Dega 667 set collection signatures

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[cornhundred]

0.26.0: SetCollection signatures, compact Clustergram controls, browser-side Enrich linking

Breaking

• Matrix no longer normalizes on construction: process() and the filter_genes / norm_col / norm_row / disable_processing arguments are removed. Call filter() / norm() explicitly.
• Marker ranking lives only in SetCollection: Matrix.marker_ranks, Matrix.set_marker_ranks() and downsample_to(rank_genes_groups=...) are removed.
• Matrix.cluster() returns the Matrix (for chaining) instead of a dict.
• calc_signature(rank_genes_groups=True) no longer silently ranks adata.raw. By default, raw counts are log-normalized (log1p(normalize_total), as Scanpy recommends) before ranking; use_raw=True explicitly ranks adata.raw.
• Clustergram ↔ Enrich linking is entirely browser-side (jslink), so live and static notebooks behave the same. Python observers removed.
• The unimplemented SetCollection.to_nbhd() stub is removed.

Added

• calc_signature: fraction_expressing_layer, rank_genes_groups_layer, var["{set_col}_marker"] (each gene's best-scoring cluster), expression-source reporting and raw-count warnings.
• Matrix(..., size_by_layer=...).
• Clustergram category-bar source dropdown (static attributes + manual category); category hover outline.
• Docs: Atera breast cancer and Visium HD human CRC Landscape + Clustergram + Enrich tutorials; sidebar toggle icon, also on gallery pages; Web Presentations moved to the bottom of the gallery.

Changed

• Compact Clustergram control panel: ROW/COL grid with order dropdowns and dendrogram sliders, DIM row, CROP | UNDO, PROP | UNIT. Category bars styled to match the Landscape.
• Changing the DIM level keeps each axis's order; a column order sorted by a gene falls back to CLUST only if that gene leaves the view.
• Logo moved into the gene search bars (Clustergram, Landscape, CellCloud, NeighborhoodCloud).
• spatial_clustergram sizes the Clustergram panel from its canvas (min 550px).
• Renames with deprecated aliases: cluster(view=), cut_tree(), size_matrix / set_size_matrix().
• Tooltip and bar-hover dwell delays; the manual-category dialog closes on outside clicks; Enrich link is blue, with logo spacing.

Fixed

• Render crash with static + manual categories; manual categories missing from the bars; new color on every keystroke.
• calc_signature: use_raw=True with an aggregation layer raised; mask_var was lost during automatic log-normalization.
• write_dega_files() without name=; .h5mu reload of SetCollection attributes.
• Wheel gestures over the Clustergram canvas or any widget control panel no longer scroll the page; scrollable boxes in the panels (bar plots, slider stacks, gene info) still scroll.

Review guide

Area	Start here
Matrix API cleanup	src/celldega/clust/matrix.py (constructor, cluster, cut_tree, set_size_matrix)
SetCollection signatures	src/celldega/set/collection.py → calc_signature (marker source / use_raw resolution, _log_normalized, {set_col}_marker)
Enrich linking	src/celldega/viz/__init__.py (_link_clustergram_to_enrich); js/global_variables/selected_genes.js (enrichmentSelection)
Control panel	js/ui/ui_containers.js (make_matrix_ui_container, block_page_scroll_in_panel); js/ui/text_buttons.js (make_reorder_dropdown, apply_reorder)
Category bars	js/ui/matrix_cat_bars.js (get_bar_sources, compute_breakdown, render_axis_cat_bar)
Order across views	js/deck-gl/matrix/rank_views.js (carry_order_across_view)
Hover / outline	js/deck-gl/matrix/cat_layers.js (ini_cat_outline_layer); js/deck-gl/matrix/matrix_layers.js (layer_filter)
Manual category editor	js/ui/attribute_editor.js (draft color, outside-click close)
Search + logo	js/ui/logo.js (embed_logo_in_search)
Layout sizing	spatial_clustergram (_clustergram_panel_width)

Skip: *.ipynb (embedded widget state), src/celldega/static/celldega.js, docs/assets/js/celldega.js (built bundle).

Testing

• 467 Python and 289 JS tests pass. New tests cover marker defaults and use_raw / mask_var, leiden_marker, panel sizing, browser link registration, enrichment selection labels, manual-category bars (jsdom), order carry-over across views and control-panel wheel handling.
• Docs notebooks re-executed; headless-Chrome render checks show no console errors.

🤖 Generated with Claude Code

[cornhundred]

Tested local notebooks and completed high-level review of Python API changes,