[package]

name = "lorikeet-rs"
version = "0.3.0"
authors = ["Rhys Newell <r.newell@uq.edu.au>"]
license = "GPL-3.0"
description = "Strain resolver for metagenomics"
homepage = "https://rhysnewell.github.io/Lorikeet/"
repository = "https://github.com/rhysnewell/Lorikeet"
documentation = "https://github.com/rhysnewell/Lorikeet"
readme = "README.md"
exclude = [
  "tests/*"
]


[features]
#openblas = ["ndarray-linalg/openblas"]
#openblas-src = ["ndarray-linalg/openblas-src"]

[dependencies]
ansi_term = "0.11"
approx = "0.3"
bio = "0.30"
bio-types = "0.5"
clap = "2"
csv = "1"
derive_builder = "0.9"
derive-new = "0.5"
env_logger = "0.6"
itertools = "0.8"
lazy_static = "1.3.0"
linregress = "0.1.6"
log = "0.4"
ordered-float = "1"
bird_tool_utils = "0.1.0"
coverm = "0.4"
ndarray = { version = "0.13", features = ["rayon"] }
ndarray-linalg = { version = "0.12" }
openblas-src = "0.7"
nymph = "0.1"
nix = "0.13"
pest = "2"
pest_derive = "2"
rayon = "1.2"
rust-htslib = "0.26"
seq_io = "0.3.*"
rand = "0.6"
strum = "0.17.1"
strum_macros = "0.17.1"
serde = "1"
serde_derive = "1"
serde_json = "1"
serde_yaml = "0.8"
statrs = "0.11"
tempdir = "0.3"
tempfile = "3.0"


[dev-dependencies]
assert_cli = "0.6"


# 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 = false        # 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
lto = false
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 = 0
debug = 2
rpath = false
lto = false
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 = false
debug-assertions = false
codegen-units = 16
panic = 'unwind'
incremental = false
overflow-checks = false