[package]
name = "lorikeet-genome"
version = "0.8.2"
authors = ["Rhys Newell <rhys.newell94@gmail.com>"]
license = "GPL-3.0"
description = "Strain resolver and variant caller via local reassembly for metagenomics"
homepage = "https://rhysnewell.github.io/Lorikeet/"
repository = "https://github.com/rhysnewell/Lorikeet"
documentation = "https://github.com/rhysnewell/Lorikeet"
readme = "README.md"
keywords = ["bioinformatics", "metagenomics", "variant-calling", "strain-anlaysis"]
categories = ["bioinformatics::metagenomics", "bioinformatics::variant-calling", "bioinformatics::strain-analysis"]
include = [
  "/src", "/LICENSE", "/README.md", "/Cargo.toml"
]
default-run = "lorikeet"
edition = "2021"

[features]
# Force openssl-sys to staticly link in the openssl library. Necessary when
# cross compiling to x86_64-unknown-linux-musl.
# vendored-openssl = ["openssl-sys/vendored"]
default = ["fst", "bam"]
fst = ["dep:pyo3"]
bam = []

[dependencies]
approx = "^0.5"
ansi_term = "^0.12"
bio = "^1.1"
bio-types = "^1.0"
bird_tool_utils = "^0.4"
bird_tool_utils-man = "^0.4"
bstr = "^0.2.17"
clap = { version="^4", features = ["cargo"] } # cargo feature required for crate_version!
clap_complete = "^4"
compare = "^0.1"
hashlink = "^0.7"
enum-ordinalize = "^3.1"
env_logger = "^0.6"
glob = "^0.3"
gkl = "^0.1.1"
indexmap = "^1.7"
itertools = "^0.8"
lazy_static = "^1.3"
log = "^0.4"
libm = "^0.2"
mathru = "^0.14"
multimap = "^0.9"
ndarray-npy = "^0.8"
ndarray = {version = "^0.15", features = ["rayon"]}
needletail = "^0.5"
nix = "0.26.2"
num = "0.4.0"
ordered-float = "1"
partitions = "^0.2"
petgraph = {version = "^0.6", features = ["stable_graph"]}
pyo3 = { version = "^0.17", optional = true }
rand = "0.6"
rayon = "^1.5.1"
roff = "^0.2"
rust-htslib = { version="^0.44", default-features = false}
serde = "^1"
serde_derive = "^1"
strum = "^0.17"
strum_macros = "^0.17"
statrs = "^0.16"
tempdir = "^0.3"
tempfile = "^3"
term = "^0.7"
indicatif = "^0.17"
scoped_threadpool = "^0.1.9"
anyhow = "1.0.70"


[lib]
bench = false

#[[bench]]
#name = "benchmarks"
#harness = false

[dev-dependencies]
assert_cli = "0.6.*"
# Run things before commit but not push
#cargo-husky = { version="1", default-features = false, features=["precommit-hook", "run-cargo-test", "run-cargo-fmt"] }


# The development profile, used for `cargo build`.
[profile.dev]
opt-level = 0      # controls the `--opt-level` the compiler builds with.
                   # 0-1 is good for debugging. 2 is well-optimized. Max is 3.
                   # 's' attempts to reduce size, 'z' reduces size even more.
debug = true       # (u32 or bool) Include debug information (debug symbols).
                   # Equivalent to `-C debuginfo=2` compiler flag.
rpath = false      # controls whether compiler should set loader paths.
                   # If true, passes `-C rpath` flag to the compiler.
lto = true        # Link Time Optimization usually reduces size of binaries
                   # and _2 libraries. Increases compilation time.
                   # If true, passes `-C lto` flag to the compiler, and if a
                   # string is specified like 'thin' then `-C lto=thin` will
                   # be passed.
debug-assertions = true # controls whether debug assertions are enabled
                   # (e.g., debug_assert!() and arithmetic overflow checks)
codegen-units = 16 # if > 1 enables parallel code generation which improves
                   # compile times, but prevents some optimizations.
                   # Passes `-C codegen-units`.
panic = 'unwind'   # panic strategy (`-C panic=...`), can also be 'abort'
incremental = true # whether or not incremental compilation is enabled
                   # This can be overridden globally with the CARGO_INCREMENTAL
                   # environment variable or `build.incremental` config
                   # variable. Incremental is only used for path sources.
overflow-checks = true # use overflow checks for integer arithmetic.
                   # Passes the `-C overflow-checks=...` flag to the compiler.

# The release profile, used for `cargo build --release` (and the dependencies
# for `cargo test --release`, including the local library or binary).
[profile.release]
opt-level = 3
debug = false
rpath = false
strip = true
lto = true
debug-assertions = false
codegen-units = 16
panic = 'unwind'
incremental = false
overflow-checks = false

# The testing profile, used for `cargo test` (for `cargo test --release` see
# the `release` and `bench` profiles).
[profile.test]
opt-level = 3
debug = 2
rpath = false
lto = true
debug-assertions = true
codegen-units = 16
panic = 'unwind'
incremental = true
overflow-checks = true

# The benchmarking profile, used for `cargo bench` (and the test targets and
# unit tests for `cargo test --release`).
[profile.bench]
opt-level = 3
debug = false
rpath = false
lto = true
debug-assertions = false
codegen-units = 16
panic = 'unwind'
incremental = false
overflow-checks = false