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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]

[0.4.0] - 2026-08-20

Added

  • spacing (default 0): pixels of blank space between the tree panel and the chart panel. 0 keeps the two butted together, as before. Distinct from shift_tree_loc, which moves the tree within its own panel by resizing the label strip. CLI form: --spacing.

Changed

  • Pin ruff to >=0.16,<0.17 and state the lint rules explicitly with [tool.ruff.lint] select. Ruff's default rule set widened in 0.16, which turned CI red on unchanged code; the selection is now a project decision rather than whatever the installed ruff defaults to. Development-only, no effect on the package.

Fixed

  • With connect_leader_to_label on, strain labels were anchored exactly on the tree panel's chart-facing edge, so the text ran up against the chart's frame and the frame line became hard to read. The pad that the label strip already reserved is now applied between the text and the chart, and the leader lines stop where the text begins rather than continuing to the panel edge. The gap is max(3, strain_label_font_size * 0.2) px, and the tree panel grows by that much, so a hand-tuned shift_tree_loc may want the same adjustment.

[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.