Cargo.toml

[package]
name = "rosalind"
version = "0.1.0"
edition = "2021"
authors = ["Logan Nye <logannye@users.noreply.github.com>"]
description = "Deterministic, low-memory genomics engine: memory as a verifiable contract (declare → predict → honor → verify) for alignment and variant calling"
repository = "https://github.com/logannye/rosalind"
license = "MIT OR Apache-2.0"
keywords = ["genomics", "alignment", "variant-calling", "bioinformatics", "bwt", "fm-index"]
categories = ["science::bioinformatics", "algorithms"]

[lib]
crate-type = ["rlib", "cdylib"]

[dependencies]
# OS bindings (used for read-only mmap of large reference/index files)
libc = "0.2"
# Finite field arithmetic - for constant-size field 𝔽_{2^c}
ff = "0.13"
# Polynomial operations - for low-degree extensions
ark-poly = "0.4"
# Fast hashing for advisory fingerprints
blake3 = "1.5"
# Transparent gzip/bgzf-sequential decompression for FASTA/FASTQ ingestion
flate2 = "1.0"
# Bit manipulation - for compact ledger representation
bitvec = "1.0"
# Error handling
thiserror = "1.0"
anyhow = "1.0"
# Logging and tracing
tracing = "0.1"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
# CLI
clap = { version = "4.5", features = ["derive"] }
# Serialization (optional, for debugging/visualization)
serde = { version = "1.0", features = ["derive"], optional = true }
# Python bindings
pyo3 = { version = "0.23.2", features = ["extension-module", "abi3-py39"], optional = true }
# BAM/VCF output
rust-htslib = { version = "0.44", default-features = false, features = ["bzip2", "lzma"] }

[dev-dependencies]
criterion = { version = "0.5", features = ["html_reports"] }
proptest = "1.4"
test-case = "3.3"

[features]
default = []
visualize = ["serde"]
profiling = []
python-bindings = ["dep:pyo3"]

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

[profile.release]
opt-level = 3
lto = true
codegen-units = 1

[profile.bench]
inherits = "release"