[package]
name = "alevin-fry"
version = "0.9.0"
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 = "2021"
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 = [
  "/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"]

[dependencies]
# for local development, look in the libradicl git repository
# but when published, pull the specified version
libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.8.2" }
anyhow = "1.0.80"
arrayvec = "0.7.4"
ahash = "0.8.11"
bincode = "1.3.3"
bstr = "1.9.1"
crossbeam-channel = "0.5.12"
crossbeam-queue = "0.3.11"
typed-builder = "0.18.1"
indicatif = "0.17.8"
needletail = "0.5.1"
petgraph = "0.6.4"
flate2 = "1.0.28"
scroll = "0.12.0"
serde = { version = "1.0.197", features = ["derive"] }
serde_json = "1.0.114"
sprs = "0.11.1"
slog = "2.7.0"
slog-term = "2.9.1"
slog-async = "2.8.0"
smallvec = "1.13.1"
snap = "1.1.1"
rand = "0.8.5"
chrono = "0.4.35"
csv = "1.3.0"
mimalloc = { version = "0.1.39", default-features = false }
num-format = "0.4.4"
num_cpus = "1.16.0"
bio-types = { version = "1.0.1", default-features = true, features = ["serde"] }
itertools = "0.12.1"
thiserror = "1.0.57"
statrs = "0.16.0"
sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }

# no shenanigans; clap makes breaking "fixes" too often to allow variability
# in the version different from what we tested with
clap = { version = "=4.5.2", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }

noodles = { version = "0.65.0", features = ["bam", "bgzf", "sam"] }
noodles-util = { version = "0.37.0", features = ["alignment"] }

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

# The profile that 'cargo dist' will build with
[profile.dist]
inherits = "release"
lto = "thin"

# Config for 'cargo dist'
[workspace.metadata.dist]
# The preferred cargo-dist version to use in CI (Cargo.toml SemVer syntax)
cargo-dist-version = "0.11.1"
# CI backends to support
ci = ["github"]
# The installers to generate for each app
installers = ["shell"]
# Target platforms to build apps for (Rust target-triple syntax)
targets = ["aarch64-apple-darwin", "x86_64-apple-darwin", "x86_64-unknown-linux-gnu"]
# Publish jobs to run in CI
pr-run-mode = "plan"

[workspace.metadata.dist.github-custom-runners]
aarch64-apple-darwin = "macos-14"