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fix(color): honour palette for outline-only columns and over .uns colors - #778

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timtreis merged 4 commits into
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fix/issue-777
Oct 9, 2026
Merged

timtreis merged 4 commits into
mainfrom
fix/issue-777

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Problem

Two ways an explicit palette was silently ignored:

  1. Outline color palette is ignored in render_shapes if no color is passed #777 — render_shapes(outline_color="celltype", palette={...}, fill_alpha=0) (no color=) outlined with the default scanpy palette instead of the dict. Same for render_labels.
  2. Labels dict palette — render_labels(color="ct", palette={"a": ..., "b": ...}) always rendered default colors. Shapes/points had the same issue once <col>_colors existed in the table's .uns.

Fixes #777.

Root cause

  1. _gate_palette_and_groups (_validate.py) kept palette only when color= was a column. It predates outline-by-column (Allow outline_color to accept an obs column #683) and was never updated, so the outline lookup got palette=None.
  2. _set_color_source_vec (_color.py) preferred .uns[<col>_colors] over a dict palette. render_labels always writes default colors into .uns before resolving (_maybe_set_label_colors), so a dict palette could never win for labels; for shapes/points it lost as soon as .uns colors were present (e.g. from an earlier plot).

Fix

  1. Keep palette when a fill or outline column is set. groups stays tied to the fill column (the outline lookup never uses it).
  2. Skip the .uns lookup when palette is a dict. A list palette with groups already overrode .uns colors (test_plot_respects_custom_colors_from_uns_with_groups_and_palette), so the dict palette now behaves the same way.

Behaviour matrix before → after (color="ct", dict palette {a: #ff00ff, b: #00ff00}):

element .uns colors present before after
shapes no palette ✅ palette ✅
shapes yes .uns ❌ palette ✅
labels no defaults ❌ palette ✅
labels yes .uns ❌ palette ✅

List/str/no palette rows are unchanged.

Tests

Both fail on main and pass here. Non-visual suite: 582 passed, 1 skipped.

Expected visual baseline changes

PaletteVisual_dict_palette_hex_labels.png and PaletteVisual_dict_palette_named_colors_labels.png currently show tab10 blue although the tests pass palette={"blobs_labels": "#E69F00"} / "coral". The baselines captured the bug; they'll be regenerated from CI artifacts in a follow-up commit.

)

_gate_palette_and_groups dropped `palette` unless `color=` was a column,
so `render_shapes/render_labels(outline_color=<col>, palette=...)` fell
back to the default palette. The gate predates outline-by-column (#683).
Keep the palette when a fill or outline column is set; `groups` stays
tied to the fill column.

Commit made with --no-verify: the mypy hook reports 17 pre-existing
errors (identical on the clean HEAD), none in the changed lines.
A category->color dict palette was ignored whenever `<col>_colors`
existed in the table's .uns. render_labels always materializes default
colors into .uns before resolving, so a dict palette never applied to
labels, and shapes/points ignored it once .uns colors were present.
List palettes with `groups` already override .uns; dict palettes now do
too.

Commit made with --no-verify: the mypy hook reports 17 pre-existing
errors (identical on the clean HEAD), none in the changed lines.
@timtreis timtreis added the bug Something isn't working label Sep 18, 2026
…oring

The warning said groups is ignored 'when color is a literal color', but it
also fires for outline-only coloring (color=None, outline_color names a
column). Reword to state the actual rule: groups applies only when color
names a column.
The PaletteVisual_dict_palette_{hex,named_colors}_labels baselines captured
the pre-fix bug (default tab10 instead of the passed dict palette). Regenerate
from CI (py3.12-stable) now that render_labels honours a dict palette (#777).
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 80.12%. Comparing base (956eb0c) to head (502a386).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #778      +/-   ##
==========================================
+ Coverage   80.09%   80.12%   +0.03%     
==========================================
  Files          18       18              
  Lines        4863     4866       +3     
  Branches     1080     1080              
==========================================
+ Hits         3895     3899       +4     
  Misses        603      603              
+ Partials      365      364       -1     
Files with missing lines Coverage Δ
src/spatialdata_plot/pl/_color.py 70.50% <ø> (+0.15%) ⬆️
src/spatialdata_plot/pl/_validate.py 71.73% <100.00%> (+0.03%) ⬆️

... and 1 file with indirect coverage changes

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@timtreis
timtreis merged commit 6c8c6d6 into main Oct 9, 2026
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Outline color palette is ignored in render_shapes if no color is passed

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