Cargo.toml

[package]
name = "genvarloader"
version = "0.2.1"
edition = "2021"
authors = ["David Laub <dlaub@ucsd.edu"]

# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

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

[dependencies]
anyhow = "1.0.102"
bigtools = "0.5.6"
coitrees = "0.4"
itertools = "0.14.0"
ndarray = "0.17.2"
numpy = "0.29.0"
rayon = "1.12.0"
seqpro-core = "0.1"
# genoray crates are pulled straight from GitHub (no crates.io publish). Cargo finds
# each package by name inside the repo — no in-repo path is given or needed. Bump `rev`
# to pull newer genoray code; both crates must share the same rev (one clone, one repo).
# Currently tag 4.0.1. Keep this rev in step with the `genoray` Python pin: the Rust
# code here reads svar2 stores that the Python package writes, so a format change that
# lands in one and not the other is invisible until it corrupts a read.
# `default-features = false` selects genoray's query-only core; since 4.0.1 that also
# excludes `tracing`/`tracing-subscriber`, which are gated behind its `conversion`
# feature (d-laub/genoray#165).
svar2-codec = { git = "https://github.com/d-laub/genoray.git", rev = "d66ec0e03d097fa8c338567b0938924be67315db" }
genoray_core = { git = "https://github.com/d-laub/genoray.git", rev = "d66ec0e03d097fa8c338567b0938924be67315db", package = "genoray", default-features = false }

[features]
extension-module = ["pyo3/extension-module"]

[dependencies.pyo3]
version = "0.29"
features = ["abi3-py310"]

[dev-dependencies]
rstest = "0.26.1"
tempfile = "3"

# Perf call-graph attribution only (`perf report --children`). Inherits release
# codegen and adds line tables + frame pointers. NEVER the gate artifact — all
# throughput/asm gate numbers come from the plain `--release` build.
[profile.profiling]
inherits = "release"
debug = "line-tables-only"
force-frame-pointers = true