feat(benchmarks): synthetic dataset template catalog (TASK 050) - #37
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Restructures genevector.benchmarks.synthetic into a unified catalog of named pathology templates. Adds three new builders (paracrine, niche, gradient) alongside the existing build_pathology, all sharing a v2.0 ground-truth schema with `phenotypes`, `genes`, and typed `pairs` collections. The new templates are smaller and more focused than build_pathology — each one cleanly exercises a specific spatial coupling mechanism: paracrine for ligand-receptor adjacency, niche for density-induced gene programs, gradient for 1D axial pathologies. Public API: list_templates() for discovery; build_*_dataset() per template; shared (adata, ground_truth) contract across all four. Documents each template in docs/synthetic_templates.md with parameter descriptions, biological intent, and rendered example layouts. Breaking: ground_truth schema bumped from v1.0 to v2.0. TASK 029 spatial eval updated to consume new schema. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
genevector.benchmarks.syntheticinto a unified catalog of named pathology templates:pathology(migrated),paracrine,niche,gradient.phenotypes/genes/pairscollections (typed pairkinds and generoles).genevector.benchmarks.spatial.evalto consume the new schema.docs/synthetic_templates.md(+ 4 rendered example layouts underdocs/_images/) and an RST stub wired into the Sphinx toctree.Templates
build_paracrine_datasetbuild_niche_datasetbuild_gradient_datasetbuild_pathologylist_templates()discovers all four; shared(adata, ground_truth)contract across the catalog.Breaking change
ground_truthschema bumped v1.0 → v2.0. The auxiliary keysadded_gene_namesandt_subtypesare removed; both are reconstructible fromgt[\"genes\"]andgt[\"phenotypes\"]. The TASK 029 spatial eval code is updated in this PR.Test plan
pytest tests/test_benchmarks_synthetic_templates.py -v(11 new tests)pytest tests/test_benchmarks_synthetic_overlay.py -v(10, all under v2.0)pytest tests/test_benchmarks_synthetic_layout.py -v(3, untouched)pytest tests/test_benchmarks_spatial_eval.py -v(5 pass, 2 pre-existing xfails)docs/_images/template_*.png)Out of scope / minor deviations from spec
added_gene_names/t_subtypes(not in the v2.0 spec; reconstructible).docs/source/synthetic_templates.rst(a brief stub that links to the canonical markdown). The markdown atdocs/synthetic_templates.mdremains the full reference per spec.🤖 Generated with Claude Code