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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[0.3.0] - 2026-05-19

Added

  • prune_chart_to_tree (default False): when on, chart rows whose chart_strain_field value isn't a tree tip are filtered out before drawing. CLI form: --prune-chart-to-tree / --no-prune-chart-to-tree. (#6)
  • -h is accepted as a short alias for --help on the tree-annotated-plot CLI.

Changed

  • Minimum supported Python lowered from 3.13 to 3.11. CI still runs on 3.13.

[0.2.2] - 2026-05-09

Fixed

  • mark_line, mark_trail, and mark_area now connect points in tree tip order regardless of other encodings on the chart. Previously, a user chart with an explicit categorical color-scale domain rendered with crisscrossing line segments because Vega-Lite's default connection-order heuristic ignored the strain-axis sort. The package now attaches a calculate transform that derives a per-row tip rank and points the order channel at that field on these marks. Any user-supplied order is left in place.
  • When color_tree_by is used together with a user chart that has its own color encoding (e.g. a titer plot colored by cell_line), the user chart's marks no longer disappear. The concat container now resolves the color scale as independent so the tree's color_value:N scale (with its tree-specific domain) is not merged with the user chart's color scale.

[0.2.1] - 2026-05-06

Fixed

  • Apply tree-tip ordering to chart axes that use untyped Altair shorthand (alt.Y("strain") without a :N / :O type suffix). Previously the sort override was silently skipped, so the chart rendered in data order instead of tree order.
  • An internal consistency check now raises if the spec-level walk and the live-object walk over the user's chart ever disagree on the number of strain-axis encodings, so silent skips like the one above can't recur in another shape.

[0.2.0] - 2026-05-06

Added

  • connect_leader_to_label (default False): extends each strain's dashed leader line all the way to its text label. When on, the chart's strain-axis labels are suppressed and replacement labels are rendered alongside the tree on its chart-facing edge.
  • strain_label_font_size (default 10), strain_label_font_weight (default "normal"), and shift_tree_loc (default 0) for tuning the size, weight, and placement of the connected labels.
  • color_tree_by (default None): color the tree's branches and tip circles by an Auspice node attribute (e.g. "subclade") or by the inferred genotype state at one or more sites (e.g. "genotype:HA1:158" or "genotype:HA1:158,189"). Colors, category ordering, and the bottom-of-plot legend match the Nextstrain view of the same tree.
  • tree_color_scale (default None): override the default coloring with an explicit {category: color} mapping. Keys must match the tree's categories one-to-one and the legend order follows the user's key order. CLI form: "value1=#hex1,value2=#hex2,...".
  • tree_color_legend_format (default None): pass any subset of Vega-Lite's Legend properties as a dict to style the tree's color legend (orient, direction, columns, padding, labelFontSize, titleFontSize, …). When orient is "left" or "right" and the user has not set columns or direction, columns=1 is forced so entries stack vertically. CLI form: a JSON object string.
  • tree_color_legend_show (default True): set to False to hide the tree's color legend entirely while still coloring the tree.
  • scale_bar_font_size (default 10): font size for the tree's scale bar label.

Changed

  • Default tree_line_width bumped from 1.5 to 2, default tree_node_size from 28 to 45. Tree branch lines and tip circles are now drawn at full opacity. The thicker / fuller defaults read better when the tree is colored (the prior values were tuned for unicolor black trees).

[0.1.0] - 2026-05-04

Initial release.