requirements.txt

# ═══════════════════════════════════════════════════════════════
# Project Confluence — Dependencies
# ═══════════════════════════════════════════════════════════════

# Core Scientific
numpy>=1.24.0
scipy>=1.10.0
pandas>=2.0.0

# ODE / Dynamical Systems
# (scipy.integrate.solve_ivp — included in scipy)

# Bayesian Inference
emcee>=3.1.0           # MCMC ensemble sampler
corner>=2.2.0          # Posterior visualization

# Complexity Metrics (optional — pure-Python fallback included)
nolds>=0.6.1           # Lyapunov exponents, correlation dimension
antropy>=0.1.6         # Multiscale entropy, fractal dimension

# Optimization
optuna>=3.0.0          # Bayesian optimization for RADO engine

# Visualization
matplotlib>=3.7.0
seaborn>=0.12.0
plotly>=5.15.0

# Machine Learning (for bioinformatics miner)
scikit-learn>=1.3.0

# Bioinformatics APIs
requests>=2.28.0       # cBioPortal REST API

# Structural Biology (AlphaFold integration)
biopython>=1.83        # PDB/mmCIF parsing for AlphaFold structures

# Testing
pytest>=7.0.0
pytest-cov>=4.0.0

# Nigeria Guidelines RAG (optional — enables NSTG 2022 integration)
# License: Dataset is CC-BY-4.0 (Federal Ministry of Health, Nigeria)
sentence-transformers>=2.2.0    # Embedding model for semantic retrieval
faiss-cpu>=1.7.0                # Vector similarity search index
datasets>=2.14.0                # HuggingFace dataset loader