koth-ms 0.12.0

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

[package]
edition = "2021"
rust-version = "1.97"
name = "koth-ms"
version = "0.12.0"
authors = ["Patrick Garrett <pgarrett@scripps.edu>"]
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
default-run = "koth_ff"
description = "High-performance LC-MS feature finder for timsTOF and mzML data"
homepage = "https://github.com/pgarrett-scripps/koth"
documentation = "https://docs.rs/koth-ms"
readme = "README.md"
keywords = [
    "mass-spectrometry",
    "proteomics",
    "lc-ms",
    "timstof",
    "feature-detection",
]
categories = [
    "science",
    "command-line-utilities",
]
license = "MIT"
repository = "https://github.com/pgarrett-scripps/koth"

[package.metadata.docs.rs]
features = [
    "cli",
    "tdf",
    "thermo",
]
rustdoc-args = [
    "--cfg",
    "docsrs",
]

[features]
cli = [
    "dep:clap",
    "dep:env_logger",
]
default = [
    "cli",
    "tdf",
    "thermo",
]
tdf = [
    "dep:dnoise",
    "dep:rusqlite",
]
thermo = ["dep:sage-plus-raw"]

[lib]
name = "koth_ms"
crate-type = ["rlib"]
path = "src/lib.rs"

[[bin]]
name = "koth_align"
path = "src/align_main.rs"
required-features = ["cli"]

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

[[example]]
name = "hill_split_lab"
path = "examples/hill_split_lab.rs"

[[example]]
name = "lfq_group_audit"
path = "examples/lfq_group_audit.rs"
required-features = ["cli"]

[[example]]
name = "lfq_member_geometry"
path = "examples/lfq_member_geometry.rs"

[[example]]
name = "lfq_permutation_audit"
path = "examples/lfq_permutation_audit.rs"
required-features = ["cli"]

[[example]]
name = "lfq_refinement"
path = "examples/lfq_refinement.rs"
required-features = ["cli"]

[[example]]
name = "replay_features"
path = "examples/replay_features.rs"
required-features = ["cli"]

[[example]]
name = "rescore_search"
path = "examples/rescore_search.rs"

[[example]]
name = "streaming_api"
path = "examples/streaming_api.rs"

[[example]]
name = "thermo_parity"
path = "examples/thermo_parity.rs"
required-features = ["thermo"]

[[example]]
name = "tims_mobility_dump"
path = "examples/tims_mobility_dump.rs"
required-features = ["tdf"]

[[example]]
name = "validate_configs"
path = "examples/validate_configs.rs"

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

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

[[test]]
name = "search_guided_cli"
path = "tests/search_guided_cli.rs"
required-features = ["cli"]

[[test]]
name = "thermo_dia_ms2"
path = "tests/thermo_dia_ms2.rs"

[dependencies.anyhow]
version = "1.0"

[dependencies.arrow]
version = "57"
features = ["ipc"]

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

[dependencies.csv]
version = "1.3"

[dependencies.dnoise]
version = "0.6.0"
optional = true
default-features = false

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

[dependencies.flate2]
version = "1"

[dependencies.koth-core]
version = "0.12.0"

[dependencies.log]
version = "0.4"

[dependencies.mzdata]
version = "0.63"
features = [
    "mzml",
    "mgf",
    "miniz_oxide",
    "nalgebra",
]
default-features = false

[dependencies.parquet]
version = "57"
features = ["arrow"]

[dependencies.rand]
version = "0.8"

[dependencies.rayon]
version = "1.10"

[dependencies.rusqlite]
version = "0.35"
features = ["bundled"]
optional = true

[dependencies.sage-plus-raw]
version = "0.1.0"
optional = true

[dependencies.serde]
version = "1.0"
features = ["derive"]

[dependencies.serde_json]
version = "1.0"

[dependencies.sha2]
version = "0.10"

[dependencies.thiserror]
version = "1.0"

[dependencies.toml]
version = "0.8"

[lints.clippy]
field_reassign_with_default = "allow"
needless_range_loop = "allow"
too_many_arguments = "allow"
uninlined_format_args = "allow"