Cargo.toml

[package]
name = "alevin-fry"
version = "0.4.3"
authors = ["Avi Srivastava <avi.srivastava@nyu.edu>", "Hirak Sarkar <hirak_sarkar@hms.harvard.edu>", "Dongze He <dhe17@umd.edu>", "Mohsen Zakeri <mzakeri@cs.umd.edu>", "Rob Patro <rob@cs.umd.edu>"]
edition = "2018"
description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data."
license-file = "LICENSE"
readme= "README.md"
repository = "https://github.com/COMBINE-lab/alevin-fry"
homepage = "https://github.com/COMBINE-lab/alevin-fry"
documentation = "https://alevin-fry.readthedocs.io/en/latest/"
include = [
    "/libradicl/src/*.rs",
    "/src/*.rs",
    "/Cargo.toml",
    "/README.md",
    "/LICENSE",
    "/CONTRIBUTING.md",
    "/CODE_OF_CONDUCT.md"
]
keywords = ["single-cell", "preprocessing", 
	    "RNA-seq", "single-nucleus", "RNA-velocity"]
categories = ["command-line-utilities", "science"]

[workspace]

[dependencies]	
# for release
libradicl = "0.4.3" 
# for local development
# libradicl = { path = "libradicl", version = "0.4.3" }
arrayvec = "0.7.1"
ahash = "0.7.6"
bincode = "1.3.3"
bstr = "0.2.17"
crossbeam-channel = "0.5.1"
crossbeam-queue = "0.3.2"
indicatif = "0.16.2"
needletail = "0.4.1"
petgraph = "0.6.0"
flate2 = "1.0.22"
scroll = "0.10.2"
serde = { version = "1.0.130", features = ["derive"] }
serde_json = "1.0.68"
sprs = "0.11.0"
slog = "2.7.0"
slog-term = "2.8.0"
slog-async = "2.6.0"
smallvec = "1.7.0"
snap = "1"
rand = "0.8.4"
chrono = "0.4.19"
csv = "1.1.6"
mimalloc = { version = "0.1.26", default-features = false }
num-format = "0.4.0"
num_cpus = "1.13.0"
bio-types = "0.12.0"
itertools = "0.10.1"
thiserror = "1.0.30"
quickersort = "3.0.1"
statrs = "0.15.0" 
rust-htslib = { version = "0.38.2", default-features = false, features = ["bzip2", "lzma"] }
sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0.1.1" }

[dependencies.clap]
version = "=3.0.0-beta.5"
features = ["wrap_help"]

[profile.release]
#debug = true
lto="thin"
#codegen-units=1
opt-level=3