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MicrobeTrace v2.2

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@dacowan404 dacowan404 released this 22 Jul 15:52
Immutable release. Only release title and notes can be modified.
v2.2
23b512c

MicrobeTrace v2.2

July 22, 2026

Commit: 76881a8 (23b512c on github)

Highlights

  • Docked Key Tables: Added ability to dock key tables (node color, link color, node shape, and group color).
  • Global Node Shapes: Node shapes are now consistent across 2D Network, Map View, and optionally Phylogenetic Tree View.
  • Addition of 46 new shapes including various places, animals, vectors and people.
  • Improved Newick File Ingestion: Allowing for larger trees to be loaded into MicrobeTrace either directly or through Nextstrain.
  • Improved file loading, session restoration, dashboard layout persistence, and restored support for loading zipped MicrobeTrace session archives.
  • Expanded visualization controls across 2D Network, Map, Phylogenetic Tree, EpiCurve, Gantt, Bubble, and dashboard/table workflows.
  • Significantly expanded Cypress automated testing coverage to include more views and previously seen bugs.

New Features and Enhancements

  • Global:
    • Added 46 node icons/shapes, global node shape support, and made node shape a global variable working across 2D Network, Map, and Tree views.
    • Added docking/undocking support for individual key tables and improved key-table display behavior.
    • Node transparency transfers across relevant views (2D Network, Map View, Phylogenetic Tree, and Bubble View).
    • Added ability to display TN93 distances as a percentage or a decimal value.
  • Files View/Loading:
    • Microbetrace session (.microbetrace) files now save the layout of the dashboard, so users can load the exact dashboard that was previously saved.
    • Added update and update+reset options for file reload workflows.
    • Improved detection of various filetypes including node files.
    • Improved Newick and Nextstrain loading for larger trees by moving patristic distance processing into a worker-backed workflow and avoiding unnecessary tree recomputation when Newick files are supplied. Added validation and guardrails for large Newick-derived networks, including duplicate-tip and invalid-branch handling.
    • Added support for loading zippedMicrobeTrace session files
    • Added Excel date parsing and clearer JSON formatting requirements.
  • 2D Network View:
    • Added context menu actions to copy node IDs, copy sequences, and view node attributes.
    • Added link label sizing setting.
  • Map View:
    • Added auto-expansion for searched/selected metanodes, with an option to disable it.
    • Added basic node-size settings.
    • Added the option to add labels to offline maps.
    • Updated basemap (online) to use English map labels.
  • Phylogenetic Tree View:
    • Added ability to view subtree and reset tree to original state.
    • Added ability to view including branch labels/support values.
  • Alignment View:
    • Added support for adjusting start and end position, by default only the first 3kb of sequence is shown which improves rendering speed.
  • EpiCurve View:
    • Added EpiCurve label and legend font-size controls, borders, and updated default color-scheme.

Bug Fixes

  • Global:
    • Fixed a bug that would reset text values in key tables (ie. link color table). Now users can edit this text and it will persist.
    • Fixed a bug that set null/missing date values to earliest date in dataset. Now that date remains null. This affected several views including Bubble and Gantt Chart.
    • Fixed manual entry of percentage thresholds and threshold launch handling.
    • Fixed a bug that prevented launching MicrobeTrace into views other than 2D Network.
  • Files View/Loading:
    • Fixed overlay uploads and file prompt behavior after files load.
  • 2D Network View:
    • Fixed incorrect bidirectional link detection.
    • Fixed a bug where group labels would reposition in response to node label position changing.
    • Fixed a 2D Network startup timing issue that could cause early visual updates to run before the network was fully initialized.
    • Fixed null/blank value normalization issues during group creation which led to nodes being assigned to a null group if they don't have a field used for grouping.
  • EpiCurve View:
    • Fixed bug where global node color changes were updating EpiCurve colors.
  • Bubble View:
    • Fixed SVG export quality for collapsed (pie-chart) nodes.
  • Gantt Chart:
    • Fixed Gantt handling of null/invalid dates and automatic width sizing.

Maintenance, Security, & Testing

  • Updated Angular, Angular CLI, Angular Material/CDK, PrimeNG, ngx-leaflet, TypeScript/module-resolution configuration, and build output handling.
  • Updated dependencies including axios, lodash, minimatch, ajv, immutable, brace-expansion, path-to-regexp, serialize-javascript, terser-webpack-plugin, hono, vite, joi, shell-quote, undici, and related build tooling.
  • Added or expanded Cypress coverage for Bubble, Map, Tree, EpiCurve, 2D Network, Gantt, dashboard export, layout restore, threshold flows, custom icons, table docking, file updates, Newick/patristic behavior, and previously seen bugs.

Full changelog: v2.1...v2.2

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