data-beans 0.6.12

Sparse genomics data backends, QC, algorithms, and simulation
Documentation 
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[package]
name = "data-beans"
license = "MIT"
authors = ["Yongjin Park <ypp@stat.ubc.ca>"]
description = "Sparse genomics data backends, QC, algorithms, and simulation"
repository = "https://github.com/causalpathlab/data-beans"
homepage = "https://github.com/causalpathlab/data-beans"
edition = "2021"
readme = "README.md"
# Own version (decoupled from workspace.version): data-beans evolves its CLI /
# QC API independently of the shared utility crates.
version = "0.6.12"
rust-version = "1.91"
exclude = ["**/.claude/**", "**/.DS_Store"]

[[bin]]
name = "data-beans"
path = "src/main.rs"

[[bin]]
name = "data-beans-sim"
path = "src/sim_main.rs"
required-features = ["sim"]

[features]
default = ["aux"]
aux = []
alg = ["aux"]
sim = ["alg"]
cuda = ["legume-numeric/cuda"]
metal = ["legume-numeric/metal"]
# Pulls in libhdf5 — opt-in so installs on hosts without HDF5 headers still
# build. When off, the HDF5 sparse backend and all H5/H5AD readers compile
# out; .zarr / .zarr.zip remain the supported formats.
hdf5 = ["dep:hdf5"]

[dependencies]
legume-numeric = { version = "0.8.10", features = ["matrix", "param", "candle"] }

anyhow = "1.0"
clap = { version = "4.5.20", features = ["derive"] }
flate2 = "1.0.34"
rayon = "1.10.0"
regex = "1"

hdf5 = { package = "hdf5-metno", version = "0.14.1", features = ["blosc"], optional = true }
libz-sys = { version = "1.1", features = ["libc"], default-features = false }
zarrs = { version = "0.23" }

tempfile = "3.2"
rand = "0.10.1"
ndarray = { version = "0.17", features = ["rayon", "serde", "approx", "blas"] }
ndarray-rand = "0.16"
rand_distr = "0.6"
approx = "0.5.1"
serde = { version = "1.0", features = ["derive"] }
serde_json = "1.0"

nalgebra = "0.34"
nalgebra-sparse = "0.11"

indicatif = { version = "^0.18", features = ["rayon"] }
indicatif-log-bridge = "0.2"
env_logger = "0.11"
log = "0.4"
dashmap = { version = "6.1.0", features = ["rayon"] }
rustc-hash = "2.1"
zip = "8"
zarrs_zip = "0.5"
petgraph = "0.8"
fastobo = "0.15"
special = "0.13"
num_cpus = "1.16.0"
statrs = { version = "0.18", default-features = false }