[package]
name = "rvdna"
version = "0.3.0"
edition = "2021"
description = "rvDNA — AI-native genomic analysis. 20-SNP biomarker risk scoring, streaming anomaly detection, 64-dim profile vectors, 23andMe genotyping, CYP2D6/CYP2C19 pharmacogenomics, variant calling, protein prediction, and HNSW vector search in pure Rust."
license = "MIT"
repository = "https://github.com/ruvnet/ruvector"
homepage = "https://github.com/ruvnet/ruvector/tree/main/examples/dna"
documentation = "https://docs.rs/rvdna"
readme = "README.md"
keywords = ["genomics", "bioinformatics", "dna", "pharmacogenomics", "23andme"]
categories = ["science", "algorithms", "wasm"]

[dependencies]
# RuVector core for HNSW vector storage
ruvector-core = { version = "2.0.2", path = "../../crates/ruvector-core" }

# Attention for sequence analysis
ruvector-attention = { version = "2.0", path = "../../crates/ruvector-attention" }

# GNN for protein structure and interaction networks
ruvector-gnn = { version = "2.0.2", path = "../../crates/ruvector-gnn" }

# Graph operations for biological networks
ruvector-graph = { version = "2.0.2", path = "../../crates/ruvector-graph" }

# DAG pipeline orchestration
ruvector-dag = { version = "2.0", path = "../../crates/ruvector-dag" }

# Math primitives
ruvector-math = { version = "2.0.2", path = "../../crates/ruvector-math" }

# Filter expressions for metadata queries
ruvector-filter = { version = "2.0.2", path = "../../crates/ruvector-filter" }

# Collections
ruvector-collections = { version = "2.0.2", path = "../../crates/ruvector-collections" }

# Serialization
serde = { version = "1.0", features = ["derive"] }
serde_json = "1.0"
bincode = { version = "2.0.0-rc.3", features = ["serde"] }

# Math and numerics
ndarray = { version = "0.16", features = ["serde"] }
rand = "0.8"
rand_distr = "0.4"

# Async runtime
tokio = { version = "1.41", features = ["rt-multi-thread", "macros", "time"] }

# Sublinear solver for k-mer graph PageRank
ruvector-solver = { version = "2.0.3", path = "../../crates/ruvector-solver", default-features = false, features = ["forward-push", "neumann", "cg"] }

# Error handling
thiserror = "2.0"
anyhow = "1.0"

# Utilities
uuid = { version = "1.11", features = ["v4"] }
chrono = "0.4"
tracing = "0.1"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }

[[bin]]
name = "rvdna-cli"
path = "src/main.rs"

[dev-dependencies]
criterion = { version = "0.5", features = ["html_reports"] }
tempfile = "3.8"

[[bench]]
name = "dna_bench"
harness = false

[[bench]]
name = "solver_bench"
harness = false

[[bench]]
name = "biomarker_bench"
harness = false