FastNLR/Cargo.toml at main · CropCoder/FastNLR · GitHub

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# FastNLR — high-speed, accurate NLR loci annotation for plant genomes.
#
# workspace root: unified dependency versions + release-optimized profile.
# Layered crate dependency graph (bottom-up):
#   nlr-core (no deps) -> nlr-config/nlr-seq -> nlr-scan -> nlr-assemble -> nlr-output/nlr-report/nlr-plot -> nlr-cli

[workspace]
resolver = "2"
members = [
    "crates/nlr-core",
    "crates/nlr-config",
    "crates/nlr-seq",
    "crates/nlr-scan",
    "crates/nlr-assemble",
    "crates/nlr-domain",
    "crates/nlr-output",
    "crates/nlr-report",
    "crates/nlr-plot",
    "crates/nlr-cli",
]

[workspace.package]
version = "1.6.0"
edition = "2021"
authors = ["Jiwen Zhao (https://github.com/CropCoder)"]
license = "GPL-3.0-only"
repository = "https://github.com/CropCoder/FastNLR"
homepage = "https://github.com/CropCoder/FastNLR"

# Unified dependency versions (workspace-level; crates declare workspace = true).
[workspace.dependencies]
# parallelism
rayon = "1.10"
# CLI parsing
clap = { version = "4.5", features = ["derive", "cargo"] }
# logging & observability
tracing = "0.1"
tracing-subscriber = { version = "0.3", features = ["env-filter", "fmt", "json"] }
# progress bar
indicatif = "0.17"
# graceful shutdown (SIGINT)
ctrlc = "3.4"
# structured serialization (stats report JSON)
serde = { version = "1.0", features = ["derive"] }
serde_json = "1.0"
# checkpoint 输入/profile 的内容指纹
sha2 = "0.10"
# local-time formatting for log timestamps and the GFF `##date` header
# (default-features off: 只需要 Local::now() 与 strftime 格式化，不引入 wasm 绑定)
chrono = { version = "0.4", default-features = false, features = ["clock", "std"] }
# gzip compression
flate2 = "1.0"
# statistics plots (default features disabled to avoid system fontconfig/freetype deps;
# ab_glyph provides a bundled font backend, enabling static/cross compilation)
plotters = { version = "0.3", default-features = false, features = ["bitmap_backend", "bitmap_encoder", "image", "ab_glyph", "all_series", "all_elements", "full_palette", "colormaps"] }
# fast hashing
rustc-hash = "2.0"
# temp directory
tempfile = "3.10"
# memory-map large files
memmap2 = "0.9"
# SIMD vectorization (cross-window parallel scoring)
wide = "0.7"
# platform process metrics (macOS peak RSS via getrusage)
libc = "0.2"
# protein-mode domain scanning (pure-Rust HMMER 3.4 port, BSD-3-Clause)
# pinned exactly: the crate is pre-1.0 and its scores feed the golden-score regression test
hmmer-pure-rs = "=0.7.4"

[profile.release]
opt-level = 3
lto = "fat"
codegen-units = 1
panic = "abort"