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base repository: scverse/spatialdata-plot
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compare: feature/render-graph
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  • 6 commits
  • 9 files changed
  • 2 contributors

Commits on Apr 16, 2026

  1. Add end-to-end tests for render_graph 

    Three visual regression tests covering the highest-value scenarios:
- Basic graph overlay on shapes (KNN connectivity edges)
- Graph overlay on labels with background image (most common real-world case)
- Group-filtered graph (only edges between specified cell types)

Tests will fail until render_graph is implemented.

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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  2. Implement render_graph for spatial connectivity visualization 

    Adds `sdata.pl.render_graph()` to render spatial graph edges from
adjacency matrices stored in table.obsp, using element centroids
for coordinates. Supports shapes, points, and labels elements via
spatialdata.get_centroids().

Key features:
- connectivity_key accepts full obsp key or prefix (auto-resolves)
- element and table_name auto-discovered when unambiguous
- groups + group_key filtering (both-endpoints semantics)
- Rasterized LineCollection for performance
- No networkx dependency (direct sparse matrix to line segments)

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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  3. Address adversarial review findings 

    - Drop **kwargs from render_graph() and _render_graph() — the deferred
  execution pattern can't forward arbitrary kwargs, matching how other
  render functions use kwargs.get() for named options only
- Add adjacency matrix shape validation against table.n_obs to catch
  subset graphs stored in multi-region tables
- Fix CS dispatch to use get_transformation() for element-level CS
  membership instead of type-level has_shapes/has_labels flags
- Vectorize edge filtering: replace Python-loop set lookups with
  numpy boolean arrays (has_coord + np.isin for groups)
- Remove dead line (dict overwritten immediately)
- Use triu(k=1) to skip self-loops at the sparse level

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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  4. Add test coverage for auto-discovery, empty graph, and error paths 

    - Auto-discovery: render_graph() with no args finds the single table/element
- Empty graph: zero-edge adjacency matrix renders without error
- Error paths: missing obsp key, missing element, groups without group_key

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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  5. Remove unreachable adjacency shape validation 

    AnnData rejects mismatched obsp matrices at assignment time,
making this check dead code.

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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  6. Replace baseline images with Linux/CI-generated versions 

    Initial baselines were generated on macOS/arm64. Matplotlib anti-aliasing
produces subtly different output on Linux, causing CI failures with RMS
values 27-37 (tolerance 15). CI-generated images are byte-identical across
Python 3.11, 3.14-stable, and 3.14-pre.

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
    @timtreis @claude
    timtreis and claude committed Apr 16, 2026
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