spacetravlr 1.3.0

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
rust-version = "1.86"
name = "spacetravlr"
version = "1.3.0"
build = "build.rs"
exclude = [
    ".agent/",
    ".agents/",
    ".claude/",
    ".cursor/",
    "skills-lock.json",
    ".github/",
    ".vscode/",
    "results/",
    "data/",
    "web/",
    "genes_human_mouse.csv.xz",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
default-run = "spacetravlr"
description = "Spatial gene regulatory network inference and in-silico perturbation (Rust port of SpaceTravLR)"
homepage = "https://github.com/Koushul/SpaceTravLR_rust"
documentation = "https://docs.rs/spacetravlr"
readme = "README.md"
keywords = [
    "spatial",
    "transcriptomics",
    "grn",
    "single-cell",
    "machine-learning",
]
categories = [
    "science",
    "command-line-utilities",
]
license = "MIT"
repository = "https://github.com/Koushul/SpaceTravLR_rust"

[package.metadata.cargo-llvm-cov]
ignore-filename-regex = [
    '/\.cargo/registry/',
    '/\.cargo/git/',
]

[features]
default = [
    "tui",
    "self-update",
]
dev-main = []
self-update = [
    "dep:ureq",
    "dep:tar",
    "dep:sha2",
    "dep:semver",
]
spatial-viewer = [
    "dep:axum",
    "dep:tokio",
    "dep:tower-http",
    "dep:tracing",
    "dep:tracing-subscriber",
    "dep:foyer",
    "dep:bincode",
    "dep:blake3",
    "dep:tempfile",
]
tui = [
    "dep:ratatui",
    "dep:ratatui-themes",
    "dep:crossterm",
    "dep:sysinfo",
    "dep:unicode-width",
    "dep:tokio",
]

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

[[bin]]
name = "spacetravlr"
path = "src/bin/spacetravlr.rs"

[[bin]]
name = "spacetravlr-perturb"
path = "src/bin/spacetravlr_perturb.rs"

[[bin]]
name = "spacetravlr-dev"
path = "src/main.rs"
required-features = ["dev-main"]

[[bin]]
name = "spatial_viewer"
path = "src/bin/spatial_viewer.rs"
required-features = ["spatial-viewer"]

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

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

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

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

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

[dependencies.anndata]
version = "0.6"

[dependencies.anndata-hdf5]
version = "0.5"

[dependencies.anyhow]
version = "1.0"

[dependencies.approx]
version = "0.5"

[dependencies.axum]
version = "0.8"
features = [
    "json",
    "query",
    "macros",
    "tokio",
    "http1",
]
optional = true
default-features = false

[dependencies.bincode]
version = "2"
features = ["serde"]
optional = true

[dependencies.blake3]
version = "1.5"
optional = true

[dependencies.build_html]
version = "2.7"

[dependencies.burn]
version = "0.16.1"
features = [
    "wgpu",
    "train",
    "ndarray",
]

[dependencies.burn-autodiff]
version = "0.16.1"

[dependencies.chrono]
version = "0.4"

[dependencies.clap]
version = "4.5"
features = [
    "derive",
    "wrap_help",
]

[dependencies.crossterm]
version = "0.29"
optional = true

[dependencies.flate2]
version = "1"

[dependencies.foyer]
version = "0.22.3"
features = ["serde"]
optional = true

[dependencies.glob]
version = "0.3"

[dependencies.indicatif]
version = "0.17"
features = ["rayon"]

[dependencies.kiddo]
version = ">=5.2, <5.3"

[dependencies.nalgebra-sparse]
version = "0.11"

[dependencies.ndarray]
version = "0.16"
features = ["rayon"]

[dependencies.ndarray-npy]
version = "0.9"

[dependencies.polars]
version = "0.51"
features = [
    "lazy",
    "ndarray",
    "parquet",
    "csv",
    "ipc",
    "decompress",
    "strings",
    "temporal",
    "fmt",
    "zip_with",
]
default-features = false

[dependencies.polars-utils]
version = "0.51"

[dependencies.pollster]
version = "0.4"

[dependencies.rand]
version = "0.8"

[dependencies.rand_chacha]
version = "0.3"

[dependencies.rand_distr]
version = "0.4"

[dependencies.ratatui]
version = "0.30"
optional = true

[dependencies.ratatui-themes]
version = "0.2.0"
optional = true

[dependencies.rayon]
version = "1.10"

[dependencies.semver]
version = "1"
optional = true

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

[dependencies.serde_json]
version = "1"

[dependencies.sha2]
version = "0.10"
optional = true

[dependencies.sysinfo]
version = "0.32"
optional = true

[dependencies.tar]
version = "0.4"
optional = true

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

[dependencies.tokio]
version = "1"
features = [
    "rt-multi-thread",
    "macros",
    "net",
    "signal",
    "sync",
    "time",
]
optional = true

[dependencies.toml]
version = "0.8"

[dependencies.tower-http]
version = "0.6"
features = [
    "cors",
    "fs",
    "trace",
    "compression-gzip",
]
optional = true

[dependencies.tracing]
version = "0.1"
optional = true

[dependencies.tracing-subscriber]
version = "0.3"
features = ["env-filter"]
optional = true

[dependencies.unicode-width]
version = "0.2"
optional = true

[dependencies.ureq]
version = "2.12"
features = ["json"]
optional = true
default-features = true

[dependencies.wgpu]
version = "23.0"

[profile.dev]
incremental = true

[profile.release]
lto = "thin"
codegen-units = 1