Cargo.toml

[workspace.lints.rust]
unsafe_code = "deny"

[workspace.lints.clippy]
# Deny unwrap/expect in production code to enforce proper error handling
unwrap_used = "deny"
expect_used = "deny"
# Lint groups with lower priority so individual overrides work
all = { level = "warn", priority = -1 }
pedantic = { level = "warn", priority = -1 }
nursery = { level = "warn", priority = -1 }

# Allow stylistic lints that are noisy without adding significant value
doc_markdown = "allow"             # BiomeOS, JSON-RPC, etc. don't need backticks internally
missing_errors_doc = "allow"       # Error handling is clear from Result types
missing_panics_doc = "allow"       # Panics are avoided via unwrap_used/expect_used warnings
uninlined_format_args = "allow"    # Format string style is a preference
module_name_repetitions = "allow"  # Module::ModuleThing is idiomatic in our codebase
similar_names = "allow"            # avg_cpu vs avg_gpu is intentionally similar
collapsible_if = "allow"           # let-chains preferred; fix incrementally (edition 2024)
must_use_candidate = "allow"       # Fix incrementally; too noisy for entire codebase at once
return_self_not_must_use = "allow" # Builders return Self; fix incrementally
missing_const_for_fn = "allow"     # Fix incrementally; many functions need const evaluation
cast_possible_truncation = "allow" # Safe: see biomeos-types/src/cast.rs for audited helpers; per-site #[expect] for new code
cast_precision_loss = "allow"      # Safe: display-only f64 values; precision beyond 2^53 is irrelevant for metrics/UI
cast_sign_loss = "allow"           # Safe: all sites verified unsigned; see biomeos-types/src/cast.rs for checked alternatives
cast_lossless = "allow"            # Widening casts are always safe; .into() preferred for new code
option_if_let_else = "allow"       # Style preference; match is often clearer
redundant_pub_crate = "allow"      # pub(crate) vs pub is a valid choice
significant_drop_tightening = "allow" # RwLock/Mutex scoping is intentional
struct_excessive_bools = "allow"   # Config structs legitimately have multiple bool fields
use_self = "allow"                 # Type::Method vs Self::Method is a style preference
unnecessary_wraps = "allow"        # Some Result wraps needed for trait conformance
items_after_statements = "allow"   # Const/type items near their usage is intentional
unused_async = "allow"             # Async trait methods may not await yet

[workspace]
resolver = "2"
default-members = [
    "crates/biomeos",
]
members = [
    "crates/neural-api-client-sync",
    "crates/neural-api-client",
    "crates/biomeos-genome-deploy",
    "crates/biomeos",
    "crates/biomeos-types",
    "crates/biomeos-core",
    "crates/biomeos-cli",
    "crates/biomeos-api",
    "crates/biomeos-manifest",
    "crates/biomeos-system",
    "crates/biomeos-primal-sdk",
    "crates/biomeos-chimera",
    "crates/biomeos-niche",
    "crates/biomeos-spore",  # USB spore system (orchestration only, BearDog handles crypto)
    "crates/biomeos-federation",  # Hierarchical federation and sub-federation management
    "crates/biomeos-compute",  # Isomorphic & fractal compute architecture
    "crates/biomeos-graph",  # Graph-based orchestration for Neural API
    "crates/biomeos-ui",  # Interactive UI orchestration - network effect of multiple primals
    "crates/biomeos-boot",
    "crates/biomeos-deploy", "crates/biomeos-test-utils", "crates/biomeos-nucleus",
    "crates/biomeos-atomic-deploy",  # Genetic lineage atomic deployment (modern Rust, no bash)
    "crates/biomeos-genomebin-v3",
    "crates/biomeos-genome-factory",
    "crates/biomeos-pseudospore",  # pseudoSpore envelope validation (NC-1.4)
]
exclude = [
    "tools",    # Standalone workspace for dev/integration tools
    "tools/harvest",  # Standalone workspace for genomeBin harvesting
]

[workspace.package]
version = "0.1.0"
edition = "2024"
rust-version = "1.87"
authors = ["biomeOS Team"]
license = "AGPL-3.0-or-later"
repository = "https://github.com/ecoPrimals/biomeOS"
homepage = "https://biomeOS.org"
documentation = "https://docs.biomeOS.org"
description = "biomeOS ecosystem workspace"
keywords = ["biomeos", "distributed", "sovereignty", "primals"]
categories = ["os", "distributed-systems", "virtualization"]

[workspace.dependencies]
# Core dependencies
tokio = { version = "1.0", default-features = false, features = ["rt-multi-thread", "macros", "sync", "time"] }
serde = { version = "1.0", features = ["derive"] }
serde_json = "1.0"
bytes = "1.0"
serde_yaml = { package = "serde-saphyr", version = "0.0.29" }
uuid = { version = "1.0", features = ["v4", "serde"] }
chrono = { version = "0.4", features = ["serde"] }
anyhow = "1.0"
thiserror = "2"
tracing = "0.1"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }
clap = { version = "4.0", features = ["derive"] }
axum = { version = "0.8", features = ["ws"] }
tower = { version = "0.5", features = [] }
ureq = { version = "2.9", default-features = false, features = ["json"] }

# Async and futures
futures = "0.3"

# Serialization
toml = "0.9"

# RPC frameworks (JSON-RPC + tarpc for performance escalation)
tarpc = { version = "0.37", features = ["serde-transport", "serde-transport-bincode", "tokio1", "unix"] }
tokio-serde = { version = "0.9", features = ["bincode"] }

# Utilities
dashmap = "6"

# Networking
hyper = { version = "1.0", default-features = false, features = ["client", "server", "http1"] }

# Testing
temp-env = { version = "0.3", features = ["async_closure"] }
tempfile = "3.8"
criterion = "0.5"
etcetera = "0.11"

rand = "0.9"
sha2 = "0.10"
base64 = "0.22"
tokio-test = "0.4"
# HTTP stack building blocks (members merge feature flags as needed)
hyper-util = { version = "0.1", default-features = false }
http-body-util = "0.1"
tower-http = { version = "0.5", default-features = false }
tokio-util = { version = "0.7", default-features = false }
tokio-stream = "0.1"

# WebSockets / async helpers
tokio-tungstenite = "0.29"
futures-util = "0.3"
async-stream = "0.3.6"

# Crypto & secrets
hmac = "0.12"
hkdf = "0.12"
chacha20poly1305 = "0.10"
zeroize = { version = "1.7", features = ["derive"] }
ed25519-dalek = "2.1"
blake3 = { version = "1.5", default-features = false, features = ["pure"] }

# Data structures / parsing
indexmap = { version = "2.0", features = ["serde"] }
url = { version = "2.5", features = ["serde"] }
semver = { version = "1.0", features = ["serde"] }
glob = "0.3"
regex = "1.11"

# OS interfaces
rustix = "1"
which = "8"
flate2 = { version = "1.0", default-features = false, features = ["rust_backend"] }
tar = { version = "0.4", default-features = false }
# Linux RTNETLINK: bridge/link ops in biomeos-deploy (transitive netlink-sys, netlink-packet-*).
# Accepted stack — kernel AF_NETLINK socket, no userspace C libs (e.g. libnl).
rtnetlink = "0.20"

# CLI / TUI helpers
indicatif = "0.17"
colored = "2.1"
console = "0.15"
comfy-table = "7.0"
humantime = "2.1"

# Storage / codecs
redb = "2.4"
lz4_flex = "0.14"
hex = "0.4"
mdns-sd = "0.20.1"

# Async I/O & bytes helpers
async-fs = "2.1"
serde_bytes = "0.11"

# Testing
proptest = "1"
wiremock = "0.6"
tracing-test = "0.2"
assert_cmd = "2"
predicates = "3"

[package]
name = "biomeos"
version.workspace = true
edition.workspace = true
rust-version.workspace = true
authors.workspace = true
license.workspace = true
repository.workspace = true
homepage.workspace = true
documentation.workspace = true
description.workspace = true
keywords.workspace = true
categories.workspace = true

[lib]
doc = false

[dependencies]
# Core BiomeOS components
biomeos-core = { path = "crates/biomeos-core", version = "0.1.0" }
biomeos-types = { path = "crates/biomeos-types", version = "0.1.0" }
biomeos-primal-sdk = { path = "crates/biomeos-primal-sdk", version = "0.1.0" }
biomeos-manifest = { path = "crates/biomeos-manifest", version = "0.1.0" }
biomeos-system = { path = "crates/biomeos-system", version = "0.1.0" }
biomeos-chimera = { path = "crates/biomeos-chimera", version = "0.1.0" }
biomeos-atomic-deploy = { path = "crates/biomeos-atomic-deploy", version = "0.1.0" }
biomeos-niche = { path = "crates/biomeos-niche", version = "0.1.0" }
biomeos-spore = { path = "crates/biomeos-spore", version = "0.1.0" }
biomeos-graph = { path = "crates/biomeos-graph", version = "0.1.0" }

# Async runtime
tokio = { workspace = true, features = ["net", "io-util", "fs", "process"] }

# Error handling
anyhow = { workspace = true }
thiserror = { workspace = true }

# Serialization
serde = { workspace = true }
serde_json = { workspace = true }
toml = { workspace = true }
serde_yaml = { workspace = true }
uuid = { workspace = true }
clap = { workspace = true }
axum = { workspace = true }

# Logging and tracing
tracing = { workspace = true }
tracing-subscriber = { workspace = true }

etcetera = { workspace = true }

# Time handling
chrono = { workspace = true }

[dev-dependencies]
tokio = { workspace = true, features = ["net", "io-util", "test-util"] }
tokio-test = { workspace = true }
anyhow = { workspace = true }
tempfile = { workspace = true }
tracing-test = { workspace = true }
wiremock = { workspace = true }
rand = { workspace = true }
biomeos-test-utils = { path = "crates/biomeos-test-utils", version = "0.1.0" }

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

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

[[example]]
name = "benchscale_p2p_test"
path = "examples/benchscale_p2p_test.rs"

# =============================================================================
# Release Profile (workspace-wide)
# =============================================================================
# NOTE: Profile settings MUST be at workspace root (non-root profiles are ignored)
[profile.release]
strip = false   # Keep symbols for debugging
lto = true      # Link-time optimization for smaller binaries
panic = "abort"  # No unwinding — faster and smaller (critical for init/PID 1)