OutbreakDetection Agent Guidelines

Build/Test Commands

Run all tests: just tests or julia --project=./OutbreakDetectionUtils -e "using Pkg; Pkg.test()"
Run single test file: julia --startup-file=no --project=./OutbreakDetectionUtils -e 'using Test; @testset "filename" include("OutbreakDetectionUtils/test/filename.jl")'
Build manuscript: just manuscript
Format code: julia -e 'using JuliaFormatter; format(".")' (uses .JuliaFormatter.toml config)

Formatting: Use Runic (https://github.com/fredrikekre/Runic.jl) style (80 char margin). Format all files before committing.
Imports: Use qualified imports (e.g., using Distributions: Distributions) to avoid namespace pollution.
Types: Use parametric types for structs. Prefer concrete types in function signatures for performance.
Naming: snake_case for functions/variables, PascalCase for types/modules. Use descriptive names (e.g., seir_mod! for in-place).
Functions: In-place functions end with !. Use keyword arguments with defaults for clarity.
Error Handling: Use Try.jl for operations with potentially invalid returns. Ensure type stability.
Testing: Include Aqua.jl and JET.jl tests for code quality and type stability. All tests must pass before committing.
Documentation: Document public functions with docstrings. Use triple-quoted strings with parameter descriptions.
Performance: Use @inbounds for performance-critical loops. Prefer StaticArrays for small fixed-size arrays.
Project Structure: Main package is OutbreakDetectionUtils/. Scripts in scripts/, plotting in src/, tests in test/.

Scripts should start with using DrWatson; @quickactivate "OutbreakDetection" for path management.
Use DrWatson helpers for data/output paths (see OutbreakDetectionUtils/src/DrWatson-helpers.jl).