Auspice Versions Save

• Add a download-JSON button within the downloads modal. This is disabled for GISAID sourced data. (#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)

Internal changes.

• Use Nextstrain CLI to create PRs on other repos. (#1765)
• Create PRs on projects which depend on Auspice by adding a label (#1767 and #1768)

• Bugfix: Restore the intended behaviour when hovering or clicking on terminal branches. (#1753)

• 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)
• 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)
• Added a link to this changelog from the Auspice view. (#1727)
• Updated "contact us"-type links to point to nextstrain.org/contact. (#1734)
• Bugfix: When showing the strain-selected modal, disabling the corresponding filter now clears the modal. (#1749)

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

• Updates to GitHub actions. (#1739, #1741)
• Updates to documentation setup. (#1730)
• Updates to PR template. (#1728)
• Updated and then reverted Webpack configuration (#1733, #1738)

• Redesigned the panel sections in the sidebar. (#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)
• Fixed a bug that prevented the narratives debugger (/edit/narratives) from working. (#1725)

• Fixed a bug that showed SVG-related errors in the development browser console when viewing a tree in the rectangular layout. (#1714)
• Added "Data updated" date under the dataset title, in addition to the existing mention in the footer. (#1715)
• Updated docs on customizing the sidebar style with sidebarTheme. (#1718)

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

• Updated Redux usage. (#1710, #1712)

• 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 or PR #1668 for more.
• Tree-specific options in the sidebar are now hidden when the tree panel is not displayed. (#1698)
• Fixed a bug where the radial trees would have their inner grid circles offset. (#1693)
• Fixed a bug where SVG export of the entropy panel was invalid. (#1694)

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

• Read the Docs build config updated. (#1700)
• CI improvements. (#1702)

• Root sequence data may be inlined in the main dataset JSON (Auspice PR #1688 and Augur PR #1295).
• Bugfix: Fixes a crash when a dataset without the entropy panel attempted to change colorings. (#1691)

• 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, and the schema changes are detailed in augur PR #1281.
• Fixed a bug where metadata TSV download was sometimes empty or incomplete, described in issue #1411. (PR #1681)
• Remove support for Node.js version 14. (#1674)
• Add support for Node.js version 20. (#1673)

• Fix a number of bugs related to continuous traits:
  • Negative (string) values are now correctly interpreted. See issue #1626 and PR #1655 for more.
  • Fix legend matching bounds (used when hovering over legend items). See PR #1657 for more.
• Dependencies updated. See PR #1669 for more.

• Fixed a bug where narratives with multiple datasets that had measurements panels would error when switching datasets. (#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)
• Minor dev docs updates (#1660)
• Overhaul of ESLint rules (#1665)