[package]
name = "simpleaf"
version = "0.17.1"
edition = "2021"
authors = [
  "Rob Patro <rob@cs.umd.edu>",
  "Dongze He <dhe17@umd.edu>",
]
description = "A rust framework to make using alevin-fry even simpler."
license-file = "LICENSE"
readme = "README.md"
repository = "https://github.com/COMBINE-lab/simpleaf"
homepage = "https://github.com/COMBINE-lab/simpleaf"
#documentation = "https://alevin-fry.readthedocs.io/en/latest/"
include = [
  "/src/*.rs",
  "/src/utils/*.rs",
  "/src/simpleaf_commands/*.rs",
  "/Cargo.toml",
  "/Cargo.lock",
  "/README.md",
  "/LICENSE",
]
keywords = [
  "single-cell",
  "preprocessing",
  "RNA-seq",
  "single-nucleus",
  "RNA-velocity",
]
categories = ["command-line-utilities", "science"]

# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
[dependencies]
seq_geom_parser = { git = "https://github.com/COMBINE-lab/seq_geom_parser", branch = "dev", version = "0.3.0" }
seq_geom_xform = { git = "https://github.com/COMBINE-lab/seq_geom_xform", branch = "dev", version = "0.4.0" }
roers = { git = "https://github.com/COMBINE-lab/roers", branch = "main", version = "0.3.0" }
anyhow = "^1.0"
clap = { version = "4.5.8", features = ["derive", "cargo", "deprecated", "wrap_help", "help", "usage", "error-context"] } 
cmd_lib = "^1.9.4"
tracing = "0.1.40"
tracing-subscriber = { version = "0.3.18", default-features = true, features = ["env-filter"] }
semver = "^1.0.23"
serde = {version = "1.0.203", features = ["derive"]}
serde_json = "1.0.119"
time = {version = "^0.3.36", features = ["macros", "formatting", "parsing", "serde", "serde-human-readable"]}
which = "^6.0.1"
jrsonnet-evaluator = "0.5.0-pre95"
jrsonnet-cli = "0.5.0-pre95"
jrsonnet-parser = "0.5.0-pre95"
thiserror = "1.0"
phf = { version = "0.11.2", features = ["macros"] }
chrono = "0.4.38"
tabled = "0.15.0"
csv = "1.3.0"
minreq = { version = "2.11.2", features = ["serde", "serde_json", "https", "json-using-serde"] }
strum = { version = "0.26.3", features = ["derive", "phf"] }
strum_macros = "0.26.4"

[profile.release]
lto = "thin"
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 = "0.16.0"
# 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"
# Whether to install an updater program
install-updater = true

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