# GitHub Copilot Instructions
## Project Context
- **Rust 1.92+** (2024 edition), source in `crates/`, not `src/`
- **Binary**: `crates/main.rs` — Library: `crates/lib.rs`
- **MCP server**: `crates/mcp/` — launched via `nsip mcp` (stdio transport)
- **Clippy**: pedantic + nursery + cargo lints with `#[deny(unwrap_used, expect_used, panic)]`
- **Error handling**: `thiserror` for error types, `Result<T>` alias, `?` propagation
- **Builder pattern**: `const fn` constructors, `#[must_use]` on value-returning functions
- **Parameters**: prefer `&str` over `String`, `&[T]` over `Vec<T>`, `Cow<'_, str>` for flexible returns
- **Formatting**: rustfmt with 100-char lines, `imports_granularity = "Crate"`, `group_imports = "StdExternalCrate"`
- **Supply chain**: `cargo-deny` enforces permissive licenses only, bans `openssl` (use rustls)
- **`unsafe` code is forbidden**
See `crates/**/*.rs` and `tests/**/*.rs` scoped instructions for detailed coding and test guidelines.
## Commands
```bash
just # List all recipes
just check # Full CI check (fmt + clippy + test + doc + deny)
just test # Run all tests
just lint # Clippy with CI flags
just fmt # Format code
just deny # Supply chain audit
```
<details>
<summary>Raw cargo commands</summary>
```bash
cargo build # Build
cargo test --all-features # Run all tests
cargo clippy --all-targets --all-features -- -D warnings # Lint
cargo fmt # Format
cargo doc --no-deps # Generate docs
cargo deny check # Supply chain audit
```
</details>
## NSIP MCP Server
The binary includes an MCP server (`nsip mcp`) for sheep genetic evaluation. Configure in `.vscode/mcp.json`. See `docs/MCP.md` for the full API reference and `docs/llm-guides/` for ready-to-use LLM instruction templates.
