v1.2.0 - Thermodynamic QC Fix, RAA Exo-Probe Architecture & Scientific Standardization

What's New in v1.2.0

🐛 Critical Thermodynamic Fixes

• ΔG Unit Normalization: Fixed unit mismatch in reranking.py where raw primer3-py ThermoAnalysis outputs (cal/mol) were compared directly against kcal/mol thresholds, ensuring precise thermodynamic filtering.
• Two-Stage Re-ranking: Fully enabled multi-candidate ranking and QC filtering across PCR, qPCR, and RAA workflows.

🧬 RAA Exo-Probe Architecture

• Automated Abasic (THF) Placement: Programmatic constraint-satisfaction algorithm enforcing TwistAmp Assay Design Manual rules (≥30 nt upstream, ≥15 nt downstream, dT-fluorophore/quencher coupling).
• Configurable Reaction Temperatures: RAA probe Tm floor is now dynamically configurable (qc.probe_tm_min) for isothermal assays (37–42°C).

📚 Scientific References & Citations

• Integrated peer-reviewed thermodynamic literature (SantaLucia 1998/2004, Owczarzy 2004/2008, Untergasser 2012, Piepenburg 2006).
• Added standardized CITATION.cff for academic repository citations.
• Added comprehensive in-silico benchmarking suite (scripts/benchmark_validation.py).

🧪 Automated Test Suite

• 1,425 tests passing (100%).