gecco 0.5.3

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# See Cargo.toml.orig for the original contents.

[package]
edition = "2021"
rust-version = "1.82"
name = "gecco"
version = "0.5.3"
build = "build.rs"
include = [
    "/src/**",
    "/benches/**",
    "/tests/**",
    "/scripts/**",
    "/bundled-data/**",
    "/build.rs",
    "/Cargo.toml",
    "/Cargo.lock",
    "/README.md",
    "/LICENSE",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Gene Cluster prediction with Conditional Random Fields"
homepage = "https://github.com/henriksson-lab/gecco-rs"
documentation = "https://docs.rs/gecco"
readme = "README.md"
keywords = [
    "bioinformatics",
    "bgc",
    "genomics",
    "hmmer",
    "crf",
]
categories = [
    "science",
    "command-line-utilities",
]
license = "GPL-3.0-or-later"
repository = "https://github.com/henriksson-lab/gecco-rs"

[features]
bench = []
bundled-data = []
cli = [
    "clap",
    "indicatif",
    "ureq",
    "env_logger",
]
default = ["cli"]

[lib]
name = "gecco"
path = "src/lib.rs"

[[bin]]
name = "bench_full"
path = "benches/bench_full.rs"
required-features = ["bench"]

[[bin]]
name = "bench_pipeline"
path = "benches/pipeline.rs"
required-features = ["bench"]

[[bin]]
name = "gecco"
path = "src/main.rs"
required-features = ["cli"]

[[test]]
name = "conformance_full_pipeline"
path = "tests/conformance_full_pipeline.rs"

[[test]]
name = "integration"
path = "tests/integration.rs"

[[test]]
name = "smoke"
path = "tests/smoke.rs"

[dependencies.anyhow]
version = "1"

[dependencies.bincode]
version = "2"

[dependencies.bio]
version = "3.0"

[dependencies.clap]
version = "4"
features = ["derive"]
optional = true

[dependencies.crfsuite-compliant-rs]
version = "0.4"

[dependencies.csv]
version = "1.3"

[dependencies.env_logger]
version = "0.11"
optional = true

[dependencies.flate2]
version = "1.0"

[dependencies.gb-io]
version = "0.9"

[dependencies.hmmer]
version = "0.7"
package = "hmmer-pure-rs"

[dependencies.indicatif]
version = "0.18"
optional = true

[dependencies.log]
version = "0.4"

[dependencies.md5]
version = "0.8"

[dependencies.ndarray]
version = "0.17"

[dependencies.noodles-fasta]
version = "0.60"

[dependencies.prodigal-rs]
version = "0.3.4"

[dependencies.quick-xml]
version = "0.39"

[dependencies.rand]
version = "0.9"

[dependencies.rayon]
version = "1.12"

[dependencies.regex-lite]
version = "0.1"

[dependencies.serde]
version = "1"
features = ["derive"]

[dependencies.serde_json]
version = "1"

[dependencies.sprs]
version = "0.11"

[dependencies.statrs]
version = "0.17"

[dependencies.thiserror]
version = "2"

[dependencies.ureq]
version = "3"
optional = true

[dependencies.zip]
version = "2.4"
features = ["deflate"]
default-features = false

[build-dependencies.flate2]
version = "1.0"

[build-dependencies.sha2]
version = "0.10"

[build-dependencies.ureq]
version = "3"

[profile.release]
lto = true