chore: promote dev → master (methods consolidation)#104
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Jaureguy760 merged 1 commit intomasterfrom Apr 19, 2026
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…e contracts) (#103) * docs(methods): consolidate statistical_models + absorb counting/dispersion/FDR Rewrite statistical_models.rst as single ~180-line page covering: - Beta-binomial model (unchanged essentials) - LRT with profile-likelihood convention (ρ held at null MLE, df=1) - Dispersion: single vs linear, AIC/BIC choice, ρ bounds (1e-6, 1-1e-6), logit clip (±10) — all WASP2-specific implementation contracts not in any paper - Phased vs unphased (uniform prior over 2^(n-1) configurations) - BH via scipy.stats.false_discovery_control - WASP2 defaults: pseudocount=1, min_count=10 - NaN-propagation warning for manual BH (matches MEMORY.md pitfall) - Output columns Extends mapping_filter.rst canonical-filter contract section with a single paragraph stating the same contract applies at the counting step (only 0x4 unmapped filter). This was previously buried in counting_algorithm.rst:69-75. Preserves four WASP2-unique contracts flagged by both the sophia decision-auditor and co-scientist hypothesis-critic: 1. Canonical filter contract at count step 2. Profile-LRT ρ convention (fix from PR #99) 3. BH-NaN trap warning 4. Default parameter values + ρ/logit bounds Next commit will delete counting_algorithm.rst, dispersion_estimation.rst, fdr_correction.rst and update toctree + cross-refs. * docs(methods): delete 3 consolidated pages + methods/index landing Removed: counting_algorithm.rst, dispersion_estimation.rst, fdr_correction.rst, methods/index.rst. All load-bearing WASP2-unique content (canonical filter contract at count step, profile-LRT ρ convention, BH-NaN trap, default values, ρ/logit bounds) was absorbed into statistical_models.rst and mapping_filter.rst in the previous commit. Updated 2 inbound cross-references: - faq.rst: methods/fdr_correction → methods/statistical_models - tutorials/bulk_workflow.rst: removed duplicate fdr_correction ref, kept single statistical_models ref Top-level index.rst toctree reduced from 6 methods entries to 2. Removed stale "Statistical Methods" landing caption was replaced by the main index.rst's own :caption: Statistical Methods toctree. Side benefit: eliminates the 3 pre-existing Sphinx duplicate-citation warnings (Kumasaka2016, vandeGeijn2015) by removing the duplicate reference definitions in methods/index.rst and the deleted pages. Methods section: 5 pages (883 lines) → 2 pages (~500 lines), a further 43% reduction on top of Tier-B + Tier-D. Agreed reframe from sophia decision-auditor + co-scientist hypothesis-critic review of the "delete all 4" proposal: consolidate instead of erase, to preserve WASP2-specific operational contracts not present in van de Geijn 2015 or in cited textbooks.
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Summary
Promote `dev` to `master`. Single new commit on dev since last promotion:
Cumulative reduction across Tier-B (PR #99) + Tier-D (PR #101) + Tier-E (PR #103):
Test plan