# `nsip`
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[](https://crates.io/crates/nsip)
[](https://docs.rs/nsip)
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Sheep genetic evaluation CLI & MCP server -- search animals, compare EBVs, plan matings, rank flocks via the NSIP database.
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<img src=".github/readme-infographic.svg" alt="NSIP Architecture Overview" width="800">
</p>
> **Try it out:** Clone [zircote/nsip-example](https://github.com/zircote/nsip-example) for a ready-to-use farm repository with MCP server configuration, sample workflows, and AI assistant instructions pre-configured.
## Features
- **Type-safe API client** with comprehensive error handling
- **Search functionality** for animals by breed group, status, and other criteria
- **Detailed animal information** including lineage and progeny
- **MCP (Model Context Protocol) integration** for AI assistant compatibility
- **CLI tool** with multiple subcommands for easy interaction
- **Async/await support** with tokio runtime
- **Full documentation** with examples in all public APIs
## Installation
Add this to your `Cargo.toml`:
```toml
[dependencies]
nsip = "0.3"
```
Or use cargo add:
```bash
cargo add nsip
```
## Quick Start
```rust,no_run
use nsip::{NsipClient, SearchCriteria};
#[tokio::main]
async fn main() -> Result<(), nsip::Error> {
// Create a new client
let client = NsipClient::new();
// List available breed groups
let breed_groups = client.breed_groups().await?;
println!("Available breed groups: {}", breed_groups.len());
// Search for animals
let criteria = SearchCriteria::new()
.with_status("CURRENT");
let results = client
.search_animals(0, 15, Some(640), None, None, Some(&criteria))
.await?;
println!("Found {} animals", results.total_count);
// Get details for a specific animal
let animal = client.animal_details("LPN_ID_HERE").await?;
println!("Animal: {}", animal.lpn_id);
Ok(())
}
```
## CLI Usage
The `nsip` CLI provides several commands for interacting with the NSIP Search API:
```bash
# Get database last-updated date
nsip date-updated
# List breed groups
nsip breed-groups
# List animal statuses
nsip statuses
# Get trait ranges for a breed
nsip trait-ranges 640
# Search for animals
nsip search --breed-id 640 --status CURRENT --page 0 --page-size 15
# Get animal details
nsip details <lpn-id>
# Get animal lineage
nsip lineage <lpn-id>
# Get animal progeny
nsip progeny <lpn-id>
# Get full profile (details + lineage + progeny)
nsip profile <lpn-id>
# Compare two or more animals side-by-side
nsip compare <lpn-id-1> <lpn-id-2>
# Generate shell completions
nsip completions bash
# Generate man pages
nsip man-pages ./man/
# Start MCP server mode
nsip mcp
```
## API Overview
### Client Methods
| `date_last_updated()` | Get database last-updated date |
| `breed_groups()` | List available breed groups |
| `statuses()` | List available animal statuses |
| `trait_ranges(breed_id)` | Get trait ranges for a breed |
| `search_animals(page, page_size, breed_id, sorted_trait, reverse, criteria)` | Search for animals |
| `animal_details(search_string)` | Get animal details |
| `lineage(lpn_id)` | Get animal lineage |
| `progeny(lpn_id, page, page_size)` | Get animal progeny |
| `search_by_lpn(lpn_id)` | Get full profile (concurrent) |
### Data Types
| `NsipClient` | Main API client |
| `SearchCriteria` | Search parameters with builder pattern |
| `AnimalDetails` | Detailed animal record with traits and contact info |
| `AnimalProfile` | Combined details + lineage + progeny |
| `Breed` | A single breed within a breed group |
| `BreedGroup` | Breed group with nested breeds |
| `ContactInfo` | Owner / flock contact information |
| `DateLastUpdated` | Response from the date-last-updated endpoint |
| `Lineage` | Animal lineage/ancestry tree |
| `LineageAnimal` | A single node in the pedigree tree |
| `Progeny` | Paginated animal offspring |
| `ProgenyAnimal` | A single offspring record |
| `SearchResults` | Paginated search results |
| `Trait` | A single EBV trait with value and accuracy |
| `TraitRange` | Min/max range for a trait within a breed |
| `TraitRangeFilter` | Min/max bounds for a trait filter |
| `Error` | Error type for operations |
| `Result<T>` | Type alias for `Result<T, Error>` |
## MCP Integration
The library includes MCP (Model Context Protocol) support for integration with AI assistants:
```rust,ignore
// Start the MCP server on stdio
nsip::mcp::serve_stdio().await?;
```
The MCP protocol exposes the following 13 tools when running `nsip mcp`:
- `search` - Search for animals with filters for breed, gender, status, date range, and flock
- `details` - Get detailed EBV data, breed, contact info, and status for an animal
- `lineage` - Get pedigree / ancestry tree including parents and grandparents
- `progeny` - Get paginated list of offspring for an animal
- `profile` - Get complete profile (details + pedigree + offspring) in one call
- `breed_groups` - List all breed groups and individual breeds
- `trait_ranges` - Get min/max EBV trait ranges for a specific breed
- `compare` - Compare 2-5 animals side-by-side on their EBV traits
- `rank` - Rank animals within a breed by weighted EBV traits
- `inbreeding_check` - Calculate Wright's coefficient of inbreeding for a sire-dam pairing
- `mating_recommendations` - Find optimal mates ranked by trait complementarity and COI
- `flock_summary` - Summarize a flock's animals: count, gender breakdown, and average EBVs
- `database_status` - Get last-updated date and available animal statuses
## Development
### Prerequisites
- Rust 1.92+ (2024 edition)
- [cargo-deny](https://github.com/EmbarkStudios/cargo-deny) for supply chain security
### Setup
```bash
# Clone the repository
git clone https://github.com/zircote/nsip.git
cd nsip
# Build
cargo build
# Run tests
cargo test
# Run linting
cargo clippy --all-targets --all-features
# Format code
cargo fmt
# Check supply chain security
cargo deny check
# Generate documentation
cargo doc --open
```
### Project Structure
```text
crates/
├── lib.rs # Library entry point
├── main.rs # Binary entry point
├── client.rs # HTTP client for the NSIP Search API
├── models.rs # Data models (SearchCriteria, AnimalDetails, etc.)
├── format.rs # Human-readable ASCII table formatting
└── mcp/ # MCP server (13 tools, prompts, resources)
tests/
├── integration_test.rs
└── cli_test.rs # CLI integration tests
Cargo.toml # Project manifest
clippy.toml # Clippy configuration
rustfmt.toml # Formatter configuration
deny.toml # cargo-deny configuration
CLAUDE.md # AI assistant instructions
AGENTS.md # AI coding agent instructions
.editorconfig # Cross-editor defaults
.devcontainer/ # Codespaces / dev container config
.vscode/ # VS Code settings and extensions
```
### Code Quality
This project maintains high code quality standards:
- **Linting**: clippy with pedantic and nursery lints
- **Formatting**: rustfmt with custom configuration
- **Testing**: Unit tests, integration tests, and property-based tests
- **Documentation**: All public APIs documented with examples
- **Supply Chain**: cargo-deny for dependency auditing
- **CI/CD**: GitHub Actions for automated testing
### Running Checks
```bash
# Run all checks
cargo fmt -- --check && \
cargo clippy --all-targets --all-features -- -D warnings && \
cargo test && \
cargo doc --no-deps && \
cargo deny check
# Run with MIRI for undefined behavior detection
cargo +nightly miri test
```
## CI/CD and Deployment
This template includes production-ready workflows:
### Continuous Integration
- **CI** (`.github/workflows/ci.yml`) - Format, lint, test, docs, supply chain security, MSRV check, coverage
- **Security Audit** (`.github/workflows/security-audit.yml`) - Daily cargo-audit scans
- **`CodeQL` Analysis** (`.github/workflows/codeql-analysis.yml`) - SAST scanning on push/PR and weekly schedule
- **Benchmark** (`.github/workflows/benchmark.yml`) - Performance tracking with criterion
- **ADR Validation** (`.github/workflows/adr-validation.yml`) - Architectural decision records validation
### Release and Deployment
- **Release** (`.github/workflows/release.yml`) - Automated GitHub releases with multi-platform binaries
- Builds for: Linux (`x86_64`, ARM64), macOS (`x86_64`, ARM64), Windows (`x86_64`)
- Automatic changelog generation
- Binary artifacts uploaded to releases
- **Changelog** (`.github/workflows/changelog.yml`) - Automated CHANGELOG.md generation
- Uses git-cliff with conventional commits
- Follows Keep a Changelog format
- Triggered on version tags
- **Docker** (`.github/workflows/docker.yml`) - Multi-platform container builds
- Platforms: linux/amd64, linux/arm64
- Distroless base image for security
- Published to GitHub Container Registry (ghcr.io)
- Tagged with version and 'latest'
- **Publish** (`.github/workflows/publish.yml`) - Automated crates.io publishing
- Full pre-publish validation
- Triggered on version tags
- Requires `CARGO_REGISTRY_TOKEN` secret
### Creating a Release
1. Update version in `Cargo.toml`
2. Create and push a version tag:
```bash
git tag -a v0.3.0 -m "Release v0.3.0"
git push origin v0.3.0
```
3. Workflows automatically:
- Generate changelog
- Build binaries for all platforms
- Create GitHub release with artifacts
- Build and push Docker images
- Publish to crates.io
### AI Coding Agent
- **Copilot Setup** (`.github/workflows/copilot-setup-steps.yml`) - Environment for GitHub Copilot coding agent
- **Agent Instructions**: `AGENTS.md`, `.github/copilot-instructions.md`, `CLAUDE.md`
- **Path-Specific Instructions**: `.github/instructions/` for Rust code and test patterns
- **Reusable Prompts**: `.github/prompts/` for common development tasks
### Docker Usage
Pull and run the container:
```bash
# Pull latest
docker pull ghcr.io/zircote/nsip:latest
# Run specific version
docker pull ghcr.io/zircote/nsip:v0.1.0
docker run --rm ghcr.io/zircote/nsip:v0.1.0 --version
```
## MSRV Policy
The Minimum Supported Rust Version (MSRV) is **1.92**. Increasing the MSRV is considered a minor breaking change.
## Contributing
See [CONTRIBUTING.md](CONTRIBUTING.md) for development setup, PR checklist, and coding standards.
Please also review:
- [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) - Community guidelines
- [SECURITY.md](SECURITY.md) - Vulnerability reporting
- [GOVERNANCE.md](GOVERNANCE.md) - Decision-making process
## License
This project is licensed under the MIT License - see the [LICENSE](https://github.com/zircote/nsip/blob/main/LICENSE) file for details.
## Acknowledgments
- [The Rust Programming Language](https://www.rust-lang.org/)
- [Cargo](https://doc.rust-lang.org/cargo/)
- [clippy](https://github.com/rust-lang/rust-clippy)