chore: promote dev → master (statistical_models removed)#108
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Jaureguy760 merged 1 commit intomasterfrom Apr 19, 2026
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chore: promote dev → master (statistical_models removed)#108Jaureguy760 merged 1 commit intomasterfrom
Jaureguy760 merged 1 commit intomasterfrom
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…_guide/analysis (#107) Per user direction, the consolidated statistical_models.rst is removed. Methods section is now a single page: mapping_filter.rst (canonical WASP filter contract, van de Geijn 2015). Rescued into user_guide/analysis.rst under a new "Defaults and contracts" section (~25 lines) to avoid losing the four WASP2-unique contracts that both the sophia decision-auditor and co-scientist hypothesis-critic flagged as load-bearing when the original "delete the stats stuff" proposal was evaluated: 1. pseudocount=1 + min_count=10 defaults 2. Profile-LRT ρ convention (ρ at null-MLE, df=1) — the scientific fix from PR #99 3. ρ bounds (1e-6, 1-1e-6) and linear-dispersion logit clip (±10) 4. BH-NaN trap warning (scipy raises; manual loop silently propagates) Plus pointer to mapping_filter.rst for the canonical filter contract that applies to both remapping and counting. Updated 6 inbound :doc: references: - index.rst toctree (removed entry) - faq.rst → points to user_guide/analysis - tutorials/bulk_workflow.rst (2 refs) → user_guide/analysis - tutorials/single_cell_workflow.rst → methods/mapping_filter - methods/mapping_filter.rst → user_guide/analysis Sphinx build clean, zero warnings.
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Summary
Promote `dev` to `master`. Single new commit:
Test plan