextstrain/auspice/pull/1665))

## version 2.45.2 - 2023/03/22


* Fixed a bug for continuous color scales where tips with values of zero wouldn't appear on legend-hover or in the frequencies panel.
See [PR #1643](https://github.com/nextstrain/auspice/pull/1643) for more.
* Fixed a bug where downloaded TSVs may have unescaped quotes which resulted in incorrect parsing.
See [PR #1649](https://github.com/nextstrain/auspice/pull/1649) for more.
* Minor documentation updates. See [PR #1638](https://github.com/nextstrain/auspice/pull/1638) for more.

## version 2.45.1 - 2023/03/14

* Small improvements to Auspice documentation. ([#1588](https://github.com/nextstrain/auspice/pull/1588))

## version 2.45.0 - 2023/03/08


* Remove support for Node.js version 12. ([#1560](https://github.com/nextstrain/auspice/pull/1560))
* Add support for Node.js version 18 and NPM version 9. ([#1560](https://github.com/nextstrain/auspice/pull/1560))

## version 2.44.0 - 2023/03/02


* Added support for [Plausible Analytics](https://plausible.io) and deprecated support for Google Analytics. See the [documentation on configuring analytics](https://docs.nextstrain.org/projects/auspice/en/stable/customise-client/api.html#tracking-analytics). ([#1597](https://github.com/nextstrain/auspice/pull/1597))

## version 2.43.0 - 2023/02/07
* Improvements to the measurements panel including multiple thresholds, jitter of raw measurements within color-by groups, and a sticky x-axis. See [PR 1631](https://github.com/nextstrain/auspice/pull/1631).

## version 2.42.0 - 2022/12/15
* You can now turn off tip labels by selecting "none" in the dropdown. See [PR #1618](https://github.com/nextstrain/auspice/pull/1618)
* A bug in the measurements panel was fixed where the mean/SD may disappear. See [PR #1593](https://github.com/nextstrain/auspice/pull/1593)

_There have been a number of internal changes with this release, most of which should not result in any different behavior while using Auspice._

* Upgraded webpack 4 → 5. See [PR #1520](https://github.com/nextstrain/auspice/pull/1520) for more.
* Upgraded lockfile to the npm 7/8 format. See [PR #1602](https://github.com/nextstrain/auspice/pull/1602) for more.
* Webpack cleanups via [PR #1605](https://github.com/nextstrain/auspice/pull/1605)
* Documentation autobuilding via [PR #1609](https://github.com/nextstrain/auspice/pull/1609)
* Spelling fixes ([PR #1619](https://github.com/nextstrain/auspice/pull/1619), [PR #1620](https://github.com/nextstrain/auspice/pull/1620))

## version 2.41.0 - 2022/11/10
* A narratives debugger has been added at `/edit/narratives`.
See [PR #1590](https://github.com/nextstrain/auspice/pull/1590) or the new [Narratives Tutorial](https://docs.nextstrain.org/en/latest/tutorials/narratives-how-to-write.html) for more details.
Note: this functionality will prevent auspice from viewing a _dataset_ JSON named `edit_narratives.json`.


## version 2.40.1 - 2022/11/07
* Fixed a bug where downloaded Newick trees may be empty - often this happens when there is no newick representation for the tree being displayed and in these cases a warning notification is shown. See [PR #1591](https://github.com/nextstrain/auspice/pull/1591) for more.
* Fixed a bug where branch labels prevented clicking on the underlying branches. See [PR #1584](https://github.com/nextstrain/auspice/pull/1584) for more.

## version 2.40.0 - 2022/10/21
* Keep the measurements panel's color-by means in a stable order while filtering. See [PR #1566](https://github.com/nextstrain/auspice/pull/1566) for more.
* Allow setting the "show all branch labels" toggle via the URL query `?showBranchLabels=all`. See [PR #1575](https://github.com/nextstrain/auspice/pull/1575) for more.
* Fix a bug where ordinal scales wouldn't be colored correctly in the frequency pane. See [Issue #843](https://github.com/nextstrain/auspice/issues/843) and [PR #1578](https://github.com/nextstrain/auspice/pull/1578) for more.
* The legend can no longer have duplicate entries (both for user provided color scales and for continuous scales), which also prevents the display bug where legend items may be overlapping when switching to a different coloring. See issues [#1521](https://github.com/nextstrain/auspice/issues/1521) and [#1547](https://github.com/nextstrain/auspice/issues/1547), and [PR 1576](https://github.com/nextstrain/auspice/pull/1576).
* Re-enable temporal confidence bars for trees which include this data. See [PR #1577](https://github.com/nextstrain/auspice/pull/1577) for more.

## version 2.39.0 - 2022/10/06
* A range of improvements to the measurements panel including reference sera coloring
and more informative tooltips. See [PR 1557](https://github.com/nextstrain/auspice/pull/1557) for more.
* Color-by genotype dropdown: nuc (nucleotide) is now the first item in the list.
See [PR 1550](https://github.com/nextstrain/auspice/pull/1550) for more.
* Fixed a bug where zooming out one level would instead jump multiple levels.
See [PR 1552](https://github.com/nextstrain/auspice/pull/1552) for more.
* Added a toggle to force the display of all branch labels, rather than only those meeting
a certain threshold. See [PR 1554](https://github.com/nextstrain/auspice/pull/1554) for more.
* Install documentation updated. See [PR 1551](https://github.com/nextstrain/auspice/pull/1551) for more.


## version 2.38.0 - 2022/09/16
* Mutations now separate out "undeletions" & add information on what the categories represent.
See [PR 1542](https://github.com/nextstrain/auspice/pull/1542) for more.
* Bugfix where certain GISAID accessions may cause a crash when clicked.
See [PR 1531](https://github.com/nextstrain/auspice/pull/1531) for more.
* Duplicate / missing node names now emit a warning to the console, not an error.
See [PR 1543](https://github.com/nextstrain/auspice/pull/1543) for more.

#### Internal (Nextstrain-related) changes
* Documentation theme added. See [PR 1535](https://github.com/nextstrain/auspice/pull/1535) for more.
* Bioconda rebuild instructions added. See [PR 1539](https://github.com/nextstrain/auspice/pull/1539) for more.
* Minor docs formatting fixes. See [PR 1533](https://github.com/nextstrain/auspice/pull/1533) for more.


## version 2.37.3 - 2022/06/16
* Allow temporal colour scales.
See [PR 1523](https://github.com/nextstrain/auspice/pull/1523) for more.
* Change ordering of sidebar tree options.
See [PR 1524](https://github.com/nextstrain/auspice/pull/1524) for more.
* (Docs) Corrected note about CORS.
See [PR 1525](https://github.com/nextstrain/auspice/pull/1525) for more.
* (Internal) Automated how we make GitHub releases.
See [PR 1518](https://github.com/nextstrain/auspice/pull/1518) for more.

## version 2.37.2 - 2022/05/27
* Allow trees with duplicate node names / missing node names (but raise an error in the console).
See [PR 1514](https://github.com/nextstrain/auspice/pull/1514) for more.
* Fix a bug where the right hand side of the tree could disappear.
See [PR 1513](https://github.com/nextstrain/auspice/pull/1513) for more.

## version 2.37.1 - 2022/05/11
* Ensure legend colours are exactly the same as the tip colours.
See [PR 1506](https://github.com/nextstrain/auspice/pull/1506) for more.
* Always show branch labels if they are the root of a subtree.
See [PR 1503](https://github.com/nextstrain/auspice/pull/1503) for more.
* Docs improvements. See [PR 1507](https://github.com/nextstrain/auspice/pull/1507) for more.
* CI improvements. See [PR 1505](https://github.com/nextstrain/auspice/pull/1505) for more.

## version 2.37.0 - 2022/04/28
* Improved footer styling of tables.
See [PR 1502](https://github.com/nextstrain/auspice/pull/1502) for more.
* Branch labels are now shown/hidden depending according to the proportion of visible tips they define.
See [PR 1501](https://github.com/nextstrain/auspice/pull/1501) for more.

## version 2.36.0 - 2022/03/28

### Functional improvements

* Dynamically update regression lines to reflect filtered data.
See [PR 1484](https://github.com/nextstrain/auspice/pull/1484) for more.
* Scatterplot axes can now use "node-order" which is the order nodes appear on the rectangular tree.
See [PR 1494](https://github.com/nextstrain/auspice/pull/1494) for more.
* Show an "experimental" icon and on-hover info text for the explode-tree functionality.
See [PR 1486](https://github.com/nextstrain/auspice/pull/1486) for more.
* You can now use the escape key to remove a tip/branch info modal over the tree.
See [PR 1485](https://github.com/nextstrain/auspice/pull/1485) for more.

### Bugfixes

* Drag-n-drop metadata now works for the second tree.
See [PR 1489](https://github.com/nextstrain/auspice/pull/1489) for more.
* Available filters are now correct when switching from a narrative to exploding the data.
See [PR 1493](https://github.com/nextstrain/auspice/pull/1493) for more.
* The auspice server only accepts valid sidecar file types.
See [PR 1495](https://github.com/nextstrain/auspice/pull/1495) for more.

## version 2.35.0 - 2022/03/16
* Upgrade how we render dropdown menus, which greatly improves the display of long options (e.g. submitting labs).
See [PR 1482](https://github.com/nextstrain/auspice/pull/1482) for more.


## version 2.34.1 - 2022/03/08
* (Minor change) expose functions for use in auspice.us. See [PR 1478](https://github.com/nextstrain/auspice/pull/1478) for more.

## version 2.34.0 - 2022/03/02

#### Major changes
* Measurements panel intended for displaying titer or DMS data where a tip in the tree has multiple values associated with it.
This function requires a dataset with a `_measurements.json` sidecar file
See [PR 1452](https://github.com/nextstrain/auspice/pull/1452) for more.

#### Minor changes
* Improved YAML parsing for narratives
See [PR 1472](https://github.com/nextstrain/auspice/pull/1472) for more.
* Remove unused properties from tip-frequencies panel.
See [PR 1471](https://github.com/nextstrain/auspice/pull/1471) for more.
* Fixed a bug where shift+clicking on branches for trees without mutations defined caused a crash.
See [PR 1475](https://github.com/nextstrain/auspice/pull/1475) for more.



## version 2.33.0 - 2022/02/15

* (Experimental) Explode phylogeny into subtrees and allow multiple trees to be provided in the dataset.
See [PR 1442](https://github.com/nextstrain/auspice/pull/1442) for more.
* Categorise mutations to better understand sequence changes on branches and tips.
See [PR 1449](https://github.com/nextstrain/auspice/pull/1449) for more.
* Add a datepicker to allow precise changes to the selected date range.
See [PR 1412](https://github.com/nextstrain/auspice/pull/1412) for more.
* Allow build-time customizable fine print.
See [PR 1448](https://github.com/nextstrain/auspice/pull/1448) for more.
* Remove scrollbar in panels when no scrolling is possible
See [PR 1439](https://github.com/nextstrain/auspice/pull/1439) for more.
* Allow searching in the color-by dropdown.
See [PR 1456](https://github.com/nextstrain/auspice/pull/1456) for more.

There have also been internal changes related to how we run CI. These should not affect using Auspice as a library / CLI.

## version 2.32.1 - 2021/11/11
* Fix URL parsing to allow the string "narratives" to be in a dataset without it being interpreted as a narrative itself.
See [PR 1428](https://github.com/nextstrain/auspice/pull/1428) for more.

## version 2.32.0 - 2021/10/20

* Tree info boxes are now improved, and you can shift+click on a branch to see more information about that branch.
See [PR 1420](https://github.com/nextstrain/auspice/pull/1420) for more.
* Filters in footer are now expandable to improve usability and discoverability of the true footer.
See [PR 1414](https://github.com/nextstrain/auspice/pull/1414) for more.
* Fixed a bug with CSV (drag & drop) parsing. See [PR 1401](https://github.com/nextstrain/auspice/pull/1401) for more.
* Removed unnecessary postinstall step. See [PR 1419](https://github.com/nextstrain/auspice/pull/1419) for more.
* Improved image sizing in narratives. See [PR 1408](https://github.com/nextstrain/auspice/pull/1408) for more.
* Improved documentation around how to build auspice documentation!


## version 2.31.0 - 2021/09/16
* Improvements to our ability to zoom out in a tree, both by exposing the root branch and via a new icon next to "Zoom to Selected".
See [PR 1392](https://github.com/nextstrain/auspice/pull/1392) for more.

## version 2.30.0 - 2021/09/07

* Narratives can now load sidecar files and second trees.
This allows allowing frequency panel display, colouring by root-sequence, and tanglegrams.
See [PR 1305](https://github.com/nextstrain/auspice/pull/1305) for more.
* Excel (`.xlsx`) files can be used as additional metadata for drag-and-drop.
See [PR 1386](https://github.com/nextstrain/auspice/pull/1386) for more.
* Trees are now clipped to improve axes visibility.
See [PR 1383](https://github.com/nextstrain/auspice/pull/1383) for more.
* Improved accession URL creation.
See [PR 1382](https://github.com/nextstrain/auspice/pull/1382) for more.
* minor documentation improvements.

## version 2.29.1 - 2021/07/16

* Update TravisCI script to improve how we publish Auspice to npm.
See [PR 1380](https://github.com/nextstrain/auspice/pull/1380) for more.

## version 2.29.0 - 2021/07/15

**Note: this version may not install from npm. Please use v2.29.1 instead**

* Branch labels are no longer displayed if the branch is not in the selected view.
See [PR 1370](https://github.com/nextstrain/auspice/pull/1370) for more.
* Clicking on a tip and then closing the info-box will result in that tip remaining as a inactivated filter.
See [PR 1372](https://github.com/nextstrain/auspice/pull/1372) for more.
* Category filters in the sidebar can now be used to inactivate all active filters in a category, and if all are inactive then this may be used to re-activate them all.
See [PR 1371](https://github.com/nextstrain/auspice/pull/1371) for more.
* On-hover tooltip widths are improved for the tree. See [PR 1375](https://github.com/nextstrain/auspice/pull/1375) for more.
* [bugfix] Colour scales can now have 37 values. See [PR 1355](https://github.com/nextstrain/auspice/pull/1355) for more.

#### Minor updates
* Docs updates
* Updated files fetched by `npm run get-data`

## version 2.28.0 - 2021/07/05

* Remove ability to download metadata TSV from GISAID datasets. Replace with acknowledgments TSV. See [PR 1366](https://github.com/nextstrain/auspice/pull/1366).
* Cleanup header fields when downloading metadata TSV, including switch to use name (eg `pango_lineage`) instead of title (eg `PANGO lineage`). See [PR 1367](https://github.com/nextstrain/auspice/pull/1367).
* Update styling of footer text. See [PR 1364](https://github.com/nextstrain/auspice/pull/1364).

## version 2.27.0 - 2021/06/05

* Adjust greyscale colour ramp.
See [PR 1353](https://github.com/nextstrain/auspice/pull/1353) for more.
* (Bugfix) Fixed the situation where the regression toggle would not appear for clock layouts.
See [PR 1352](https://github.com/nextstrain/auspice/pull/1352) for more.

## version 2.26.0 - 2021/05/25
* Scatterplot improvements:
  * Non-continuous variables can now be used, which allows all colourings (including Genotype, if that's the current colouring) to be scatterplot variables.
  * Jittering is applied when the spacing between axis variables is more than 50 pixels.
  * See [PR 1346](https://github.com/nextstrain/auspice/pull/1346) for more.
* Normalized frequency values now tend to zero in the absence of data.
See [PR 1325](https://github.com/nextstrain/auspice/pull/1325) for more.
* Colour scale improvements:
  * Continuous colourings can provide a scale, which we interpolate between to get the colour scheme
  * Custom legend data can be provided, including display text and, for continuous variables, bounds to map legend entries to values in the data.
  * Displayed legend entires may be restricted by specifying them in the dataset JSON.
  * See [PR 1340](https://github.com/nextstrain/auspice/pull/1340) for more.
* Filtering via the sidebar UI now returns options which match each of the space-separated queries, rather than requiring an exact match of the query.
See [PR 1344](https://github.com/nextstrain/auspice/pull/1344) for more.
* Legend text now takes the maximum available space.
See [PR 1328](https://github.com/nextstrain/auspice/pull/1328) for more.

## version 2.25.1 - 2021/04/07
* Bugfix for cases where certain interactions with scatterplot variables would cause auspice to crash.
See [PR 1332](https://github.com/nextstrain/auspice/pull/1332) for more.


## version 2.25.0 - 2021/03/31

* Scatterplots are now available as a tree layout.
These allow graphs to be created between any two continuous traits (colourings), similar to the "clock" layout but with user-definable variables
Branches and regression lines can be toggled on/off, and nodes which do not define valid values for both variables will be hidden.
Note that the regression line is calculated with a free intercept, which differs from the clock view where we force it to pass through the root.
See [PR 1310](https://github.com/nextstrain/auspice/pull/1310) and [PR 1326](https://github.com/nextstrain/auspice/pull/1326) for more.
* Datasets may now define "data provenance" which will be rendered in the byline.
See [PR 1313](https://github.com/nextstrain/auspice/pull/1313) for more.
* Names within the filtering UI now use the metadata-provided title, which is clearer.
See [PR 1327](https://github.com/nextstrain/auspice/pull/1327) for more.
* Frequency rounding is improved for small values.
See [PR 1301](https://github.com/nextstrain/auspice/pull/1301) for more.
* Node traits may define a URL which will result in the value being displayed as a link.
See [PR 1308](https://github.com/nextstrain/auspice/pull/1308) for more.
* A bug was fixed which caused some datasets to crash auspice when metadata files were dragged on.
See [PR 1319](https://github.com/nextstrain/auspice/pull/1319) for more.

## version 2.24.1 - 2021/03/19

* [bugfix] Fixes a bug introduced in v2.24.0 where certain datasets wouldn't load

## version 2.24.0 - 2021/03/17

* Frequencies are no longer normalized when the data is lacking.
See [PR 1278](https://github.com/nextstrain/auspice/pull/1278) for more.
* Fixed a stack size bug, which mainly affected the TB dataset on certain browsers.
See [PR 1293](https://github.com/nextstrain/auspice/pull/1293) for more.
* Root-to-tip mutations are now displayed in the tip-clicked info box.
See [PR 1280](https://github.com/nextstrain/auspice/pull/1280) for more.
* Datasets may now define the default language.
See [PR 1303](https://github.com/nextstrain/auspice/pull/1303) for more.
* Polish language added.
See [PR 1288](https://github.com/nextstrain/auspice/pull/1288) for more.
* Tips in the tree should no longer be obscured behind the legend.
See [PR 1302](https://github.com/nextstrain/auspice/pull/1302) for more.
* Dates BCE are now correctly displayed in the phylogeny axis.
See [PR 1297](https://github.com/nextstrain/auspice/pull/1297) for more.


## version 2.23.0 - 2021/01/28
* [feature] Implement genotype filtering.
The sidebar, typing-based filter UI now includes genotypes (for datasets which define mutations on branches).
See [PR 1265](https://github.com/nextstrain/auspice/pull/1265) for more.
* [bugfix] Update how we generate the bundle hashes as the fix introduced in v2.22.2 was insufficient.
See [PR 1272](https://github.com/nextstrain/auspice/pull/1272) for more.

## version 2.22.2 - 2021/01/14
* [bugfix] Updated how we generate hashes for the transpiled, chunked client bundles.
This prevents subtle bugs where bundles could have the same hash, but different contents, and thus stale (browser cached) chunks may be used in certain situations.
This bug most probably arose in v2.22.0, so please update to this version if possible!
See [PR 1263](https://github.com/nextstrain/auspice/pull/1263) for more.

## version 2.22.1 - 2021/01/13
* Updated package-lock JSON file

## version 2.22.0 - 2021/01/11

* The address Auspice uses to fetch map tiles, including the API token, has been updated and will now only work for local installs of auspice.
For help on how to specify your own address, which lets you specify custom map tile sets, see [the Auspice docs](https://docs.nextstrain.org/projects/auspice/en/stable/customise-client/api.html#specifying-the-api-server-address).
See [PR 1261](https://github.com/nextstrain/auspice/pull/1261) for more.
* Animation controls have moved and are now in the sidebar, underneath the date-slider.
See [PR 1262](https://github.com/nextstrain/auspice/pull/1262) for more.
* The footer has been updated to streamline the Nextstrain accreditation and now displays "Powered by Nextstrain".
If you are serving your own version of auspice we ask for this accreditation to remain be maintained, in keeping with the spirit of scientific citations.
Please also remember that customised version of auspice must make their source code available, as per Auspice's licence.
See [PR 1260](https://github.com/nextstrain/auspice/pull/1260) for more.

## version 2.21.0 - 2021/01/06

### Improved Functionality

* Tree rendering and zooming has been improved.
  * A new **Zoom to Selected** button has been added which allows you to zoom the tree to the clade containing the currently selected tips ([PR 1257](https://github.com/nextstrain/auspice/pull/1257)).
  * Branches ancestral to the common ancestor of the currently selected tips are now correctly rendered ([PR 1248](https://github.com/nextstrain/auspice/pull/1248)).
* The **Download Data** functionality has been improved to export data reflecting the currently viewed subset of data.
Additionally we export annotated Nexus trees which can be parsed by [FigTree](http://tree.bio.ed.ac.uk/software/figtree/).
See [PR 1245](https://github.com/nextstrain/auspice/pull/1245) for more.
* The **drag & drop metadata** functionality has been improved to facilitate easier filtering, custom locations and colours.
See [PR 1244](https://github.com/nextstrain/auspice/pull/1244) or [these docs](https://docs.nextstrain.org/projects/auspice/en/latest/advanced-functionality/drag-drop-csv-tsv.html) for more.
* **Tip labels** are now user-selectable via a drop-down in the sidebar.
See [PR 1246](https://github.com/nextstrain/auspice/pull/1246) for more.
* **Legend values** now dynamically update to reflect those in the current view.
See [PR 1250](https://github.com/nextstrain/auspice/pull/1250) for more.


#### Other Changes

* Italian translation added. See [PR 1256](https://github.com/nextstrain/auspice/pull/1256).
* Amino acid labels are only shown on branches leading to big clades.
See [PR 1249](https://github.com/nextstrain/auspice/pull/1249) for more.
* Colour scale generation has been refactored and a (rare) bug fixed where color-bys which defined a scale in the JSON could cause tips with no trait value set to have a colour rather than a shade of grey.
See [PR 1237](https://github.com/nextstrain/auspice/pull/1237).
* Warnings added to documentation pages which