Obs store ctrl panel clean - #322
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merging in small quality of life improvements for the 3D point cloud
Resolve conflicts from the squash-merged Align module (broadinstitute#314) now on main. The align module (calc_landmarks, calc_alignment_transform, align_serial_slices, _transform, _slices, serial_slices) landed on main via broadinstitute#314's squash-merge, so it conflicted with this branch's independent align development. This branch is a strict superset of that module (it adds the Landmark widget, plot_alignment, write_alignment_point_cloud, TPS area/shape regularization, the degree param, numeric slice-id ordering, and the Landscape `alignment` trait + gene-panel auto-hide), so align source and align tests resolve to this branch's versions. Preserved from main: test_yearbook_cluster_attr_synced_for_custom_cluster_key in tests/unit/test_viz/test_widget.py. Rebuilt the JS bundle from the uncontested js/ source. Full suite: 249 passed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Alpha pre-release to make the Landmark widget and point-cloud alignment views easier to test on Manifold.ai. Bumps pyproject.toml + package.json to 0.19.0a3 and adds the CHANGELOG entry (Landmark widget, TPS area/shape regularization, plot_alignment, write_alignment_point_cloud, Landscape alignment= arg, gene-panel auto-hide). Also notes in _slice_centroids that the Landmark centroid payload is an extensible per-cell columnar schema, so future gene-expression coloring (red-fill + expression-driven opacity, matching Landscape) is an additive column + alpha branch rather than a rework. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Landmark is a visualization widget, so it now lives in celldega.viz alongside Landscape, Yearbook, Clustergram, and Enrich — importable as dega.viz.Landmark (and still dega.Landmark). - git-rename src/celldega/align/widget.py -> src/celldega/viz/landmark_widget.py (pure rename: its imports of celldega.viz.widget and celldega.align._slices are absolute and stay valid; no content change). - viz/__init__: export Landmark. align/__init__: drop Landmark export + update the roadmap docstring cross-ref. celldega/__init__: import Landmark from viz. - Update ~celldega.align.widget.Landmark docstring cross-refs to ~celldega.viz.Landmark. - Move the widget test to tests/unit/test_viz/. No import cycle: only align/widget.py imported viz, and it moved out, so align no longer depends on viz; the moved widget's one-directional viz -> align._slices dependency is fine. 249 tests pass, ruff clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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