2.5.88

[spond]

Version 2.5.88: SIMD Refactoring, Matrix Kernel Additions, and Optimization

Description

This PR introduces a series of optimizations, refactoring, and bug fixes leading up to version 2.5.88. Key changes include improvements to SIMD operations, the addition of missing matrix kernels, and updates to core formula evaluation logic.

Key Changes

🚀 Optimizations & Refactoring

• SIMD Enhancements: Implemented SIMD refactoring and AI-guided improvements to enhance performance (e4a1c6f9).
• Core Optimizations: General changes and optimizations in associative_list.cpp and global_things.cpp (1dec4eef, 36322dc8).
• Formula Evaluation: Significant updates to formula.cpp and formula.h, optimizing formula processing and evaluation (9dea386c).

🐛 Fixes & Maintenance

• Matrix Kernels: Added a missing matrix kernel to address computation gaps (fedeee2e, 574d80bb, 0eff2de8).
• Debug Cleanup: Removed extraneous MPI debug prints to clean up output logs (fedeee2e, 574d80bb, 0eff2de8).
• Reformatting: Code reformatting for better style consistency (f03e65d0).

🧬 Template Batch Files

• Workflow Updates: Modifications to CleanStopCodons.bf and SelectionAnalyses/RELAX.bf (9dea386c).

📦 Release

• Version Bump: Bumped version to 2.5.88 (28f83598).

Commits

• 28f8359 - 2.5.88
• 9dea386 - WIP (Formula and Batch File updates)
• f03e65d - Reformatting
• fedeee2 - Adding a missing matrix kernel; removing mpi debug prints
• 574d80b - Adding a missing matrix kernel; removing mpi debug prints
• 0eff2de - Adding a missing matrix kernel; removing mpi debug prints
• 1dec4ee - Changes and optimizations
• 36322dc - Changes and optimizations
• e4a1c6f - Some SIMD refactoring and AI-guided improvements

[sonarqubecloud]

Quality Gate failed

Failed conditions
27.5% Duplication on New Code (required ≤ 3%)
C Reliability Rating on New Code (required ≥ A)

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