Fix docstrings and remove dead code across public API#583
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Systematic audit of all public method docstrings against their implementations, fixing mismatches and removing dead/broken code. Docstring fixes: - Fix `norm` type/default in render_shapes, render_points (was `bool | Normalize, default False`, now `Normalize | None`) - Fix `palette` type across all render methods (add `dict[str, str]`) - Remove false claim that palette defaults to lightgray when groups given - Fix `cmap` description: continuous only, not discrete (render_shapes, render_points) - Fix `scale` description in render_shapes: applies to polygons too - Fix `method` description: "or" not "and", add >10k threshold - Fix `show()` return type: `Axes | list[Axes] | None`, not `sd.SpatialData` - Document all 13 missing `show()` parameters - Fix `render_labels` return type (was `None`) - Fix `render_points` return saying "shapes" (copy-paste) - Fix `render_labels` broadcasting example referencing render_images - Add Notes section to render_images: RGB auto-detection, compositing, cmap broadcast - Add type annotations to colorbar/colorbar_params across all methods - Fix `make_palette_from_data` color column lookup description - Fix OutlineParams docstring (was "Cmap params") - Fix typo "precendence" → "precedence" Dead code removal: - Remove `share_extent` from `show()` (accepted but never used) - Remove `na_color` from `render_images()` (no use case for images) - Remove `**kwargs` from `render_images()` (broken: crashed or was silently dropped) - Remove dead `transfunc` from `LabelsRenderParams` (stored but never read) - Remove vestigial `LabelsRenderParams.outline` field - Remove vestigial `ShapesRenderParams.contour_px` field New behavior: - Warn when user requests `colorbar=True` for 5+ channel images Related: #463, #582 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Change 5+ channel colorbar message to logger.info on auto mode only (explicit colorbar=True is not blocked) - Fix double periods in dataclass docstrings Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Align render_labels cmap/norm docstrings with shapes/points style - Remove misleading kwargs docstring entry from render_labels - Guard na_color processing in _type_check_params to skip images Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #583 +/- ##
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+ Coverage 76.28% 76.33% +0.05%
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Files 11 11
Lines 3259 3254 -5
Branches 756 756
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- Hits 2486 2484 -2
+ Misses 468 467 -1
+ Partials 305 303 -2
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Summary
share_extent,render_images(**kwargs),render_images(na_color=...), deadtransfuncin labels, vestigial dataclass fieldscolorbar=Truefor 5+ channel imagesDocstring fixes
normtype/default (bool | Normalize, default False→Normalize | None)palettetype: adddict[str, str]cmap: "discrete or continuous" → continuous onlyscale: "circles" → "shapes (circles and polygons)"method: "and" → "or", add >10k thresholdshow()return type:sd.SpatialData→Axes | list[Axes] | Noneshow()parametersrender_labelsreturn type:None→sd.SpatialDatarender_pointsreturn: "shapes" → "points"colorbar/colorbar_paramstype annotationsmake_palette_from_datacolor lookup descriptionDead code removal
show(share_extent=...)render_images(na_color=...)set_bad()never triggers.render_images(**kwargs)_prepare_cmap_norm()which doesn't accept them (would crash).vmin/vmaxdeprecated 18 months ago.LabelsRenderParams.transfunc_render_labels()never reads it. Filed #582 for the broader transfunc inconsistency.LabelsRenderParams.outlineFalse, never set or read.ShapesRenderParams.contour_px