v0.1.0b2 — Score-gated expression, WAL durability, ΣĒMA cold-storage

What's New

Score-gated expression & retrieval quality

• Coverage metric now uses extracted domain/entity signals instead of raw word splits — coverage: 0.19 → 0.85-1.0
• Ellipticity improved from 0.37 avg → 0.60-0.74 (approaching aligned threshold)
• Score-gated trimming drops weak-scoring tail candidates (< 20% of top score)
• Dynamic density denominator scales by expressed/max ratio

WAL durability

• checkpoint() method with PASSIVE/FULL/TRUNCATE modes
• Periodic checkpoint in upsert (every 50/500 genes) + background 60s timer in server
• Max crash loss reduced from ~13,700 genes to ~50

ΣĒMA cold-storage compression tiers

• Three tiers: OPEN (full fidelity), EUCHROMATIN (summary + ΣĒMA), HETEROCHROMATIN (ΣĒMA + metadata only)
• compact_genome() retroactive sweep with configurable thresholds
• Density gate at ingest routes low-signal content directly to cold tiers
• /admin/compact and /admin/checkpoint endpoints

Domain tagging

• spaCy EntityRuler with project vocabulary (before statistical NER)
• SPLADE weight boosted 2.5 → 3.5 as semantic safety net

Performance

• Dedicated read-only SQLite connection — WAL readers no longer block writers
• ΣĒMA vector cache: pre-materialized numpy matrix replaces 7K json_loads() per query
• Mode B scan: 120s → <100ms

All 179 tests passing.

🤖 Generated with Claude Code